2-GSVA.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Understand the effect of Interferons in Pancreatic Adenocarcinoma\n",
    "\n",
    "Interferons (IFNs) are a group of signaling proteins made and released by host cells in response to\n",
    "the presence of several pathogens, such as viruses, bacteria, parasites, and also tumor cells. Type I\n",
    "interferons (IFNs) are a large subgroup of interferon proteins that help regulate the activity of the\n",
    "immune system. The genes responsible for type 1 Interferons is called Type 1 IFN signature and\n",
    "consists of a set of 25 genes in homo sapiens."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Part 2 \n",
    "\n",
    "Run the GSVA (a single sample gene set enrichment) algorithm with 25 gene IFN signature as the gene set and the subsetted pancreatic cancer data as the expression dataset. \n",
    "\n",
    "#### Simple Intro to GSVA: \n",
    "\n",
    "It is an unsupervised and non-parametric method for performing gene set enrichment analysis. It performs the change in coordinates system and transforms data from a gene by sample matrix to a gene set by sample matrix [1]. This transformation does not rely on any specific phenotype, which makes it powerful and is suitable for understanding the complex data. \n",
    "\n",
    "Here we are trying is look at how the expression of IFNs genes causes variation within the Pancreatic Adenocarcinoma (well-defined sample) cases. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "## Read expression set \n",
    "exp_set = read.csv(\"expression_set.csv\", row.names=\"rid\" )\n",
    "# exp_set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A matrix: 14098 × 175 of type dbl</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>aab1.Primary.solid.Tumor</th><th scope=col>aab4.Primary.solid.Tumor</th><th scope=col>aab6.Primary.solid.Tumor</th><th scope=col>aab8.Primary.solid.Tumor</th><th scope=col>aab9.Primary.solid.Tumor</th><th scope=col>aaba.Primary.solid.Tumor</th><th scope=col>aabe.Primary.solid.Tumor</th><th scope=col>aabf.Primary.solid.Tumor</th><th scope=col>aabh.Primary.solid.Tumor</th><th scope=col>aabi.Primary.solid.Tumor</th><th scope=col>...</th><th scope=col>aauh.Primary.solid.Tumor</th><th scope=col>aaui.Primary.solid.Tumor</th><th scope=col>aaul.Primary.solid.Tumor</th><th scope=col>a8t3.Primary.solid.Tumor</th><th scope=col>a8t5.Primary.solid.Tumor</th><th scope=col>a89d.Solid.Tissue.Normal</th><th scope=col>a89d.Primary.solid.Tumor</th><th scope=col>a8sy.Primary.solid.Tumor</th><th scope=col>a8lh.Primary.solid.Tumor</th><th scope=col>aapl.Primary.solid.Tumor</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>SLC35E2</th><td> 7.45</td><td> 8.1</td><td> 7.2</td><td> 8.0</td><td> 7.65</td><td> 8.1</td><td> 8.2</td><td> 8.2</td><td> 7.55</td><td> 8.45</td><td>...</td><td> 8.45</td><td> 7.95</td><td> 8.3</td><td> 8.05</td><td> 8.2</td><td> 7.25</td><td> 7.4</td><td> 7.35</td><td> 7.2</td><td> 9.05</td></tr>\n",
       "\t<tr><th scope=row>A1BG</th><td> 6.40</td><td> 5.8</td><td> 6.4</td><td> 5.8</td><td> 6.70</td><td> 6.6</td><td> 6.3</td><td> 6.5</td><td> 5.70</td><td> 6.30</td><td>...</td><td> 7.10</td><td> 7.10</td><td> 6.7</td><td> 7.00</td><td> 6.9</td><td> 7.10</td><td> 7.3</td><td> 7.90</td><td> 6.0</td><td> 6.90</td></tr>\n",
       "\t<tr><th scope=row>A2LD1</th><td> 7.50</td><td> 6.8</td><td> 7.3</td><td> 7.5</td><td> 7.40</td><td> 6.6</td><td> 7.1</td><td> 6.8</td><td> 8.00</td><td> 5.80</td><td>...</td><td> 6.50</td><td> 7.30</td><td> 6.1</td><td> 6.70</td><td> 6.5</td><td> 6.70</td><td> 6.7</td><td> 6.50</td><td> 6.9</td><td> 6.70</td></tr>\n",
       "\t<tr><th scope=row>A2M</th><td>14.30</td><td>14.0</td><td>13.1</td><td>13.8</td><td>14.60</td><td>13.3</td><td>13.4</td><td>14.2</td><td>13.90</td><td>11.90</td><td>...</td><td>14.50</td><td>14.30</td><td>14.5</td><td>14.20</td><td>14.3</td><td>14.90</td><td>14.5</td><td>13.00</td><td>12.1</td><td>13.30</td></tr>\n",
       "\t<tr><th scope=row>A4GALT</th><td>10.60</td><td>10.2</td><td>10.1</td><td> 8.6</td><td>10.10</td><td> 9.3</td><td> 9.5</td><td> 8.4</td><td> 8.40</td><td> 7.90</td><td>...</td><td> 9.10</td><td> 9.50</td><td>10.0</td><td> 9.50</td><td> 9.1</td><td>10.50</td><td> 9.8</td><td>10.80</td><td> 8.3</td><td> 9.00</td></tr>\n",
       "\t<tr><th scope=row>AAAS</th><td> 9.40</td><td> 9.1</td><td> 9.7</td><td> 9.6</td><td> 9.80</td><td> 9.3</td><td> 9.5</td><td> 9.3</td><td> 9.00</td><td> 9.30</td><td>...</td><td> 9.20</td><td> 9.40</td><td> 9.3</td><td> 9.50</td><td> 9.0</td><td> 9.20</td><td> 9.2</td><td> 9.30</td><td> 9.6</td><td> 9.60</td></tr>\n",
       "\t<tr><th scope=row>AACS</th><td>10.20</td><td>10.3</td><td> 9.2</td><td> 9.4</td><td> 9.30</td><td> 9.9</td><td>10.3</td><td>10.0</td><td> 9.70</td><td> 9.10</td><td>...</td><td>10.50</td><td>10.20</td><td> 9.6</td><td>10.00</td><td> 9.9</td><td> 9.50</td><td>10.1</td><td> 9.50</td><td>10.0</td><td> 8.60</td></tr>\n",
       "\t<tr><th scope=row>AADAT</th><td> 4.80</td><td> 6.3</td><td> 5.9</td><td> 6.4</td><td> 6.50</td><td> 6.0</td><td> 6.6</td><td> 6.3</td><td> 5.40</td><td> 4.10</td><td>...</td><td> 6.40</td><td> 5.80</td><td> 5.6</td><td> 6.70</td><td> 6.4</td><td> 5.50</td><td> 6.2</td><td> 6.20</td><td> 6.0</td><td> 4.90</td></tr>\n",
       "\t<tr><th scope=row>AAGAB</th><td>10.20</td><td>10.4</td><td> 9.9</td><td>10.5</td><td>10.10</td><td>10.3</td><td> 9.4</td><td>10.1</td><td> 9.70</td><td> 9.80</td><td>...</td><td>10.00</td><td> 9.90</td><td>10.2</td><td> 9.90</td><td>10.2</td><td> 9.90</td><td>10.0</td><td> 9.70</td><td>10.5</td><td>10.10</td></tr>\n",
       "\t<tr><th scope=row>AAK1</th><td> 9.60</td><td> 9.8</td><td> 9.8</td><td> 9.2</td><td> 9.80</td><td> 9.7</td><td> 9.5</td><td> 9.9</td><td> 9.70</td><td>10.50</td><td>...</td><td>10.20</td><td> 9.90</td><td> 9.7</td><td>10.00</td><td>10.0</td><td>10.00</td><td> 9.5</td><td> 9.60</td><td> 8.9</td><td>10.50</td></tr>\n",
       "\t<tr><th scope=row>AAMP</th><td>11.80</td><td>11.4</td><td>11.1</td><td>11.6</td><td>11.20</td><td>11.6</td><td>11.7</td><td>11.3</td><td>11.80</td><td>12.00</td><td>...</td><td>11.30</td><td>11.70</td><td>11.5</td><td>11.20</td><td>11.4</td><td>11.30</td><td>11.5</td><td>11.60</td><td>11.9</td><td>11.10</td></tr>\n",
       "\t<tr><th scope=row>AARS2</th><td> 8.60</td><td> 8.4</td><td> 8.4</td><td> 8.7</td><td> 8.40</td><td> 8.7</td><td> 8.6</td><td> 9.1</td><td> 8.50</td><td> 8.60</td><td>...</td><td> 8.70</td><td> 8.30</td><td> 8.3</td><td> 9.00</td><td> 8.7</td><td> 8.40</td><td> 8.3</td><td> 8.60</td><td> 8.9</td><td> 8.80</td></tr>\n",
       "\t<tr><th scope=row>AARSD1</th><td> 8.90</td><td> 8.7</td><td> 8.8</td><td> 9.1</td><td> 9.30</td><td> 9.0</td><td> 9.1</td><td> 8.8</td><td> 8.90</td><td> 9.60</td><td>...</td><td> 9.00</td><td> 9.10</td><td> 8.8</td><td> 9.10</td><td> 9.1</td><td> 9.20</td><td> 8.9</td><td> 9.50</td><td> 9.1</td><td> 9.00</td></tr>\n",
       "\t<tr><th scope=row>AARS</th><td>11.30</td><td>11.6</td><td>11.4</td><td>11.4</td><td>11.40</td><td>11.3</td><td>11.3</td><td>11.6</td><td>11.40</td><td>11.60</td><td>...</td><td>11.60</td><td>12.10</td><td>11.2</td><td>11.00</td><td>11.5</td><td>11.40</td><td>11.7</td><td>11.20</td><td>12.0</td><td>11.10</td></tr>\n",
       "\t<tr><th scope=row>AASDHPPT</th><td> 8.60</td><td> 9.0</td><td> 9.3</td><td> 9.4</td><td> 9.40</td><td> 9.0</td><td> 8.8</td><td> 9.2</td><td> 8.80</td><td> 9.10</td><td>...</td><td> 9.10</td><td> 9.00</td><td> 9.0</td><td> 9.30</td><td> 9.3</td><td> 8.90</td><td> 9.0</td><td> 8.70</td><td> 8.7</td><td> 9.50</td></tr>\n",
       "\t<tr><th scope=row>AASDH</th><td> 7.50</td><td> 7.5</td><td> 6.7</td><td> 7.7</td><td> 7.20</td><td> 8.2</td><td> 7.8</td><td> 7.6</td><td> 7.30</td><td> 8.30</td><td>...</td><td> 8.10</td><td> 7.30</td><td> 7.2</td><td> 7.40</td><td> 7.8</td><td> 6.80</td><td> 7.0</td><td> 6.90</td><td> 7.0</td><td> 8.00</td></tr>\n",
       "\t<tr><th scope=row>AASS</th><td> 8.10</td><td> 8.2</td><td> 7.3</td><td> 7.8</td><td> 8.30</td><td> 8.7</td><td> 7.9</td><td> 8.4</td><td> 8.60</td><td> 7.60</td><td>...</td><td> 8.80</td><td> 8.80</td><td> 8.5</td><td> 8.70</td><td> 8.6</td><td> 8.30</td><td> 8.4</td><td> 8.20</td><td> 7.3</td><td> 8.10</td></tr>\n",
       "\t<tr><th scope=row>AATF</th><td>10.60</td><td>10.2</td><td>10.3</td><td>10.1</td><td>10.30</td><td>10.2</td><td>10.3</td><td>10.1</td><td>10.40</td><td>10.90</td><td>...</td><td>10.10</td><td>10.80</td><td>10.1</td><td>10.00</td><td>10.2</td><td>10.30</td><td>10.3</td><td>10.50</td><td>10.9</td><td>10.50</td></tr>\n",
       "\t<tr><th scope=row>AATK</th><td>10.00</td><td> 8.1</td><td> 7.3</td><td> 8.3</td><td> 8.60</td><td> 8.7</td><td> 9.2</td><td> 7.9</td><td> 9.10</td><td> 6.20</td><td>...</td><td> 7.70</td><td> 7.70</td><td> 7.5</td><td> 6.70</td><td> 9.2</td><td> 7.40</td><td> 7.9</td><td> 9.20</td><td> 7.8</td><td> 7.00</td></tr>\n",
       "\t<tr><th scope=row>ABAT</th><td> 9.40</td><td> 9.3</td><td> 8.4</td><td> 8.4</td><td> 9.40</td><td> 7.4</td><td> 8.7</td><td> 9.8</td><td>10.00</td><td> 7.30</td><td>...</td><td>11.40</td><td> 8.90</td><td> 8.5</td><td> 8.90</td><td> 9.2</td><td> 8.70</td><td>10.1</td><td> 7.60</td><td> 8.5</td><td> 8.10</td></tr>\n",
       "\t<tr><th scope=row>ABCA10</th><td> 4.40</td><td> 4.9</td><td> 4.7</td><td> 5.4</td><td> 5.90</td><td> 7.7</td><td> 4.6</td><td> 6.3</td><td> 4.00</td><td> 4.70</td><td>...</td><td> 6.80</td><td> 6.10</td><td> 5.6</td><td> 6.10</td><td> 7.1</td><td> 6.20</td><td> 5.8</td><td> 4.20</td><td> 3.7</td><td> 4.70</td></tr>\n",
       "\t<tr><th scope=row>ABCA11P</th><td> 5.80</td><td> 5.7</td><td> 6.1</td><td> 6.6</td><td> 6.20</td><td> 6.9</td><td> 6.4</td><td> 6.5</td><td> 6.60</td><td> 6.80</td><td>...</td><td> 7.20</td><td> 6.30</td><td> 6.0</td><td> 6.70</td><td> 6.7</td><td> 5.80</td><td> 6.6</td><td> 6.40</td><td> 6.2</td><td> 7.70</td></tr>\n",
       "\t<tr><th scope=row>ABCA1</th><td> 7.80</td><td> 8.5</td><td> 9.2</td><td> 9.0</td><td> 8.70</td><td> 9.9</td><td> 9.3</td><td> 9.7</td><td> 8.70</td><td> 8.30</td><td>...</td><td>10.00</td><td> 9.00</td><td> 9.3</td><td>10.00</td><td>10.4</td><td>10.60</td><td> 9.5</td><td>10.40</td><td> 7.8</td><td> 9.90</td></tr>\n",
       "\t<tr><th scope=row>ABCA2</th><td>10.40</td><td>10.9</td><td>10.6</td><td>10.0</td><td>10.00</td><td>11.1</td><td>11.0</td><td>10.4</td><td>10.70</td><td>12.00</td><td>...</td><td>11.10</td><td>10.40</td><td>10.5</td><td>11.00</td><td>11.4</td><td>10.50</td><td>10.9</td><td>10.30</td><td>10.7</td><td> 9.80</td></tr>\n",
       "\t<tr><th scope=row>ABCA3</th><td> 9.70</td><td> 9.5</td><td> 8.0</td><td> 7.9</td><td> 9.30</td><td> 8.1</td><td> 8.4</td><td> 9.7</td><td> 9.20</td><td> 9.10</td><td>...</td><td>10.70</td><td> 9.10</td><td> 9.9</td><td> 9.10</td><td> 9.7</td><td> 8.80</td><td> 9.5</td><td> 6.30</td><td> 9.2</td><td> 8.80</td></tr>\n",
       "\t<tr><th scope=row>ABCA5</th><td> 8.10</td><td> 9.0</td><td> 7.7</td><td> 7.6</td><td> 8.80</td><td> 8.6</td><td> 7.6</td><td> 8.8</td><td> 8.50</td><td> 8.30</td><td>...</td><td> 9.50</td><td> 8.40</td><td> 8.6</td><td> 8.90</td><td> 8.3</td><td> 8.00</td><td> 8.5</td><td> 7.50</td><td> 7.4</td><td> 9.10</td></tr>\n",
       "\t<tr><th scope=row>ABCA6</th><td> 7.90</td><td> 6.0</td><td> 5.7</td><td> 6.7</td><td> 7.70</td><td> 9.3</td><td> 6.2</td><td> 8.0</td><td> 6.50</td><td> 9.70</td><td>...</td><td> 8.50</td><td> 7.90</td><td> 7.0</td><td> 7.20</td><td> 8.5</td><td> 8.40</td><td> 8.1</td><td> 6.50</td><td> 3.9</td><td> 7.60</td></tr>\n",
       "\t<tr><th scope=row>ABCA7</th><td> 9.30</td><td> 9.7</td><td>10.4</td><td>10.4</td><td> 9.20</td><td> 9.8</td><td>10.3</td><td>10.0</td><td>10.60</td><td>10.00</td><td>...</td><td> 9.60</td><td> 9.70</td><td> 9.5</td><td> 9.70</td><td>10.4</td><td> 9.30</td><td> 9.8</td><td> 8.20</td><td> 9.9</td><td>11.00</td></tr>\n",
       "\t<tr><th scope=row>ABCA8</th><td> 6.90</td><td> 6.7</td><td> 6.9</td><td> 7.7</td><td> 6.40</td><td> 9.6</td><td> 5.0</td><td> 8.2</td><td> 6.40</td><td> 3.80</td><td>...</td><td>10.60</td><td> 8.10</td><td> 4.8</td><td> 8.00</td><td>10.7</td><td> 9.20</td><td> 8.1</td><td> 3.90</td><td> 4.5</td><td> 7.90</td></tr>\n",
       "\t<tr><th scope=row>ABCA9</th><td> 7.00</td><td> 6.7</td><td> 5.9</td><td> 6.2</td><td> 7.50</td><td> 9.1</td><td> 5.7</td><td> 8.1</td><td> 6.10</td><td> 6.40</td><td>...</td><td> 8.80</td><td> 7.00</td><td> 6.9</td><td> 7.00</td><td> 8.4</td><td> 8.40</td><td> 8.1</td><td> 5.80</td><td> 4.2</td><td> 6.20</td></tr>\n",
       "\t<tr><th scope=row>...</th><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td></td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td><td>...</td></tr>\n",
       "\t<tr><th scope=row>ZRANB2</th><td> 9.4</td><td>10.2</td><td>10.4</td><td>10.6</td><td> 9.7</td><td>10.7</td><td>10.2</td><td>10.4</td><td> 9.6</td><td> 9.9</td><td>...</td><td>10.5</td><td>10.0</td><td>10.0</td><td>10.3</td><td>10.3</td><td> 9.8</td><td>10.2</td><td>10.5</td><td>10.2</td><td>11.1</td></tr>\n",
       "\t<tr><th scope=row>ZRANB3</th><td> 5.5</td><td> 5.4</td><td> 4.9</td><td> 5.7</td><td> 4.8</td><td> 5.4</td><td> 5.8</td><td> 6.0</td><td> 5.1</td><td> 5.6</td><td>...</td><td> 5.9</td><td> 5.0</td><td> 5.0</td><td> 5.5</td><td> 5.6</td><td> 4.9</td><td> 5.1</td><td> 3.5</td><td> 4.6</td><td> 5.8</td></tr>\n",
       "\t<tr><th scope=row>ZRSR2</th><td> 8.1</td><td> 7.9</td><td> 7.8</td><td> 8.0</td><td> 8.1</td><td> 8.1</td><td> 7.7</td><td> 8.0</td><td> 7.8</td><td> 9.0</td><td>...</td><td> 8.7</td><td> 8.6</td><td> 7.8</td><td> 7.9</td><td> 8.6</td><td> 8.0</td><td> 7.9</td><td> 8.5</td><td> 8.7</td><td> 9.5</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN12P1</th><td> 4.0</td><td> 5.0</td><td> 5.2</td><td> 6.0</td><td> 5.1</td><td> 5.4</td><td> 5.1</td><td> 6.2</td><td> 4.3</td><td> 3.2</td><td>...</td><td> 4.6</td><td> 4.5</td><td> 4.8</td><td> 4.7</td><td> 4.8</td><td> 4.0</td><td> 4.7</td><td> 4.9</td><td> 2.6</td><td> 5.0</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN12</th><td> 7.2</td><td> 7.0</td><td> 6.6</td><td> 7.6</td><td> 7.3</td><td> 7.9</td><td> 6.4</td><td> 7.6</td><td> 7.1</td><td> 6.6</td><td>...</td><td> 7.4</td><td> 7.6</td><td> 7.0</td><td> 7.3</td><td> 7.7</td><td> 6.8</td><td> 7.0</td><td> 6.8</td><td> 7.0</td><td> 8.1</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN16</th><td> 6.9</td><td> 6.1</td><td> 5.4</td><td> 6.5</td><td> 6.2</td><td> 6.8</td><td> 7.1</td><td> 7.1</td><td> 6.5</td><td> 6.0</td><td>...</td><td> 6.2</td><td> 6.5</td><td> 6.2</td><td> 5.7</td><td> 6.5</td><td> 5.7</td><td> 5.4</td><td> 6.3</td><td> 7.0</td><td> 7.2</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN18</th><td> 9.1</td><td> 9.8</td><td> 9.9</td><td> 9.2</td><td>10.1</td><td> 9.3</td><td> 9.1</td><td> 9.5</td><td>10.1</td><td> 8.3</td><td>...</td><td>10.5</td><td>10.4</td><td> 9.5</td><td>10.0</td><td>10.4</td><td>10.0</td><td> 9.6</td><td> 9.3</td><td> 8.2</td><td>10.2</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN20</th><td> 6.0</td><td> 6.0</td><td> 6.3</td><td> 5.9</td><td> 5.7</td><td> 6.1</td><td> 5.9</td><td> 6.2</td><td> 5.9</td><td> 5.7</td><td>...</td><td> 5.8</td><td> 5.9</td><td> 6.3</td><td> 6.2</td><td> 5.9</td><td> 5.9</td><td> 5.7</td><td> 5.6</td><td> 5.6</td><td> 5.6</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN21</th><td> 8.0</td><td> 7.6</td><td> 7.7</td><td> 7.1</td><td> 7.9</td><td> 7.9</td><td> 7.6</td><td> 7.8</td><td> 7.6</td><td> 7.8</td><td>...</td><td> 7.9</td><td> 7.8</td><td> 7.9</td><td> 7.6</td><td> 7.6</td><td> 7.4</td><td> 7.2</td><td> 7.4</td><td> 7.6</td><td> 7.4</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN22</th><td> 7.3</td><td> 6.2</td><td> 6.6</td><td> 6.8</td><td> 7.0</td><td> 7.2</td><td> 6.3</td><td> 6.9</td><td> 6.8</td><td> 6.6</td><td>...</td><td> 7.1</td><td> 6.8</td><td> 6.4</td><td> 7.2</td><td> 6.5</td><td> 6.5</td><td> 6.6</td><td> 6.3</td><td> 6.7</td><td> 6.4</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN29</th><td> 8.7</td><td> 8.5</td><td> 7.9</td><td> 8.9</td><td> 8.6</td><td> 9.1</td><td> 8.4</td><td> 9.1</td><td> 8.5</td><td> 9.1</td><td>...</td><td> 8.8</td><td> 8.5</td><td> 8.3</td><td> 8.9</td><td> 8.6</td><td> 8.1</td><td> 8.2</td><td> 8.3</td><td> 8.8</td><td> 9.3</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN2</th><td> 7.1</td><td> 7.5</td><td> 6.9</td><td> 7.4</td><td> 8.0</td><td> 7.4</td><td> 7.5</td><td> 7.6</td><td> 7.4</td><td> 8.2</td><td>...</td><td> 8.0</td><td> 7.3</td><td> 7.5</td><td> 7.7</td><td> 7.6</td><td> 7.2</td><td> 7.1</td><td> 7.5</td><td> 7.3</td><td> 7.6</td></tr>\n",
       "\t<tr><th scope=row>ZSCAN5A</th><td> 6.0</td><td> 5.7</td><td> 5.7</td><td> 6.1</td><td> 6.1</td><td> 5.7</td><td> 5.4</td><td> 6.6</td><td> 5.6</td><td> 4.8</td><td>...</td><td> 6.3</td><td> 5.1</td><td> 5.0</td><td> 6.4</td><td> 6.1</td><td> 5.5</td><td> 5.2</td><td> 5.2</td><td> 5.4</td><td> 6.2</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM1</th><td> 8.6</td><td> 7.9</td><td> 8.2</td><td> 8.0</td><td> 8.4</td><td> 8.1</td><td> 8.1</td><td> 8.3</td><td> 7.9</td><td> 8.8</td><td>...</td><td> 8.1</td><td> 8.5</td><td> 7.9</td><td> 8.4</td><td> 7.9</td><td> 7.9</td><td> 7.9</td><td> 8.1</td><td> 8.4</td><td> 8.2</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM3</th><td> 7.1</td><td> 6.2</td><td> 5.7</td><td> 6.1</td><td> 7.0</td><td> 6.7</td><td> 6.6</td><td> 7.7</td><td> 6.3</td><td> 6.9</td><td>...</td><td> 7.2</td><td> 7.4</td><td> 7.2</td><td> 6.8</td><td> 6.6</td><td> 6.7</td><td> 6.0</td><td> 6.6</td><td> 6.8</td><td> 6.7</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM4</th><td> 8.8</td><td> 9.2</td><td> 8.8</td><td> 9.8</td><td> 9.9</td><td> 9.0</td><td> 9.8</td><td> 9.3</td><td> 9.8</td><td> 9.7</td><td>...</td><td> 8.5</td><td> 9.0</td><td>10.0</td><td> 8.9</td><td> 9.3</td><td> 9.9</td><td> 9.5</td><td>10.6</td><td> 9.7</td><td> 8.5</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM5</th><td> 8.2</td><td> 6.9</td><td> 5.3</td><td> 6.3</td><td> 6.9</td><td> 8.5</td><td> 7.2</td><td> 6.7</td><td> 6.3</td><td> 5.7</td><td>...</td><td> 7.9</td><td> 6.1</td><td> 6.7</td><td> 6.4</td><td> 6.5</td><td> 5.4</td><td> 6.9</td><td> 3.5</td><td> 7.5</td><td> 7.0</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM6</th><td> 8.8</td><td> 9.4</td><td> 8.7</td><td> 8.8</td><td> 8.6</td><td> 8.4</td><td> 9.1</td><td> 8.9</td><td> 9.5</td><td> 9.0</td><td>...</td><td> 9.0</td><td> 8.8</td><td> 8.6</td><td> 8.9</td><td> 9.2</td><td> 9.3</td><td> 8.8</td><td> 9.1</td><td> 9.1</td><td> 8.9</td></tr>\n",
       "\t<tr><th scope=row>ZSWIM7</th><td> 8.1</td><td> 8.1</td><td> 7.3</td><td> 8.0</td><td> 8.0</td><td> 8.2</td><td> 8.0</td><td> 7.9</td><td> 7.6</td><td> 7.9</td><td>...</td><td> 8.2</td><td> 7.8</td><td> 7.6</td><td> 8.1</td><td> 8.2</td><td> 8.2</td><td> 7.5</td><td> 7.3</td><td> 7.4</td><td> 7.9</td></tr>\n",
       "\t<tr><th scope=row>ZUFSP</th><td> 7.0</td><td> 7.5</td><td> 7.0</td><td> 7.4</td><td> 7.0</td><td> 6.7</td><td> 6.3</td><td> 7.6</td><td> 6.6</td><td> 6.6</td><td>...</td><td> 7.3</td><td> 7.5</td><td> 7.4</td><td> 6.8</td><td> 7.3</td><td> 7.3</td><td> 6.9</td><td> 7.0</td><td> 6.8</td><td> 7.6</td></tr>\n",
       "\t<tr><th scope=row>ZW10</th><td> 8.6</td><td> 8.7</td><td> 8.8</td><td> 8.6</td><td> 8.9</td><td> 8.6</td><td> 8.3</td><td> 8.6</td><td> 8.5</td><td> 9.0</td><td>...</td><td> 8.5</td><td> 8.0</td><td> 8.3</td><td> 8.5</td><td> 8.4</td><td> 8.2</td><td> 8.2</td><td> 8.1</td><td> 8.6</td><td> 8.5</td></tr>\n",
       "\t<tr><th scope=row>ZWILCH</th><td> 8.1</td><td> 8.1</td><td> 8.4</td><td> 8.6</td><td> 8.2</td><td> 8.0</td><td> 7.6</td><td> 8.5</td><td> 7.3</td><td> 8.4</td><td>...</td><td> 7.5</td><td> 7.9</td><td> 8.0</td><td> 8.2</td><td> 8.0</td><td> 7.7</td><td> 7.5</td><td> 8.4</td><td> 8.0</td><td> 8.6</td></tr>\n",
       "\t<tr><th scope=row>ZWINT</th><td> 8.6</td><td> 8.8</td><td> 9.1</td><td> 8.9</td><td> 8.4</td><td> 7.5</td><td> 7.9</td><td> 9.0</td><td> 8.6</td><td> 9.2</td><td>...</td><td> 7.0</td><td> 8.6</td><td> 8.4</td><td> 9.1</td><td> 7.6</td><td> 7.8</td><td> 7.9</td><td> 9.4</td><td> 8.8</td><td> 9.1</td></tr>\n",
       "\t<tr><th scope=row>ZXDA</th><td> 6.2</td><td> 5.8</td><td> 3.9</td><td> 5.2</td><td> 5.9</td><td> 5.7</td><td> 5.8</td><td> 5.8</td><td> 6.4</td><td> 5.6</td><td>...</td><td> 5.9</td><td> 5.6</td><td> 5.6</td><td> 5.4</td><td> 5.9</td><td> 5.3</td><td> 5.3</td><td> 5.0</td><td> 5.4</td><td> 6.3</td></tr>\n",
       "\t<tr><th scope=row>ZXDB</th><td> 9.0</td><td> 8.5</td><td> 8.1</td><td> 8.5</td><td> 8.6</td><td> 8.2</td><td> 8.8</td><td> 8.7</td><td> 9.4</td><td> 9.0</td><td>...</td><td> 8.9</td><td> 8.5</td><td> 8.7</td><td> 8.0</td><td> 8.6</td><td> 8.4</td><td> 8.8</td><td> 8.2</td><td> 8.7</td><td> 8.9</td></tr>\n",
       "\t<tr><th scope=row>ZXDC</th><td> 9.9</td><td>10.0</td><td>10.0</td><td> 9.7</td><td> 9.9</td><td>10.6</td><td>10.1</td><td> 9.9</td><td> 9.8</td><td>10.7</td><td>...</td><td>10.1</td><td>10.1</td><td> 9.9</td><td>10.1</td><td> 9.8</td><td> 9.5</td><td> 9.5</td><td> 9.4</td><td> 9.5</td><td>10.4</td></tr>\n",
       "\t<tr><th scope=row>ZYG11B</th><td> 9.2</td><td> 9.3</td><td> 9.4</td><td> 9.4</td><td> 9.3</td><td> 9.9</td><td> 9.1</td><td> 9.5</td><td> 8.9</td><td> 8.3</td><td>...</td><td> 9.7</td><td> 9.2</td><td> 9.5</td><td> 9.5</td><td> 9.4</td><td> 9.4</td><td> 9.6</td><td> 9.2</td><td> 8.3</td><td> 9.5</td></tr>\n",
       "\t<tr><th scope=row>ZYX</th><td>12.9</td><td>12.4</td><td>13.5</td><td>12.5</td><td>13.0</td><td>12.2</td><td>12.9</td><td>12.6</td><td>12.7</td><td>12.5</td><td>...</td><td>12.4</td><td>12.6</td><td>13.5</td><td>12.5</td><td>12.7</td><td>13.6</td><td>13.1</td><td>13.2</td><td>12.3</td><td>12.3</td></tr>\n",
       "\t<tr><th scope=row>ZZEF1</th><td>10.1</td><td> 9.8</td><td> 9.8</td><td> 9.7</td><td>10.1</td><td>10.4</td><td> 9.7</td><td>10.6</td><td>10.0</td><td> 9.9</td><td>...</td><td>10.6</td><td> 9.9</td><td> 9.8</td><td>10.3</td><td>10.4</td><td>10.2</td><td> 9.9</td><td> 9.8</td><td> 9.6</td><td>10.9</td></tr>\n",
       "\t<tr><th scope=row>ZZZ3</th><td> 9.3</td><td> 8.9</td><td> 9.2</td><td> 9.3</td><td> 9.2</td><td> 9.6</td><td> 8.9</td><td> 9.8</td><td> 8.8</td><td> 8.6</td><td>...</td><td> 9.6</td><td> 9.0</td><td> 9.0</td><td> 9.5</td><td> 9.2</td><td> 8.5</td><td> 8.8</td><td> 8.6</td><td> 8.4</td><td> 9.4</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A matrix: 14098 × 175 of type dbl\n",
       "\\begin{tabular}{r|lllllllllllllllllllll}\n",
       "  & aab1.Primary.solid.Tumor & aab4.Primary.solid.Tumor & aab6.Primary.solid.Tumor & aab8.Primary.solid.Tumor & aab9.Primary.solid.Tumor & aaba.Primary.solid.Tumor & aabe.Primary.solid.Tumor & aabf.Primary.solid.Tumor & aabh.Primary.solid.Tumor & aabi.Primary.solid.Tumor & ... & aauh.Primary.solid.Tumor & aaui.Primary.solid.Tumor & aaul.Primary.solid.Tumor & a8t3.Primary.solid.Tumor & a8t5.Primary.solid.Tumor & a89d.Solid.Tissue.Normal & a89d.Primary.solid.Tumor & a8sy.Primary.solid.Tumor & a8lh.Primary.solid.Tumor & aapl.Primary.solid.Tumor\\\\\n",
       "\\hline\n",
       "\tSLC35E2 &  7.45 &  8.1 &  7.2 &  8.0 &  7.65 &  8.1 &  8.2 &  8.2 &  7.55 &  8.45 & ... &  8.45 &  7.95 &  8.3 &  8.05 &  8.2 &  7.25 &  7.4 &  7.35 &  7.2 &  9.05\\\\\n",
       "\tA1BG &  6.40 &  5.8 &  6.4 &  5.8 &  6.70 &  6.6 &  6.3 &  6.5 &  5.70 &  6.30 & ... &  7.10 &  7.10 &  6.7 &  7.00 &  6.9 &  7.10 &  7.3 &  7.90 &  6.0 &  6.90\\\\\n",
       "\tA2LD1 &  7.50 &  6.8 &  7.3 &  7.5 &  7.40 &  6.6 &  7.1 &  6.8 &  8.00 &  5.80 & ... &  6.50 &  7.30 &  6.1 &  6.70 &  6.5 &  6.70 &  6.7 &  6.50 &  6.9 &  6.70\\\\\n",
       "\tA2M & 14.30 & 14.0 & 13.1 & 13.8 & 14.60 & 13.3 & 13.4 & 14.2 & 13.90 & 11.90 & ... & 14.50 & 14.30 & 14.5 & 14.20 & 14.3 & 14.90 & 14.5 & 13.00 & 12.1 & 13.30\\\\\n",
       "\tA4GALT & 10.60 & 10.2 & 10.1 &  8.6 & 10.10 &  9.3 &  9.5 &  8.4 &  8.40 &  7.90 & ... &  9.10 &  9.50 & 10.0 &  9.50 &  9.1 & 10.50 &  9.8 & 10.80 &  8.3 &  9.00\\\\\n",
       "\tAAAS &  9.40 &  9.1 &  9.7 &  9.6 &  9.80 &  9.3 &  9.5 &  9.3 &  9.00 &  9.30 & ... &  9.20 &  9.40 &  9.3 &  9.50 &  9.0 &  9.20 &  9.2 &  9.30 &  9.6 &  9.60\\\\\n",
       "\tAACS & 10.20 & 10.3 &  9.2 &  9.4 &  9.30 &  9.9 & 10.3 & 10.0 &  9.70 &  9.10 & ... & 10.50 & 10.20 &  9.6 & 10.00 &  9.9 &  9.50 & 10.1 &  9.50 & 10.0 &  8.60\\\\\n",
       "\tAADAT &  4.80 &  6.3 &  5.9 &  6.4 &  6.50 &  6.0 &  6.6 &  6.3 &  5.40 &  4.10 & ... &  6.40 &  5.80 &  5.6 &  6.70 &  6.4 &  5.50 &  6.2 &  6.20 &  6.0 &  4.90\\\\\n",
       "\tAAGAB & 10.20 & 10.4 &  9.9 & 10.5 & 10.10 & 10.3 &  9.4 & 10.1 &  9.70 &  9.80 & ... & 10.00 &  9.90 & 10.2 &  9.90 & 10.2 &  9.90 & 10.0 &  9.70 & 10.5 & 10.10\\\\\n",
       "\tAAK1 &  9.60 &  9.8 &  9.8 &  9.2 &  9.80 &  9.7 &  9.5 &  9.9 &  9.70 & 10.50 & ... & 10.20 &  9.90 &  9.7 & 10.00 & 10.0 & 10.00 &  9.5 &  9.60 &  8.9 & 10.50\\\\\n",
       "\tAAMP & 11.80 & 11.4 & 11.1 & 11.6 & 11.20 & 11.6 & 11.7 & 11.3 & 11.80 & 12.00 & ... & 11.30 & 11.70 & 11.5 & 11.20 & 11.4 & 11.30 & 11.5 & 11.60 & 11.9 & 11.10\\\\\n",
       "\tAARS2 &  8.60 &  8.4 &  8.4 &  8.7 &  8.40 &  8.7 &  8.6 &  9.1 &  8.50 &  8.60 & ... &  8.70 &  8.30 &  8.3 &  9.00 &  8.7 &  8.40 &  8.3 &  8.60 &  8.9 &  8.80\\\\\n",
       "\tAARSD1 &  8.90 &  8.7 &  8.8 &  9.1 &  9.30 &  9.0 &  9.1 &  8.8 &  8.90 &  9.60 & ... &  9.00 &  9.10 &  8.8 &  9.10 &  9.1 &  9.20 &  8.9 &  9.50 &  9.1 &  9.00\\\\\n",
       "\tAARS & 11.30 & 11.6 & 11.4 & 11.4 & 11.40 & 11.3 & 11.3 & 11.6 & 11.40 & 11.60 & ... & 11.60 & 12.10 & 11.2 & 11.00 & 11.5 & 11.40 & 11.7 & 11.20 & 12.0 & 11.10\\\\\n",
       "\tAASDHPPT &  8.60 &  9.0 &  9.3 &  9.4 &  9.40 &  9.0 &  8.8 &  9.2 &  8.80 &  9.10 & ... &  9.10 &  9.00 &  9.0 &  9.30 &  9.3 &  8.90 &  9.0 &  8.70 &  8.7 &  9.50\\\\\n",
       "\tAASDH &  7.50 &  7.5 &  6.7 &  7.7 &  7.20 &  8.2 &  7.8 &  7.6 &  7.30 &  8.30 & ... &  8.10 &  7.30 &  7.2 &  7.40 &  7.8 &  6.80 &  7.0 &  6.90 &  7.0 &  8.00\\\\\n",
       "\tAASS &  8.10 &  8.2 &  7.3 &  7.8 &  8.30 &  8.7 &  7.9 &  8.4 &  8.60 &  7.60 & ... &  8.80 &  8.80 &  8.5 &  8.70 &  8.6 &  8.30 &  8.4 &  8.20 &  7.3 &  8.10\\\\\n",
       "\tAATF & 10.60 & 10.2 & 10.3 & 10.1 & 10.30 & 10.2 & 10.3 & 10.1 & 10.40 & 10.90 & ... & 10.10 & 10.80 & 10.1 & 10.00 & 10.2 & 10.30 & 10.3 & 10.50 & 10.9 & 10.50\\\\\n",
       "\tAATK & 10.00 &  8.1 &  7.3 &  8.3 &  8.60 &  8.7 &  9.2 &  7.9 &  9.10 &  6.20 & ... &  7.70 &  7.70 &  7.5 &  6.70 &  9.2 &  7.40 &  7.9 &  9.20 &  7.8 &  7.00\\\\\n",
       "\tABAT &  9.40 &  9.3 &  8.4 &  8.4 &  9.40 &  7.4 &  8.7 &  9.8 & 10.00 &  7.30 & ... & 11.40 &  8.90 &  8.5 &  8.90 &  9.2 &  8.70 & 10.1 &  7.60 &  8.5 &  8.10\\\\\n",
       "\tABCA10 &  4.40 &  4.9 &  4.7 &  5.4 &  5.90 &  7.7 &  4.6 &  6.3 &  4.00 &  4.70 & ... &  6.80 &  6.10 &  5.6 &  6.10 &  7.1 &  6.20 &  5.8 &  4.20 &  3.7 &  4.70\\\\\n",
       "\tABCA11P &  5.80 &  5.7 &  6.1 &  6.6 &  6.20 &  6.9 &  6.4 &  6.5 &  6.60 &  6.80 & ... &  7.20 &  6.30 &  6.0 &  6.70 &  6.7 &  5.80 &  6.6 &  6.40 &  6.2 &  7.70\\\\\n",
       "\tABCA1 &  7.80 &  8.5 &  9.2 &  9.0 &  8.70 &  9.9 &  9.3 &  9.7 &  8.70 &  8.30 & ... & 10.00 &  9.00 &  9.3 & 10.00 & 10.4 & 10.60 &  9.5 & 10.40 &  7.8 &  9.90\\\\\n",
       "\tABCA2 & 10.40 & 10.9 & 10.6 & 10.0 & 10.00 & 11.1 & 11.0 & 10.4 & 10.70 & 12.00 & ... & 11.10 & 10.40 & 10.5 & 11.00 & 11.4 & 10.50 & 10.9 & 10.30 & 10.7 &  9.80\\\\\n",
       "\tABCA3 &  9.70 &  9.5 &  8.0 &  7.9 &  9.30 &  8.1 &  8.4 &  9.7 &  9.20 &  9.10 & ... & 10.70 &  9.10 &  9.9 &  9.10 &  9.7 &  8.80 &  9.5 &  6.30 &  9.2 &  8.80\\\\\n",
       "\tABCA5 &  8.10 &  9.0 &  7.7 &  7.6 &  8.80 &  8.6 &  7.6 &  8.8 &  8.50 &  8.30 & ... &  9.50 &  8.40 &  8.6 &  8.90 &  8.3 &  8.00 &  8.5 &  7.50 &  7.4 &  9.10\\\\\n",
       "\tABCA6 &  7.90 &  6.0 &  5.7 &  6.7 &  7.70 &  9.3 &  6.2 &  8.0 &  6.50 &  9.70 & ... &  8.50 &  7.90 &  7.0 &  7.20 &  8.5 &  8.40 &  8.1 &  6.50 &  3.9 &  7.60\\\\\n",
       "\tABCA7 &  9.30 &  9.7 & 10.4 & 10.4 &  9.20 &  9.8 & 10.3 & 10.0 & 10.60 & 10.00 & ... &  9.60 &  9.70 &  9.5 &  9.70 & 10.4 &  9.30 &  9.8 &  8.20 &  9.9 & 11.00\\\\\n",
       "\tABCA8 &  6.90 &  6.7 &  6.9 &  7.7 &  6.40 &  9.6 &  5.0 &  8.2 &  6.40 &  3.80 & ... & 10.60 &  8.10 &  4.8 &  8.00 & 10.7 &  9.20 &  8.1 &  3.90 &  4.5 &  7.90\\\\\n",
       "\tABCA9 &  7.00 &  6.7 &  5.9 &  6.2 &  7.50 &  9.1 &  5.7 &  8.1 &  6.10 &  6.40 & ... &  8.80 &  7.00 &  6.9 &  7.00 &  8.4 &  8.40 &  8.1 &  5.80 &  4.2 &  6.20\\\\\n",
       "\t... & ... & ... & ... & ... & ... & ... & ... & ... & ... & ... &  & ... & ... & ... & ... & ... & ... & ... & ... & ... & ...\\\\\n",
       "\tZRANB2 &  9.4 & 10.2 & 10.4 & 10.6 &  9.7 & 10.7 & 10.2 & 10.4 &  9.6 &  9.9 & ... & 10.5 & 10.0 & 10.0 & 10.3 & 10.3 &  9.8 & 10.2 & 10.5 & 10.2 & 11.1\\\\\n",
       "\tZRANB3 &  5.5 &  5.4 &  4.9 &  5.7 &  4.8 &  5.4 &  5.8 &  6.0 &  5.1 &  5.6 & ... &  5.9 &  5.0 &  5.0 &  5.5 &  5.6 &  4.9 &  5.1 &  3.5 &  4.6 &  5.8\\\\\n",
       "\tZRSR2 &  8.1 &  7.9 &  7.8 &  8.0 &  8.1 &  8.1 &  7.7 &  8.0 &  7.8 &  9.0 & ... &  8.7 &  8.6 &  7.8 &  7.9 &  8.6 &  8.0 &  7.9 &  8.5 &  8.7 &  9.5\\\\\n",
       "\tZSCAN12P1 &  4.0 &  5.0 &  5.2 &  6.0 &  5.1 &  5.4 &  5.1 &  6.2 &  4.3 &  3.2 & ... &  4.6 &  4.5 &  4.8 &  4.7 &  4.8 &  4.0 &  4.7 &  4.9 &  2.6 &  5.0\\\\\n",
       "\tZSCAN12 &  7.2 &  7.0 &  6.6 &  7.6 &  7.3 &  7.9 &  6.4 &  7.6 &  7.1 &  6.6 & ... &  7.4 &  7.6 &  7.0 &  7.3 &  7.7 &  6.8 &  7.0 &  6.8 &  7.0 &  8.1\\\\\n",
       "\tZSCAN16 &  6.9 &  6.1 &  5.4 &  6.5 &  6.2 &  6.8 &  7.1 &  7.1 &  6.5 &  6.0 & ... &  6.2 &  6.5 &  6.2 &  5.7 &  6.5 &  5.7 &  5.4 &  6.3 &  7.0 &  7.2\\\\\n",
       "\tZSCAN18 &  9.1 &  9.8 &  9.9 &  9.2 & 10.1 &  9.3 &  9.1 &  9.5 & 10.1 &  8.3 & ... & 10.5 & 10.4 &  9.5 & 10.0 & 10.4 & 10.0 &  9.6 &  9.3 &  8.2 & 10.2\\\\\n",
       "\tZSCAN20 &  6.0 &  6.0 &  6.3 &  5.9 &  5.7 &  6.1 &  5.9 &  6.2 &  5.9 &  5.7 & ... &  5.8 &  5.9 &  6.3 &  6.2 &  5.9 &  5.9 &  5.7 &  5.6 &  5.6 &  5.6\\\\\n",
       "\tZSCAN21 &  8.0 &  7.6 &  7.7 &  7.1 &  7.9 &  7.9 &  7.6 &  7.8 &  7.6 &  7.8 & ... &  7.9 &  7.8 &  7.9 &  7.6 &  7.6 &  7.4 &  7.2 &  7.4 &  7.6 &  7.4\\\\\n",
       "\tZSCAN22 &  7.3 &  6.2 &  6.6 &  6.8 &  7.0 &  7.2 &  6.3 &  6.9 &  6.8 &  6.6 & ... &  7.1 &  6.8 &  6.4 &  7.2 &  6.5 &  6.5 &  6.6 &  6.3 &  6.7 &  6.4\\\\\n",
       "\tZSCAN29 &  8.7 &  8.5 &  7.9 &  8.9 &  8.6 &  9.1 &  8.4 &  9.1 &  8.5 &  9.1 & ... &  8.8 &  8.5 &  8.3 &  8.9 &  8.6 &  8.1 &  8.2 &  8.3 &  8.8 &  9.3\\\\\n",
       "\tZSCAN2 &  7.1 &  7.5 &  6.9 &  7.4 &  8.0 &  7.4 &  7.5 &  7.6 &  7.4 &  8.2 & ... &  8.0 &  7.3 &  7.5 &  7.7 &  7.6 &  7.2 &  7.1 &  7.5 &  7.3 &  7.6\\\\\n",
       "\tZSCAN5A &  6.0 &  5.7 &  5.7 &  6.1 &  6.1 &  5.7 &  5.4 &  6.6 &  5.6 &  4.8 & ... &  6.3 &  5.1 &  5.0 &  6.4 &  6.1 &  5.5 &  5.2 &  5.2 &  5.4 &  6.2\\\\\n",
       "\tZSWIM1 &  8.6 &  7.9 &  8.2 &  8.0 &  8.4 &  8.1 &  8.1 &  8.3 &  7.9 &  8.8 & ... &  8.1 &  8.5 &  7.9 &  8.4 &  7.9 &  7.9 &  7.9 &  8.1 &  8.4 &  8.2\\\\\n",
       "\tZSWIM3 &  7.1 &  6.2 &  5.7 &  6.1 &  7.0 &  6.7 &  6.6 &  7.7 &  6.3 &  6.9 & ... &  7.2 &  7.4 &  7.2 &  6.8 &  6.6 &  6.7 &  6.0 &  6.6 &  6.8 &  6.7\\\\\n",
       "\tZSWIM4 &  8.8 &  9.2 &  8.8 &  9.8 &  9.9 &  9.0 &  9.8 &  9.3 &  9.8 &  9.7 & ... &  8.5 &  9.0 & 10.0 &  8.9 &  9.3 &  9.9 &  9.5 & 10.6 &  9.7 &  8.5\\\\\n",
       "\tZSWIM5 &  8.2 &  6.9 &  5.3 &  6.3 &  6.9 &  8.5 &  7.2 &  6.7 &  6.3 &  5.7 & ... &  7.9 &  6.1 &  6.7 &  6.4 &  6.5 &  5.4 &  6.9 &  3.5 &  7.5 &  7.0\\\\\n",
       "\tZSWIM6 &  8.8 &  9.4 &  8.7 &  8.8 &  8.6 &  8.4 &  9.1 &  8.9 &  9.5 &  9.0 & ... &  9.0 &  8.8 &  8.6 &  8.9 &  9.2 &  9.3 &  8.8 &  9.1 &  9.1 &  8.9\\\\\n",
       "\tZSWIM7 &  8.1 &  8.1 &  7.3 &  8.0 &  8.0 &  8.2 &  8.0 &  7.9 &  7.6 &  7.9 & ... &  8.2 &  7.8 &  7.6 &  8.1 &  8.2 &  8.2 &  7.5 &  7.3 &  7.4 &  7.9\\\\\n",
       "\tZUFSP &  7.0 &  7.5 &  7.0 &  7.4 &  7.0 &  6.7 &  6.3 &  7.6 &  6.6 &  6.6 & ... &  7.3 &  7.5 &  7.4 &  6.8 &  7.3 &  7.3 &  6.9 &  7.0 &  6.8 &  7.6\\\\\n",
       "\tZW10 &  8.6 &  8.7 &  8.8 &  8.6 &  8.9 &  8.6 &  8.3 &  8.6 &  8.5 &  9.0 & ... &  8.5 &  8.0 &  8.3 &  8.5 &  8.4 &  8.2 &  8.2 &  8.1 &  8.6 &  8.5\\\\\n",
       "\tZWILCH &  8.1 &  8.1 &  8.4 &  8.6 &  8.2 &  8.0 &  7.6 &  8.5 &  7.3 &  8.4 & ... &  7.5 &  7.9 &  8.0 &  8.2 &  8.0 &  7.7 &  7.5 &  8.4 &  8.0 &  8.6\\\\\n",
       "\tZWINT &  8.6 &  8.8 &  9.1 &  8.9 &  8.4 &  7.5 &  7.9 &  9.0 &  8.6 &  9.2 & ... &  7.0 &  8.6 &  8.4 &  9.1 &  7.6 &  7.8 &  7.9 &  9.4 &  8.8 &  9.1\\\\\n",
       "\tZXDA &  6.2 &  5.8 &  3.9 &  5.2 &  5.9 &  5.7 &  5.8 &  5.8 &  6.4 &  5.6 & ... &  5.9 &  5.6 &  5.6 &  5.4 &  5.9 &  5.3 &  5.3 &  5.0 &  5.4 &  6.3\\\\\n",
       "\tZXDB &  9.0 &  8.5 &  8.1 &  8.5 &  8.6 &  8.2 &  8.8 &  8.7 &  9.4 &  9.0 & ... &  8.9 &  8.5 &  8.7 &  8.0 &  8.6 &  8.4 &  8.8 &  8.2 &  8.7 &  8.9\\\\\n",
       "\tZXDC &  9.9 & 10.0 & 10.0 &  9.7 &  9.9 & 10.6 & 10.1 &  9.9 &  9.8 & 10.7 & ... & 10.1 & 10.1 &  9.9 & 10.1 &  9.8 &  9.5 &  9.5 &  9.4 &  9.5 & 10.4\\\\\n",
       "\tZYG11B &  9.2 &  9.3 &  9.4 &  9.4 &  9.3 &  9.9 &  9.1 &  9.5 &  8.9 &  8.3 & ... &  9.7 &  9.2 &  9.5 &  9.5 &  9.4 &  9.4 &  9.6 &  9.2 &  8.3 &  9.5\\\\\n",
       "\tZYX & 12.9 & 12.4 & 13.5 & 12.5 & 13.0 & 12.2 & 12.9 & 12.6 & 12.7 & 12.5 & ... & 12.4 & 12.6 & 13.5 & 12.5 & 12.7 & 13.6 & 13.1 & 13.2 & 12.3 & 12.3\\\\\n",
       "\tZZEF1 & 10.1 &  9.8 &  9.8 &  9.7 & 10.1 & 10.4 &  9.7 & 10.6 & 10.0 &  9.9 & ... & 10.6 &  9.9 &  9.8 & 10.3 & 10.4 & 10.2 &  9.9 &  9.8 &  9.6 & 10.9\\\\\n",
       "\tZZZ3 &  9.3 &  8.9 &  9.2 &  9.3 &  9.2 &  9.6 &  8.9 &  9.8 &  8.8 &  8.6 & ... &  9.6 &  9.0 &  9.0 &  9.5 &  9.2 &  8.5 &  8.8 &  8.6 &  8.4 &  9.4\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A matrix: 14098 × 175 of type dbl\n",
       "\n",
       "| <!--/--> | aab1.Primary.solid.Tumor | aab4.Primary.solid.Tumor | aab6.Primary.solid.Tumor | aab8.Primary.solid.Tumor | aab9.Primary.solid.Tumor | aaba.Primary.solid.Tumor | aabe.Primary.solid.Tumor | aabf.Primary.solid.Tumor | aabh.Primary.solid.Tumor | aabi.Primary.solid.Tumor | ... | aauh.Primary.solid.Tumor | aaui.Primary.solid.Tumor | aaul.Primary.solid.Tumor | a8t3.Primary.solid.Tumor | a8t5.Primary.solid.Tumor | a89d.Solid.Tissue.Normal | a89d.Primary.solid.Tumor | a8sy.Primary.solid.Tumor | a8lh.Primary.solid.Tumor | aapl.Primary.solid.Tumor |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| SLC35E2 |  7.45 |  8.1 |  7.2 |  8.0 |  7.65 |  8.1 |  8.2 |  8.2 |  7.55 |  8.45 | ... |  8.45 |  7.95 |  8.3 |  8.05 |  8.2 |  7.25 |  7.4 |  7.35 |  7.2 |  9.05 |\n",
       "| A1BG |  6.40 |  5.8 |  6.4 |  5.8 |  6.70 |  6.6 |  6.3 |  6.5 |  5.70 |  6.30 | ... |  7.10 |  7.10 |  6.7 |  7.00 |  6.9 |  7.10 |  7.3 |  7.90 |  6.0 |  6.90 |\n",
       "| A2LD1 |  7.50 |  6.8 |  7.3 |  7.5 |  7.40 |  6.6 |  7.1 |  6.8 |  8.00 |  5.80 | ... |  6.50 |  7.30 |  6.1 |  6.70 |  6.5 |  6.70 |  6.7 |  6.50 |  6.9 |  6.70 |\n",
       "| A2M | 14.30 | 14.0 | 13.1 | 13.8 | 14.60 | 13.3 | 13.4 | 14.2 | 13.90 | 11.90 | ... | 14.50 | 14.30 | 14.5 | 14.20 | 14.3 | 14.90 | 14.5 | 13.00 | 12.1 | 13.30 |\n",
       "| A4GALT | 10.60 | 10.2 | 10.1 |  8.6 | 10.10 |  9.3 |  9.5 |  8.4 |  8.40 |  7.90 | ... |  9.10 |  9.50 | 10.0 |  9.50 |  9.1 | 10.50 |  9.8 | 10.80 |  8.3 |  9.00 |\n",
       "| AAAS |  9.40 |  9.1 |  9.7 |  9.6 |  9.80 |  9.3 |  9.5 |  9.3 |  9.00 |  9.30 | ... |  9.20 |  9.40 |  9.3 |  9.50 |  9.0 |  9.20 |  9.2 |  9.30 |  9.6 |  9.60 |\n",
       "| AACS | 10.20 | 10.3 |  9.2 |  9.4 |  9.30 |  9.9 | 10.3 | 10.0 |  9.70 |  9.10 | ... | 10.50 | 10.20 |  9.6 | 10.00 |  9.9 |  9.50 | 10.1 |  9.50 | 10.0 |  8.60 |\n",
       "| AADAT |  4.80 |  6.3 |  5.9 |  6.4 |  6.50 |  6.0 |  6.6 |  6.3 |  5.40 |  4.10 | ... |  6.40 |  5.80 |  5.6 |  6.70 |  6.4 |  5.50 |  6.2 |  6.20 |  6.0 |  4.90 |\n",
       "| AAGAB | 10.20 | 10.4 |  9.9 | 10.5 | 10.10 | 10.3 |  9.4 | 10.1 |  9.70 |  9.80 | ... | 10.00 |  9.90 | 10.2 |  9.90 | 10.2 |  9.90 | 10.0 |  9.70 | 10.5 | 10.10 |\n",
       "| AAK1 |  9.60 |  9.8 |  9.8 |  9.2 |  9.80 |  9.7 |  9.5 |  9.9 |  9.70 | 10.50 | ... | 10.20 |  9.90 |  9.7 | 10.00 | 10.0 | 10.00 |  9.5 |  9.60 |  8.9 | 10.50 |\n",
       "| AAMP | 11.80 | 11.4 | 11.1 | 11.6 | 11.20 | 11.6 | 11.7 | 11.3 | 11.80 | 12.00 | ... | 11.30 | 11.70 | 11.5 | 11.20 | 11.4 | 11.30 | 11.5 | 11.60 | 11.9 | 11.10 |\n",
       "| AARS2 |  8.60 |  8.4 |  8.4 |  8.7 |  8.40 |  8.7 |  8.6 |  9.1 |  8.50 |  8.60 | ... |  8.70 |  8.30 |  8.3 |  9.00 |  8.7 |  8.40 |  8.3 |  8.60 |  8.9 |  8.80 |\n",
       "| AARSD1 |  8.90 |  8.7 |  8.8 |  9.1 |  9.30 |  9.0 |  9.1 |  8.8 |  8.90 |  9.60 | ... |  9.00 |  9.10 |  8.8 |  9.10 |  9.1 |  9.20 |  8.9 |  9.50 |  9.1 |  9.00 |\n",
       "| AARS | 11.30 | 11.6 | 11.4 | 11.4 | 11.40 | 11.3 | 11.3 | 11.6 | 11.40 | 11.60 | ... | 11.60 | 12.10 | 11.2 | 11.00 | 11.5 | 11.40 | 11.7 | 11.20 | 12.0 | 11.10 |\n",
       "| AASDHPPT |  8.60 |  9.0 |  9.3 |  9.4 |  9.40 |  9.0 |  8.8 |  9.2 |  8.80 |  9.10 | ... |  9.10 |  9.00 |  9.0 |  9.30 |  9.3 |  8.90 |  9.0 |  8.70 |  8.7 |  9.50 |\n",
       "| AASDH |  7.50 |  7.5 |  6.7 |  7.7 |  7.20 |  8.2 |  7.8 |  7.6 |  7.30 |  8.30 | ... |  8.10 |  7.30 |  7.2 |  7.40 |  7.8 |  6.80 |  7.0 |  6.90 |  7.0 |  8.00 |\n",
       "| AASS |  8.10 |  8.2 |  7.3 |  7.8 |  8.30 |  8.7 |  7.9 |  8.4 |  8.60 |  7.60 | ... |  8.80 |  8.80 |  8.5 |  8.70 |  8.6 |  8.30 |  8.4 |  8.20 |  7.3 |  8.10 |\n",
       "| AATF | 10.60 | 10.2 | 10.3 | 10.1 | 10.30 | 10.2 | 10.3 | 10.1 | 10.40 | 10.90 | ... | 10.10 | 10.80 | 10.1 | 10.00 | 10.2 | 10.30 | 10.3 | 10.50 | 10.9 | 10.50 |\n",
       "| AATK | 10.00 |  8.1 |  7.3 |  8.3 |  8.60 |  8.7 |  9.2 |  7.9 |  9.10 |  6.20 | ... |  7.70 |  7.70 |  7.5 |  6.70 |  9.2 |  7.40 |  7.9 |  9.20 |  7.8 |  7.00 |\n",
       "| ABAT |  9.40 |  9.3 |  8.4 |  8.4 |  9.40 |  7.4 |  8.7 |  9.8 | 10.00 |  7.30 | ... | 11.40 |  8.90 |  8.5 |  8.90 |  9.2 |  8.70 | 10.1 |  7.60 |  8.5 |  8.10 |\n",
       "| ABCA10 |  4.40 |  4.9 |  4.7 |  5.4 |  5.90 |  7.7 |  4.6 |  6.3 |  4.00 |  4.70 | ... |  6.80 |  6.10 |  5.6 |  6.10 |  7.1 |  6.20 |  5.8 |  4.20 |  3.7 |  4.70 |\n",
       "| ABCA11P |  5.80 |  5.7 |  6.1 |  6.6 |  6.20 |  6.9 |  6.4 |  6.5 |  6.60 |  6.80 | ... |  7.20 |  6.30 |  6.0 |  6.70 |  6.7 |  5.80 |  6.6 |  6.40 |  6.2 |  7.70 |\n",
       "| ABCA1 |  7.80 |  8.5 |  9.2 |  9.0 |  8.70 |  9.9 |  9.3 |  9.7 |  8.70 |  8.30 | ... | 10.00 |  9.00 |  9.3 | 10.00 | 10.4 | 10.60 |  9.5 | 10.40 |  7.8 |  9.90 |\n",
       "| ABCA2 | 10.40 | 10.9 | 10.6 | 10.0 | 10.00 | 11.1 | 11.0 | 10.4 | 10.70 | 12.00 | ... | 11.10 | 10.40 | 10.5 | 11.00 | 11.4 | 10.50 | 10.9 | 10.30 | 10.7 |  9.80 |\n",
       "| ABCA3 |  9.70 |  9.5 |  8.0 |  7.9 |  9.30 |  8.1 |  8.4 |  9.7 |  9.20 |  9.10 | ... | 10.70 |  9.10 |  9.9 |  9.10 |  9.7 |  8.80 |  9.5 |  6.30 |  9.2 |  8.80 |\n",
       "| ABCA5 |  8.10 |  9.0 |  7.7 |  7.6 |  8.80 |  8.6 |  7.6 |  8.8 |  8.50 |  8.30 | ... |  9.50 |  8.40 |  8.6 |  8.90 |  8.3 |  8.00 |  8.5 |  7.50 |  7.4 |  9.10 |\n",
       "| ABCA6 |  7.90 |  6.0 |  5.7 |  6.7 |  7.70 |  9.3 |  6.2 |  8.0 |  6.50 |  9.70 | ... |  8.50 |  7.90 |  7.0 |  7.20 |  8.5 |  8.40 |  8.1 |  6.50 |  3.9 |  7.60 |\n",
       "| ABCA7 |  9.30 |  9.7 | 10.4 | 10.4 |  9.20 |  9.8 | 10.3 | 10.0 | 10.60 | 10.00 | ... |  9.60 |  9.70 |  9.5 |  9.70 | 10.4 |  9.30 |  9.8 |  8.20 |  9.9 | 11.00 |\n",
       "| ABCA8 |  6.90 |  6.7 |  6.9 |  7.7 |  6.40 |  9.6 |  5.0 |  8.2 |  6.40 |  3.80 | ... | 10.60 |  8.10 |  4.8 |  8.00 | 10.7 |  9.20 |  8.1 |  3.90 |  4.5 |  7.90 |\n",
       "| ABCA9 |  7.00 |  6.7 |  5.9 |  6.2 |  7.50 |  9.1 |  5.7 |  8.1 |  6.10 |  6.40 | ... |  8.80 |  7.00 |  6.9 |  7.00 |  8.4 |  8.40 |  8.1 |  5.80 |  4.2 |  6.20 |\n",
       "| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | <!----> | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |\n",
       "| ZRANB2 |  9.4 | 10.2 | 10.4 | 10.6 |  9.7 | 10.7 | 10.2 | 10.4 |  9.6 |  9.9 | ... | 10.5 | 10.0 | 10.0 | 10.3 | 10.3 |  9.8 | 10.2 | 10.5 | 10.2 | 11.1 |\n",
       "| ZRANB3 |  5.5 |  5.4 |  4.9 |  5.7 |  4.8 |  5.4 |  5.8 |  6.0 |  5.1 |  5.6 | ... |  5.9 |  5.0 |  5.0 |  5.5 |  5.6 |  4.9 |  5.1 |  3.5 |  4.6 |  5.8 |\n",
       "| ZRSR2 |  8.1 |  7.9 |  7.8 |  8.0 |  8.1 |  8.1 |  7.7 |  8.0 |  7.8 |  9.0 | ... |  8.7 |  8.6 |  7.8 |  7.9 |  8.6 |  8.0 |  7.9 |  8.5 |  8.7 |  9.5 |\n",
       "| ZSCAN12P1 |  4.0 |  5.0 |  5.2 |  6.0 |  5.1 |  5.4 |  5.1 |  6.2 |  4.3 |  3.2 | ... |  4.6 |  4.5 |  4.8 |  4.7 |  4.8 |  4.0 |  4.7 |  4.9 |  2.6 |  5.0 |\n",
       "| ZSCAN12 |  7.2 |  7.0 |  6.6 |  7.6 |  7.3 |  7.9 |  6.4 |  7.6 |  7.1 |  6.6 | ... |  7.4 |  7.6 |  7.0 |  7.3 |  7.7 |  6.8 |  7.0 |  6.8 |  7.0 |  8.1 |\n",
       "| ZSCAN16 |  6.9 |  6.1 |  5.4 |  6.5 |  6.2 |  6.8 |  7.1 |  7.1 |  6.5 |  6.0 | ... |  6.2 |  6.5 |  6.2 |  5.7 |  6.5 |  5.7 |  5.4 |  6.3 |  7.0 |  7.2 |\n",
       "| ZSCAN18 |  9.1 |  9.8 |  9.9 |  9.2 | 10.1 |  9.3 |  9.1 |  9.5 | 10.1 |  8.3 | ... | 10.5 | 10.4 |  9.5 | 10.0 | 10.4 | 10.0 |  9.6 |  9.3 |  8.2 | 10.2 |\n",
       "| ZSCAN20 |  6.0 |  6.0 |  6.3 |  5.9 |  5.7 |  6.1 |  5.9 |  6.2 |  5.9 |  5.7 | ... |  5.8 |  5.9 |  6.3 |  6.2 |  5.9 |  5.9 |  5.7 |  5.6 |  5.6 |  5.6 |\n",
       "| ZSCAN21 |  8.0 |  7.6 |  7.7 |  7.1 |  7.9 |  7.9 |  7.6 |  7.8 |  7.6 |  7.8 | ... |  7.9 |  7.8 |  7.9 |  7.6 |  7.6 |  7.4 |  7.2 |  7.4 |  7.6 |  7.4 |\n",
       "| ZSCAN22 |  7.3 |  6.2 |  6.6 |  6.8 |  7.0 |  7.2 |  6.3 |  6.9 |  6.8 |  6.6 | ... |  7.1 |  6.8 |  6.4 |  7.2 |  6.5 |  6.5 |  6.6 |  6.3 |  6.7 |  6.4 |\n",
       "| ZSCAN29 |  8.7 |  8.5 |  7.9 |  8.9 |  8.6 |  9.1 |  8.4 |  9.1 |  8.5 |  9.1 | ... |  8.8 |  8.5 |  8.3 |  8.9 |  8.6 |  8.1 |  8.2 |  8.3 |  8.8 |  9.3 |\n",
       "| ZSCAN2 |  7.1 |  7.5 |  6.9 |  7.4 |  8.0 |  7.4 |  7.5 |  7.6 |  7.4 |  8.2 | ... |  8.0 |  7.3 |  7.5 |  7.7 |  7.6 |  7.2 |  7.1 |  7.5 |  7.3 |  7.6 |\n",
       "| ZSCAN5A |  6.0 |  5.7 |  5.7 |  6.1 |  6.1 |  5.7 |  5.4 |  6.6 |  5.6 |  4.8 | ... |  6.3 |  5.1 |  5.0 |  6.4 |  6.1 |  5.5 |  5.2 |  5.2 |  5.4 |  6.2 |\n",
       "| ZSWIM1 |  8.6 |  7.9 |  8.2 |  8.0 |  8.4 |  8.1 |  8.1 |  8.3 |  7.9 |  8.8 | ... |  8.1 |  8.5 |  7.9 |  8.4 |  7.9 |  7.9 |  7.9 |  8.1 |  8.4 |  8.2 |\n",
       "| ZSWIM3 |  7.1 |  6.2 |  5.7 |  6.1 |  7.0 |  6.7 |  6.6 |  7.7 |  6.3 |  6.9 | ... |  7.2 |  7.4 |  7.2 |  6.8 |  6.6 |  6.7 |  6.0 |  6.6 |  6.8 |  6.7 |\n",
       "| ZSWIM4 |  8.8 |  9.2 |  8.8 |  9.8 |  9.9 |  9.0 |  9.8 |  9.3 |  9.8 |  9.7 | ... |  8.5 |  9.0 | 10.0 |  8.9 |  9.3 |  9.9 |  9.5 | 10.6 |  9.7 |  8.5 |\n",
       "| ZSWIM5 |  8.2 |  6.9 |  5.3 |  6.3 |  6.9 |  8.5 |  7.2 |  6.7 |  6.3 |  5.7 | ... |  7.9 |  6.1 |  6.7 |  6.4 |  6.5 |  5.4 |  6.9 |  3.5 |  7.5 |  7.0 |\n",
       "| ZSWIM6 |  8.8 |  9.4 |  8.7 |  8.8 |  8.6 |  8.4 |  9.1 |  8.9 |  9.5 |  9.0 | ... |  9.0 |  8.8 |  8.6 |  8.9 |  9.2 |  9.3 |  8.8 |  9.1 |  9.1 |  8.9 |\n",
       "| ZSWIM7 |  8.1 |  8.1 |  7.3 |  8.0 |  8.0 |  8.2 |  8.0 |  7.9 |  7.6 |  7.9 | ... |  8.2 |  7.8 |  7.6 |  8.1 |  8.2 |  8.2 |  7.5 |  7.3 |  7.4 |  7.9 |\n",
       "| ZUFSP |  7.0 |  7.5 |  7.0 |  7.4 |  7.0 |  6.7 |  6.3 |  7.6 |  6.6 |  6.6 | ... |  7.3 |  7.5 |  7.4 |  6.8 |  7.3 |  7.3 |  6.9 |  7.0 |  6.8 |  7.6 |\n",
       "| ZW10 |  8.6 |  8.7 |  8.8 |  8.6 |  8.9 |  8.6 |  8.3 |  8.6 |  8.5 |  9.0 | ... |  8.5 |  8.0 |  8.3 |  8.5 |  8.4 |  8.2 |  8.2 |  8.1 |  8.6 |  8.5 |\n",
       "| ZWILCH |  8.1 |  8.1 |  8.4 |  8.6 |  8.2 |  8.0 |  7.6 |  8.5 |  7.3 |  8.4 | ... |  7.5 |  7.9 |  8.0 |  8.2 |  8.0 |  7.7 |  7.5 |  8.4 |  8.0 |  8.6 |\n",
       "| ZWINT |  8.6 |  8.8 |  9.1 |  8.9 |  8.4 |  7.5 |  7.9 |  9.0 |  8.6 |  9.2 | ... |  7.0 |  8.6 |  8.4 |  9.1 |  7.6 |  7.8 |  7.9 |  9.4 |  8.8 |  9.1 |\n",
       "| ZXDA |  6.2 |  5.8 |  3.9 |  5.2 |  5.9 |  5.7 |  5.8 |  5.8 |  6.4 |  5.6 | ... |  5.9 |  5.6 |  5.6 |  5.4 |  5.9 |  5.3 |  5.3 |  5.0 |  5.4 |  6.3 |\n",
       "| ZXDB |  9.0 |  8.5 |  8.1 |  8.5 |  8.6 |  8.2 |  8.8 |  8.7 |  9.4 |  9.0 | ... |  8.9 |  8.5 |  8.7 |  8.0 |  8.6 |  8.4 |  8.8 |  8.2 |  8.7 |  8.9 |\n",
       "| ZXDC |  9.9 | 10.0 | 10.0 |  9.7 |  9.9 | 10.6 | 10.1 |  9.9 |  9.8 | 10.7 | ... | 10.1 | 10.1 |  9.9 | 10.1 |  9.8 |  9.5 |  9.5 |  9.4 |  9.5 | 10.4 |\n",
       "| ZYG11B |  9.2 |  9.3 |  9.4 |  9.4 |  9.3 |  9.9 |  9.1 |  9.5 |  8.9 |  8.3 | ... |  9.7 |  9.2 |  9.5 |  9.5 |  9.4 |  9.4 |  9.6 |  9.2 |  8.3 |  9.5 |\n",
       "| ZYX | 12.9 | 12.4 | 13.5 | 12.5 | 13.0 | 12.2 | 12.9 | 12.6 | 12.7 | 12.5 | ... | 12.4 | 12.6 | 13.5 | 12.5 | 12.7 | 13.6 | 13.1 | 13.2 | 12.3 | 12.3 |\n",
       "| ZZEF1 | 10.1 |  9.8 |  9.8 |  9.7 | 10.1 | 10.4 |  9.7 | 10.6 | 10.0 |  9.9 | ... | 10.6 |  9.9 |  9.8 | 10.3 | 10.4 | 10.2 |  9.9 |  9.8 |  9.6 | 10.9 |\n",
       "| ZZZ3 |  9.3 |  8.9 |  9.2 |  9.3 |  9.2 |  9.6 |  8.9 |  9.8 |  8.8 |  8.6 | ... |  9.6 |  9.0 |  9.0 |  9.5 |  9.2 |  8.5 |  8.8 |  8.6 |  8.4 |  9.4 |\n",
       "\n"
      ],
      "text/plain": [
       "          aab1.Primary.solid.Tumor aab4.Primary.solid.Tumor\n",
       "SLC35E2    7.45                     8.1                    \n",
       "A1BG       6.40                     5.8                    \n",
       "A2LD1      7.50                     6.8                    \n",
       "A2M       14.30                    14.0                    \n",
       "A4GALT    10.60                    10.2                    \n",
       "AAAS       9.40                     9.1                    \n",
       "AACS      10.20                    10.3                    \n",
       "AADAT      4.80                     6.3                    \n",
       "AAGAB     10.20                    10.4                    \n",
       "AAK1       9.60                     9.8                    \n",
       "AAMP      11.80                    11.4                    \n",
       "AARS2      8.60                     8.4                    \n",
       "AARSD1     8.90                     8.7                    \n",
       "AARS      11.30                    11.6                    \n",
       "AASDHPPT   8.60                     9.0                    \n",
       "AASDH      7.50                     7.5                    \n",
       "AASS       8.10                     8.2                    \n",
       "AATF      10.60                    10.2                    \n",
       "AATK      10.00                     8.1                    \n",
       "ABAT       9.40                     9.3                    \n",
       "ABCA10     4.40                     4.9                    \n",
       "ABCA11P    5.80                     5.7                    \n",
       "ABCA1      7.80                     8.5                    \n",
       "ABCA2     10.40                    10.9                    \n",
       "ABCA3      9.70                     9.5                    \n",
       "ABCA5      8.10                     9.0                    \n",
       "ABCA6      7.90                     6.0                    \n",
       "ABCA7      9.30                     9.7                    \n",
       "ABCA8      6.90                     6.7                    \n",
       "ABCA9      7.00                     6.7                    \n",
       "...       ...                      ...                     \n",
       "ZRANB2     9.4                     10.2                    \n",
       "ZRANB3     5.5                      5.4                    \n",
       "ZRSR2      8.1                      7.9                    \n",
       "ZSCAN12P1  4.0                      5.0                    \n",
       "ZSCAN12    7.2                      7.0                    \n",
       "ZSCAN16    6.9                      6.1                    \n",
       "ZSCAN18    9.1                      9.8                    \n",
       "ZSCAN20    6.0                      6.0                    \n",
       "ZSCAN21    8.0                      7.6                    \n",
       "ZSCAN22    7.3                      6.2                    \n",
       "ZSCAN29    8.7                      8.5                    \n",
       "ZSCAN2     7.1                      7.5                    \n",
       "ZSCAN5A    6.0                      5.7                    \n",
       "ZSWIM1     8.6                      7.9                    \n",
       "ZSWIM3     7.1                      6.2                    \n",
       "ZSWIM4     8.8                      9.2                    \n",
       "ZSWIM5     8.2                      6.9                    \n",
       "ZSWIM6     8.8                      9.4                    \n",
       "ZSWIM7     8.1                      8.1                    \n",
       "ZUFSP      7.0                      7.5                    \n",
       "ZW10       8.6                      8.7                    \n",
       "ZWILCH     8.1                      8.1                    \n",
       "ZWINT      8.6                      8.8                    \n",
       "ZXDA       6.2                      5.8                    \n",
       "ZXDB       9.0                      8.5                    \n",
       "ZXDC       9.9                     10.0                    \n",
       "ZYG11B     9.2                      9.3                    \n",
       "ZYX       12.9                     12.4                    \n",
       "ZZEF1     10.1                      9.8                    \n",
       "ZZZ3       9.3                      8.9                    \n",
       "          aab6.Primary.solid.Tumor aab8.Primary.solid.Tumor\n",
       "SLC35E2    7.2                      8.0                    \n",
       "A1BG       6.4                      5.8                    \n",
       "A2LD1      7.3                      7.5                    \n",
       "A2M       13.1                     13.8                    \n",
       "A4GALT    10.1                      8.6                    \n",
       "AAAS       9.7                      9.6                    \n",
       "AACS       9.2                      9.4                    \n",
       "AADAT      5.9                      6.4                    \n",
       "AAGAB      9.9                     10.5                    \n",
       "AAK1       9.8                      9.2                    \n",
       "AAMP      11.1                     11.6                    \n",
       "AARS2      8.4                      8.7                    \n",
       "AARSD1     8.8                      9.1                    \n",
       "AARS      11.4                     11.4                    \n",
       "AASDHPPT   9.3                      9.4                    \n",
       "AASDH      6.7                      7.7                    \n",
       "AASS       7.3                      7.8                    \n",
       "AATF      10.3                     10.1                    \n",
       "AATK       7.3                      8.3                    \n",
       "ABAT       8.4                      8.4                    \n",
       "ABCA10     4.7                      5.4                    \n",
       "ABCA11P    6.1                      6.6                    \n",
       "ABCA1      9.2                      9.0                    \n",
       "ABCA2     10.6                     10.0                    \n",
       "ABCA3      8.0                      7.9                    \n",
       "ABCA5      7.7                      7.6                    \n",
       "ABCA6      5.7                      6.7                    \n",
       "ABCA7     10.4                     10.4                    \n",
       "ABCA8      6.9                      7.7                    \n",
       "ABCA9      5.9                      6.2                    \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.4                     10.6                    \n",
       "ZRANB3     4.9                      5.7                    \n",
       "ZRSR2      7.8                      8.0                    \n",
       "ZSCAN12P1  5.2                      6.0                    \n",
       "ZSCAN12    6.6                      7.6                    \n",
       "ZSCAN16    5.4                      6.5                    \n",
       "ZSCAN18    9.9                      9.2                    \n",
       "ZSCAN20    6.3                      5.9                    \n",
       "ZSCAN21    7.7                      7.1                    \n",
       "ZSCAN22    6.6                      6.8                    \n",
       "ZSCAN29    7.9                      8.9                    \n",
       "ZSCAN2     6.9                      7.4                    \n",
       "ZSCAN5A    5.7                      6.1                    \n",
       "ZSWIM1     8.2                      8.0                    \n",
       "ZSWIM3     5.7                      6.1                    \n",
       "ZSWIM4     8.8                      9.8                    \n",
       "ZSWIM5     5.3                      6.3                    \n",
       "ZSWIM6     8.7                      8.8                    \n",
       "ZSWIM7     7.3                      8.0                    \n",
       "ZUFSP      7.0                      7.4                    \n",
       "ZW10       8.8                      8.6                    \n",
       "ZWILCH     8.4                      8.6                    \n",
       "ZWINT      9.1                      8.9                    \n",
       "ZXDA       3.9                      5.2                    \n",
       "ZXDB       8.1                      8.5                    \n",
       "ZXDC      10.0                      9.7                    \n",
       "ZYG11B     9.4                      9.4                    \n",
       "ZYX       13.5                     12.5                    \n",
       "ZZEF1      9.8                      9.7                    \n",
       "ZZZ3       9.2                      9.3                    \n",
       "          aab9.Primary.solid.Tumor aaba.Primary.solid.Tumor\n",
       "SLC35E2    7.65                     8.1                    \n",
       "A1BG       6.70                     6.6                    \n",
       "A2LD1      7.40                     6.6                    \n",
       "A2M       14.60                    13.3                    \n",
       "A4GALT    10.10                     9.3                    \n",
       "AAAS       9.80                     9.3                    \n",
       "AACS       9.30                     9.9                    \n",
       "AADAT      6.50                     6.0                    \n",
       "AAGAB     10.10                    10.3                    \n",
       "AAK1       9.80                     9.7                    \n",
       "AAMP      11.20                    11.6                    \n",
       "AARS2      8.40                     8.7                    \n",
       "AARSD1     9.30                     9.0                    \n",
       "AARS      11.40                    11.3                    \n",
       "AASDHPPT   9.40                     9.0                    \n",
       "AASDH      7.20                     8.2                    \n",
       "AASS       8.30                     8.7                    \n",
       "AATF      10.30                    10.2                    \n",
       "AATK       8.60                     8.7                    \n",
       "ABAT       9.40                     7.4                    \n",
       "ABCA10     5.90                     7.7                    \n",
       "ABCA11P    6.20                     6.9                    \n",
       "ABCA1      8.70                     9.9                    \n",
       "ABCA2     10.00                    11.1                    \n",
       "ABCA3      9.30                     8.1                    \n",
       "ABCA5      8.80                     8.6                    \n",
       "ABCA6      7.70                     9.3                    \n",
       "ABCA7      9.20                     9.8                    \n",
       "ABCA8      6.40                     9.6                    \n",
       "ABCA9      7.50                     9.1                    \n",
       "...       ...                      ...                     \n",
       "ZRANB2     9.7                     10.7                    \n",
       "ZRANB3     4.8                      5.4                    \n",
       "ZRSR2      8.1                      8.1                    \n",
       "ZSCAN12P1  5.1                      5.4                    \n",
       "ZSCAN12    7.3                      7.9                    \n",
       "ZSCAN16    6.2                      6.8                    \n",
       "ZSCAN18   10.1                      9.3                    \n",
       "ZSCAN20    5.7                      6.1                    \n",
       "ZSCAN21    7.9                      7.9                    \n",
       "ZSCAN22    7.0                      7.2                    \n",
       "ZSCAN29    8.6                      9.1                    \n",
       "ZSCAN2     8.0                      7.4                    \n",
       "ZSCAN5A    6.1                      5.7                    \n",
       "ZSWIM1     8.4                      8.1                    \n",
       "ZSWIM3     7.0                      6.7                    \n",
       "ZSWIM4     9.9                      9.0                    \n",
       "ZSWIM5     6.9                      8.5                    \n",
       "ZSWIM6     8.6                      8.4                    \n",
       "ZSWIM7     8.0                      8.2                    \n",
       "ZUFSP      7.0                      6.7                    \n",
       "ZW10       8.9                      8.6                    \n",
       "ZWILCH     8.2                      8.0                    \n",
       "ZWINT      8.4                      7.5                    \n",
       "ZXDA       5.9                      5.7                    \n",
       "ZXDB       8.6                      8.2                    \n",
       "ZXDC       9.9                     10.6                    \n",
       "ZYG11B     9.3                      9.9                    \n",
       "ZYX       13.0                     12.2                    \n",
       "ZZEF1     10.1                     10.4                    \n",
       "ZZZ3       9.2                      9.6                    \n",
       "          aabe.Primary.solid.Tumor aabf.Primary.solid.Tumor\n",
       "SLC35E2    8.2                      8.2                    \n",
       "A1BG       6.3                      6.5                    \n",
       "A2LD1      7.1                      6.8                    \n",
       "A2M       13.4                     14.2                    \n",
       "A4GALT     9.5                      8.4                    \n",
       "AAAS       9.5                      9.3                    \n",
       "AACS      10.3                     10.0                    \n",
       "AADAT      6.6                      6.3                    \n",
       "AAGAB      9.4                     10.1                    \n",
       "AAK1       9.5                      9.9                    \n",
       "AAMP      11.7                     11.3                    \n",
       "AARS2      8.6                      9.1                    \n",
       "AARSD1     9.1                      8.8                    \n",
       "AARS      11.3                     11.6                    \n",
       "AASDHPPT   8.8                      9.2                    \n",
       "AASDH      7.8                      7.6                    \n",
       "AASS       7.9                      8.4                    \n",
       "AATF      10.3                     10.1                    \n",
       "AATK       9.2                      7.9                    \n",
       "ABAT       8.7                      9.8                    \n",
       "ABCA10     4.6                      6.3                    \n",
       "ABCA11P    6.4                      6.5                    \n",
       "ABCA1      9.3                      9.7                    \n",
       "ABCA2     11.0                     10.4                    \n",
       "ABCA3      8.4                      9.7                    \n",
       "ABCA5      7.6                      8.8                    \n",
       "ABCA6      6.2                      8.0                    \n",
       "ABCA7     10.3                     10.0                    \n",
       "ABCA8      5.0                      8.2                    \n",
       "ABCA9      5.7                      8.1                    \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.2                     10.4                    \n",
       "ZRANB3     5.8                      6.0                    \n",
       "ZRSR2      7.7                      8.0                    \n",
       "ZSCAN12P1  5.1                      6.2                    \n",
       "ZSCAN12    6.4                      7.6                    \n",
       "ZSCAN16    7.1                      7.1                    \n",
       "ZSCAN18    9.1                      9.5                    \n",
       "ZSCAN20    5.9                      6.2                    \n",
       "ZSCAN21    7.6                      7.8                    \n",
       "ZSCAN22    6.3                      6.9                    \n",
       "ZSCAN29    8.4                      9.1                    \n",
       "ZSCAN2     7.5                      7.6                    \n",
       "ZSCAN5A    5.4                      6.6                    \n",
       "ZSWIM1     8.1                      8.3                    \n",
       "ZSWIM3     6.6                      7.7                    \n",
       "ZSWIM4     9.8                      9.3                    \n",
       "ZSWIM5     7.2                      6.7                    \n",
       "ZSWIM6     9.1                      8.9                    \n",
       "ZSWIM7     8.0                      7.9                    \n",
       "ZUFSP      6.3                      7.6                    \n",
       "ZW10       8.3                      8.6                    \n",
       "ZWILCH     7.6                      8.5                    \n",
       "ZWINT      7.9                      9.0                    \n",
       "ZXDA       5.8                      5.8                    \n",
       "ZXDB       8.8                      8.7                    \n",
       "ZXDC      10.1                      9.9                    \n",
       "ZYG11B     9.1                      9.5                    \n",
       "ZYX       12.9                     12.6                    \n",
       "ZZEF1      9.7                     10.6                    \n",
       "ZZZ3       8.9                      9.8                    \n",
       "          aabh.Primary.solid.Tumor aabi.Primary.solid.Tumor ...\n",
       "SLC35E2    7.55                     8.45                    ...\n",
       "A1BG       5.70                     6.30                    ...\n",
       "A2LD1      8.00                     5.80                    ...\n",
       "A2M       13.90                    11.90                    ...\n",
       "A4GALT     8.40                     7.90                    ...\n",
       "AAAS       9.00                     9.30                    ...\n",
       "AACS       9.70                     9.10                    ...\n",
       "AADAT      5.40                     4.10                    ...\n",
       "AAGAB      9.70                     9.80                    ...\n",
       "AAK1       9.70                    10.50                    ...\n",
       "AAMP      11.80                    12.00                    ...\n",
       "AARS2      8.50                     8.60                    ...\n",
       "AARSD1     8.90                     9.60                    ...\n",
       "AARS      11.40                    11.60                    ...\n",
       "AASDHPPT   8.80                     9.10                    ...\n",
       "AASDH      7.30                     8.30                    ...\n",
       "AASS       8.60                     7.60                    ...\n",
       "AATF      10.40                    10.90                    ...\n",
       "AATK       9.10                     6.20                    ...\n",
       "ABAT      10.00                     7.30                    ...\n",
       "ABCA10     4.00                     4.70                    ...\n",
       "ABCA11P    6.60                     6.80                    ...\n",
       "ABCA1      8.70                     8.30                    ...\n",
       "ABCA2     10.70                    12.00                    ...\n",
       "ABCA3      9.20                     9.10                    ...\n",
       "ABCA5      8.50                     8.30                    ...\n",
       "ABCA6      6.50                     9.70                    ...\n",
       "ABCA7     10.60                    10.00                    ...\n",
       "ABCA8      6.40                     3.80                    ...\n",
       "ABCA9      6.10                     6.40                    ...\n",
       "...       ...                      ...                         \n",
       "ZRANB2     9.6                      9.9                     ...\n",
       "ZRANB3     5.1                      5.6                     ...\n",
       "ZRSR2      7.8                      9.0                     ...\n",
       "ZSCAN12P1  4.3                      3.2                     ...\n",
       "ZSCAN12    7.1                      6.6                     ...\n",
       "ZSCAN16    6.5                      6.0                     ...\n",
       "ZSCAN18   10.1                      8.3                     ...\n",
       "ZSCAN20    5.9                      5.7                     ...\n",
       "ZSCAN21    7.6                      7.8                     ...\n",
       "ZSCAN22    6.8                      6.6                     ...\n",
       "ZSCAN29    8.5                      9.1                     ...\n",
       "ZSCAN2     7.4                      8.2                     ...\n",
       "ZSCAN5A    5.6                      4.8                     ...\n",
       "ZSWIM1     7.9                      8.8                     ...\n",
       "ZSWIM3     6.3                      6.9                     ...\n",
       "ZSWIM4     9.8                      9.7                     ...\n",
       "ZSWIM5     6.3                      5.7                     ...\n",
       "ZSWIM6     9.5                      9.0                     ...\n",
       "ZSWIM7     7.6                      7.9                     ...\n",
       "ZUFSP      6.6                      6.6                     ...\n",
       "ZW10       8.5                      9.0                     ...\n",
       "ZWILCH     7.3                      8.4                     ...\n",
       "ZWINT      8.6                      9.2                     ...\n",
       "ZXDA       6.4                      5.6                     ...\n",
       "ZXDB       9.4                      9.0                     ...\n",
       "ZXDC       9.8                     10.7                     ...\n",
       "ZYG11B     8.9                      8.3                     ...\n",
       "ZYX       12.7                     12.5                     ...\n",
       "ZZEF1     10.0                      9.9                     ...\n",
       "ZZZ3       8.8                      8.6                     ...\n",
       "          aauh.Primary.solid.Tumor aaui.Primary.solid.Tumor\n",
       "SLC35E2    8.45                     7.95                   \n",
       "A1BG       7.10                     7.10                   \n",
       "A2LD1      6.50                     7.30                   \n",
       "A2M       14.50                    14.30                   \n",
       "A4GALT     9.10                     9.50                   \n",
       "AAAS       9.20                     9.40                   \n",
       "AACS      10.50                    10.20                   \n",
       "AADAT      6.40                     5.80                   \n",
       "AAGAB     10.00                     9.90                   \n",
       "AAK1      10.20                     9.90                   \n",
       "AAMP      11.30                    11.70                   \n",
       "AARS2      8.70                     8.30                   \n",
       "AARSD1     9.00                     9.10                   \n",
       "AARS      11.60                    12.10                   \n",
       "AASDHPPT   9.10                     9.00                   \n",
       "AASDH      8.10                     7.30                   \n",
       "AASS       8.80                     8.80                   \n",
       "AATF      10.10                    10.80                   \n",
       "AATK       7.70                     7.70                   \n",
       "ABAT      11.40                     8.90                   \n",
       "ABCA10     6.80                     6.10                   \n",
       "ABCA11P    7.20                     6.30                   \n",
       "ABCA1     10.00                     9.00                   \n",
       "ABCA2     11.10                    10.40                   \n",
       "ABCA3     10.70                     9.10                   \n",
       "ABCA5      9.50                     8.40                   \n",
       "ABCA6      8.50                     7.90                   \n",
       "ABCA7      9.60                     9.70                   \n",
       "ABCA8     10.60                     8.10                   \n",
       "ABCA9      8.80                     7.00                   \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.5                     10.0                    \n",
       "ZRANB3     5.9                      5.0                    \n",
       "ZRSR2      8.7                      8.6                    \n",
       "ZSCAN12P1  4.6                      4.5                    \n",
       "ZSCAN12    7.4                      7.6                    \n",
       "ZSCAN16    6.2                      6.5                    \n",
       "ZSCAN18   10.5                     10.4                    \n",
       "ZSCAN20    5.8                      5.9                    \n",
       "ZSCAN21    7.9                      7.8                    \n",
       "ZSCAN22    7.1                      6.8                    \n",
       "ZSCAN29    8.8                      8.5                    \n",
       "ZSCAN2     8.0                      7.3                    \n",
       "ZSCAN5A    6.3                      5.1                    \n",
       "ZSWIM1     8.1                      8.5                    \n",
       "ZSWIM3     7.2                      7.4                    \n",
       "ZSWIM4     8.5                      9.0                    \n",
       "ZSWIM5     7.9                      6.1                    \n",
       "ZSWIM6     9.0                      8.8                    \n",
       "ZSWIM7     8.2                      7.8                    \n",
       "ZUFSP      7.3                      7.5                    \n",
       "ZW10       8.5                      8.0                    \n",
       "ZWILCH     7.5                      7.9                    \n",
       "ZWINT      7.0                      8.6                    \n",
       "ZXDA       5.9                      5.6                    \n",
       "ZXDB       8.9                      8.5                    \n",
       "ZXDC      10.1                     10.1                    \n",
       "ZYG11B     9.7                      9.2                    \n",
       "ZYX       12.4                     12.6                    \n",
       "ZZEF1     10.6                      9.9                    \n",
       "ZZZ3       9.6                      9.0                    \n",
       "          aaul.Primary.solid.Tumor a8t3.Primary.solid.Tumor\n",
       "SLC35E2    8.3                      8.05                   \n",
       "A1BG       6.7                      7.00                   \n",
       "A2LD1      6.1                      6.70                   \n",
       "A2M       14.5                     14.20                   \n",
       "A4GALT    10.0                      9.50                   \n",
       "AAAS       9.3                      9.50                   \n",
       "AACS       9.6                     10.00                   \n",
       "AADAT      5.6                      6.70                   \n",
       "AAGAB     10.2                      9.90                   \n",
       "AAK1       9.7                     10.00                   \n",
       "AAMP      11.5                     11.20                   \n",
       "AARS2      8.3                      9.00                   \n",
       "AARSD1     8.8                      9.10                   \n",
       "AARS      11.2                     11.00                   \n",
       "AASDHPPT   9.0                      9.30                   \n",
       "AASDH      7.2                      7.40                   \n",
       "AASS       8.5                      8.70                   \n",
       "AATF      10.1                     10.00                   \n",
       "AATK       7.5                      6.70                   \n",
       "ABAT       8.5                      8.90                   \n",
       "ABCA10     5.6                      6.10                   \n",
       "ABCA11P    6.0                      6.70                   \n",
       "ABCA1      9.3                     10.00                   \n",
       "ABCA2     10.5                     11.00                   \n",
       "ABCA3      9.9                      9.10                   \n",
       "ABCA5      8.6                      8.90                   \n",
       "ABCA6      7.0                      7.20                   \n",
       "ABCA7      9.5                      9.70                   \n",
       "ABCA8      4.8                      8.00                   \n",
       "ABCA9      6.9                      7.00                   \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.0                     10.3                    \n",
       "ZRANB3     5.0                      5.5                    \n",
       "ZRSR2      7.8                      7.9                    \n",
       "ZSCAN12P1  4.8                      4.7                    \n",
       "ZSCAN12    7.0                      7.3                    \n",
       "ZSCAN16    6.2                      5.7                    \n",
       "ZSCAN18    9.5                     10.0                    \n",
       "ZSCAN20    6.3                      6.2                    \n",
       "ZSCAN21    7.9                      7.6                    \n",
       "ZSCAN22    6.4                      7.2                    \n",
       "ZSCAN29    8.3                      8.9                    \n",
       "ZSCAN2     7.5                      7.7                    \n",
       "ZSCAN5A    5.0                      6.4                    \n",
       "ZSWIM1     7.9                      8.4                    \n",
       "ZSWIM3     7.2                      6.8                    \n",
       "ZSWIM4    10.0                      8.9                    \n",
       "ZSWIM5     6.7                      6.4                    \n",
       "ZSWIM6     8.6                      8.9                    \n",
       "ZSWIM7     7.6                      8.1                    \n",
       "ZUFSP      7.4                      6.8                    \n",
       "ZW10       8.3                      8.5                    \n",
       "ZWILCH     8.0                      8.2                    \n",
       "ZWINT      8.4                      9.1                    \n",
       "ZXDA       5.6                      5.4                    \n",
       "ZXDB       8.7                      8.0                    \n",
       "ZXDC       9.9                     10.1                    \n",
       "ZYG11B     9.5                      9.5                    \n",
       "ZYX       13.5                     12.5                    \n",
       "ZZEF1      9.8                     10.3                    \n",
       "ZZZ3       9.0                      9.5                    \n",
       "          a8t5.Primary.solid.Tumor a89d.Solid.Tissue.Normal\n",
       "SLC35E2    8.2                      7.25                   \n",
       "A1BG       6.9                      7.10                   \n",
       "A2LD1      6.5                      6.70                   \n",
       "A2M       14.3                     14.90                   \n",
       "A4GALT     9.1                     10.50                   \n",
       "AAAS       9.0                      9.20                   \n",
       "AACS       9.9                      9.50                   \n",
       "AADAT      6.4                      5.50                   \n",
       "AAGAB     10.2                      9.90                   \n",
       "AAK1      10.0                     10.00                   \n",
       "AAMP      11.4                     11.30                   \n",
       "AARS2      8.7                      8.40                   \n",
       "AARSD1     9.1                      9.20                   \n",
       "AARS      11.5                     11.40                   \n",
       "AASDHPPT   9.3                      8.90                   \n",
       "AASDH      7.8                      6.80                   \n",
       "AASS       8.6                      8.30                   \n",
       "AATF      10.2                     10.30                   \n",
       "AATK       9.2                      7.40                   \n",
       "ABAT       9.2                      8.70                   \n",
       "ABCA10     7.1                      6.20                   \n",
       "ABCA11P    6.7                      5.80                   \n",
       "ABCA1     10.4                     10.60                   \n",
       "ABCA2     11.4                     10.50                   \n",
       "ABCA3      9.7                      8.80                   \n",
       "ABCA5      8.3                      8.00                   \n",
       "ABCA6      8.5                      8.40                   \n",
       "ABCA7     10.4                      9.30                   \n",
       "ABCA8     10.7                      9.20                   \n",
       "ABCA9      8.4                      8.40                   \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.3                      9.8                    \n",
       "ZRANB3     5.6                      4.9                    \n",
       "ZRSR2      8.6                      8.0                    \n",
       "ZSCAN12P1  4.8                      4.0                    \n",
       "ZSCAN12    7.7                      6.8                    \n",
       "ZSCAN16    6.5                      5.7                    \n",
       "ZSCAN18   10.4                     10.0                    \n",
       "ZSCAN20    5.9                      5.9                    \n",
       "ZSCAN21    7.6                      7.4                    \n",
       "ZSCAN22    6.5                      6.5                    \n",
       "ZSCAN29    8.6                      8.1                    \n",
       "ZSCAN2     7.6                      7.2                    \n",
       "ZSCAN5A    6.1                      5.5                    \n",
       "ZSWIM1     7.9                      7.9                    \n",
       "ZSWIM3     6.6                      6.7                    \n",
       "ZSWIM4     9.3                      9.9                    \n",
       "ZSWIM5     6.5                      5.4                    \n",
       "ZSWIM6     9.2                      9.3                    \n",
       "ZSWIM7     8.2                      8.2                    \n",
       "ZUFSP      7.3                      7.3                    \n",
       "ZW10       8.4                      8.2                    \n",
       "ZWILCH     8.0                      7.7                    \n",
       "ZWINT      7.6                      7.8                    \n",
       "ZXDA       5.9                      5.3                    \n",
       "ZXDB       8.6                      8.4                    \n",
       "ZXDC       9.8                      9.5                    \n",
       "ZYG11B     9.4                      9.4                    \n",
       "ZYX       12.7                     13.6                    \n",
       "ZZEF1     10.4                     10.2                    \n",
       "ZZZ3       9.2                      8.5                    \n",
       "          a89d.Primary.solid.Tumor a8sy.Primary.solid.Tumor\n",
       "SLC35E2    7.4                      7.35                   \n",
       "A1BG       7.3                      7.90                   \n",
       "A2LD1      6.7                      6.50                   \n",
       "A2M       14.5                     13.00                   \n",
       "A4GALT     9.8                     10.80                   \n",
       "AAAS       9.2                      9.30                   \n",
       "AACS      10.1                      9.50                   \n",
       "AADAT      6.2                      6.20                   \n",
       "AAGAB     10.0                      9.70                   \n",
       "AAK1       9.5                      9.60                   \n",
       "AAMP      11.5                     11.60                   \n",
       "AARS2      8.3                      8.60                   \n",
       "AARSD1     8.9                      9.50                   \n",
       "AARS      11.7                     11.20                   \n",
       "AASDHPPT   9.0                      8.70                   \n",
       "AASDH      7.0                      6.90                   \n",
       "AASS       8.4                      8.20                   \n",
       "AATF      10.3                     10.50                   \n",
       "AATK       7.9                      9.20                   \n",
       "ABAT      10.1                      7.60                   \n",
       "ABCA10     5.8                      4.20                   \n",
       "ABCA11P    6.6                      6.40                   \n",
       "ABCA1      9.5                     10.40                   \n",
       "ABCA2     10.9                     10.30                   \n",
       "ABCA3      9.5                      6.30                   \n",
       "ABCA5      8.5                      7.50                   \n",
       "ABCA6      8.1                      6.50                   \n",
       "ABCA7      9.8                      8.20                   \n",
       "ABCA8      8.1                      3.90                   \n",
       "ABCA9      8.1                      5.80                   \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.2                     10.5                    \n",
       "ZRANB3     5.1                      3.5                    \n",
       "ZRSR2      7.9                      8.5                    \n",
       "ZSCAN12P1  4.7                      4.9                    \n",
       "ZSCAN12    7.0                      6.8                    \n",
       "ZSCAN16    5.4                      6.3                    \n",
       "ZSCAN18    9.6                      9.3                    \n",
       "ZSCAN20    5.7                      5.6                    \n",
       "ZSCAN21    7.2                      7.4                    \n",
       "ZSCAN22    6.6                      6.3                    \n",
       "ZSCAN29    8.2                      8.3                    \n",
       "ZSCAN2     7.1                      7.5                    \n",
       "ZSCAN5A    5.2                      5.2                    \n",
       "ZSWIM1     7.9                      8.1                    \n",
       "ZSWIM3     6.0                      6.6                    \n",
       "ZSWIM4     9.5                     10.6                    \n",
       "ZSWIM5     6.9                      3.5                    \n",
       "ZSWIM6     8.8                      9.1                    \n",
       "ZSWIM7     7.5                      7.3                    \n",
       "ZUFSP      6.9                      7.0                    \n",
       "ZW10       8.2                      8.1                    \n",
       "ZWILCH     7.5                      8.4                    \n",
       "ZWINT      7.9                      9.4                    \n",
       "ZXDA       5.3                      5.0                    \n",
       "ZXDB       8.8                      8.2                    \n",
       "ZXDC       9.5                      9.4                    \n",
       "ZYG11B     9.6                      9.2                    \n",
       "ZYX       13.1                     13.2                    \n",
       "ZZEF1      9.9                      9.8                    \n",
       "ZZZ3       8.8                      8.6                    \n",
       "          a8lh.Primary.solid.Tumor aapl.Primary.solid.Tumor\n",
       "SLC35E2    7.2                      9.05                   \n",
       "A1BG       6.0                      6.90                   \n",
       "A2LD1      6.9                      6.70                   \n",
       "A2M       12.1                     13.30                   \n",
       "A4GALT     8.3                      9.00                   \n",
       "AAAS       9.6                      9.60                   \n",
       "AACS      10.0                      8.60                   \n",
       "AADAT      6.0                      4.90                   \n",
       "AAGAB     10.5                     10.10                   \n",
       "AAK1       8.9                     10.50                   \n",
       "AAMP      11.9                     11.10                   \n",
       "AARS2      8.9                      8.80                   \n",
       "AARSD1     9.1                      9.00                   \n",
       "AARS      12.0                     11.10                   \n",
       "AASDHPPT   8.7                      9.50                   \n",
       "AASDH      7.0                      8.00                   \n",
       "AASS       7.3                      8.10                   \n",
       "AATF      10.9                     10.50                   \n",
       "AATK       7.8                      7.00                   \n",
       "ABAT       8.5                      8.10                   \n",
       "ABCA10     3.7                      4.70                   \n",
       "ABCA11P    6.2                      7.70                   \n",
       "ABCA1      7.8                      9.90                   \n",
       "ABCA2     10.7                      9.80                   \n",
       "ABCA3      9.2                      8.80                   \n",
       "ABCA5      7.4                      9.10                   \n",
       "ABCA6      3.9                      7.60                   \n",
       "ABCA7      9.9                     11.00                   \n",
       "ABCA8      4.5                      7.90                   \n",
       "ABCA9      4.2                      6.20                   \n",
       "...       ...                      ...                     \n",
       "ZRANB2    10.2                     11.1                    \n",
       "ZRANB3     4.6                      5.8                    \n",
       "ZRSR2      8.7                      9.5                    \n",
       "ZSCAN12P1  2.6                      5.0                    \n",
       "ZSCAN12    7.0                      8.1                    \n",
       "ZSCAN16    7.0                      7.2                    \n",
       "ZSCAN18    8.2                     10.2                    \n",
       "ZSCAN20    5.6                      5.6                    \n",
       "ZSCAN21    7.6                      7.4                    \n",
       "ZSCAN22    6.7                      6.4                    \n",
       "ZSCAN29    8.8                      9.3                    \n",
       "ZSCAN2     7.3                      7.6                    \n",
       "ZSCAN5A    5.4                      6.2                    \n",
       "ZSWIM1     8.4                      8.2                    \n",
       "ZSWIM3     6.8                      6.7                    \n",
       "ZSWIM4     9.7                      8.5                    \n",
       "ZSWIM5     7.5                      7.0                    \n",
       "ZSWIM6     9.1                      8.9                    \n",
       "ZSWIM7     7.4                      7.9                    \n",
       "ZUFSP      6.8                      7.6                    \n",
       "ZW10       8.6                      8.5                    \n",
       "ZWILCH     8.0                      8.6                    \n",
       "ZWINT      8.8                      9.1                    \n",
       "ZXDA       5.4                      6.3                    \n",
       "ZXDB       8.7                      8.9                    \n",
       "ZXDC       9.5                     10.4                    \n",
       "ZYG11B     8.3                      9.5                    \n",
       "ZYX       12.3                     12.3                    \n",
       "ZZEF1      9.6                     10.9                    \n",
       "ZZZ3       8.4                      9.4                    "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## convert data frame to matrix\n",
    "exp_set <- as.matrix(exp_set) \n",
    "exp_set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<strong>$IFN</strong> = <style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>IFIT1</li><li>IFI44</li><li>IFIT3</li><li>MX2</li><li>OAS1</li><li>OAS3</li><li>BST2</li><li>IFITM1</li><li>MX1</li><li>STAT1</li><li>IFI27</li><li>CXCL10</li><li>IFI16</li><li>IFI30</li><li>IFIH1</li><li>IFIT2</li><li>IFITM2</li><li>IRF1</li><li>IRF9</li><li>ISG15</li><li>OAS2</li><li>PSME1</li><li>SOCS1</li><li>STAT2</li></ol>\n",
       "\n",
       "<details>\n",
       "\t<summary style=display:list-item;cursor:pointer>\n",
       "\t\t<strong>Levels</strong>:\n",
       "\t</summary>\n",
       "\t<style>\n",
       "\t.list-inline {list-style: none; margin:0; padding: 0}\n",
       "\t.list-inline>li {display: inline-block}\n",
       "\t.list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "\t</style>\n",
       "\t<ol class=list-inline><li>'BST2'</li><li>'CXCL10'</li><li>'IFI16'</li><li>'IFI27'</li><li>'IFI30'</li><li>'IFI44'</li><li>'IFIH1'</li><li>'IFIT1'</li><li>'IFIT2'</li><li>'IFIT3'</li><li>'IFITM1'</li><li>'IFITM2'</li><li>'IRF1'</li><li>'IRF9'</li><li>'ISG15'</li><li>'MX1'</li><li>'MX2'</li><li>'OAS1'</li><li>'OAS2'</li><li>'OAS3'</li><li>'PSME1'</li><li>'SOCS1'</li><li>'STAT1'</li><li>'STAT2'</li></ol>\n",
       "</details>"
      ],
      "text/latex": [
       "\\textbf{\\$IFN} = \\begin{enumerate*}\n",
       "\\item IFIT1\n",
       "\\item IFI44\n",
       "\\item IFIT3\n",
       "\\item MX2\n",
       "\\item OAS1\n",
       "\\item OAS3\n",
       "\\item BST2\n",
       "\\item IFITM1\n",
       "\\item MX1\n",
       "\\item STAT1\n",
       "\\item IFI27\n",
       "\\item CXCL10\n",
       "\\item IFI16\n",
       "\\item IFI30\n",
       "\\item IFIH1\n",
       "\\item IFIT2\n",
       "\\item IFITM2\n",
       "\\item IRF1\n",
       "\\item IRF9\n",
       "\\item ISG15\n",
       "\\item OAS2\n",
       "\\item PSME1\n",
       "\\item SOCS1\n",
       "\\item STAT2\n",
       "\\end{enumerate*}\n",
       "\n",
       "\\emph{Levels}: \\begin{enumerate*}\n",
       "\\item 'BST2'\n",
       "\\item 'CXCL10'\n",
       "\\item 'IFI16'\n",
       "\\item 'IFI27'\n",
       "\\item 'IFI30'\n",
       "\\item 'IFI44'\n",
       "\\item 'IFIH1'\n",
       "\\item 'IFIT1'\n",
       "\\item 'IFIT2'\n",
       "\\item 'IFIT3'\n",
       "\\item 'IFITM1'\n",
       "\\item 'IFITM2'\n",
       "\\item 'IRF1'\n",
       "\\item 'IRF9'\n",
       "\\item 'ISG15'\n",
       "\\item 'MX1'\n",
       "\\item 'MX2'\n",
       "\\item 'OAS1'\n",
       "\\item 'OAS2'\n",
       "\\item 'OAS3'\n",
       "\\item 'PSME1'\n",
       "\\item 'SOCS1'\n",
       "\\item 'STAT1'\n",
       "\\item 'STAT2'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "**$IFN** = 1. IFIT1\n",
       "2. IFI44\n",
       "3. IFIT3\n",
       "4. MX2\n",
       "5. OAS1\n",
       "6. OAS3\n",
       "7. BST2\n",
       "8. IFITM1\n",
       "9. MX1\n",
       "10. STAT1\n",
       "11. IFI27\n",
       "12. CXCL10\n",
       "13. IFI16\n",
       "14. IFI30\n",
       "15. IFIH1\n",
       "16. IFIT2\n",
       "17. IFITM2\n",
       "18. IRF1\n",
       "19. IRF9\n",
       "20. ISG15\n",
       "21. OAS2\n",
       "22. PSME1\n",
       "23. SOCS1\n",
       "24. STAT2\n",
       "\n",
       "\n",
       "\n",
       "**Levels**: 1. 'BST2'\n",
       "2. 'CXCL10'\n",
       "3. 'IFI16'\n",
       "4. 'IFI27'\n",
       "5. 'IFI30'\n",
       "6. 'IFI44'\n",
       "7. 'IFIH1'\n",
       "8. 'IFIT1'\n",
       "9. 'IFIT2'\n",
       "10. 'IFIT3'\n",
       "11. 'IFITM1'\n",
       "12. 'IFITM2'\n",
       "13. 'IRF1'\n",
       "14. 'IRF9'\n",
       "15. 'ISG15'\n",
       "16. 'MX1'\n",
       "17. 'MX2'\n",
       "18. 'OAS1'\n",
       "19. 'OAS2'\n",
       "20. 'OAS3'\n",
       "21. 'PSME1'\n",
       "22. 'SOCS1'\n",
       "23. 'STAT1'\n",
       "24. 'STAT2'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "$IFN\n",
       " [1] IFIT1  IFI44  IFIT3  MX2    OAS1   OAS3   BST2   IFITM1 MX1    STAT1 \n",
       "[11] IFI27  CXCL10 IFI16  IFI30  IFIH1  IFIT2  IFITM2 IRF1   IRF9   ISG15 \n",
       "[21] OAS2   PSME1  SOCS1  STAT2 \n",
       "24 Levels: BST2 CXCL10 IFI16 IFI27 IFI30 IFI44 IFIH1 IFIT1 IFIT2 ... STAT2\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## Read gene set file \n",
    "ifn <- read.delim(\"type1_IFN.txt\", header = FALSE, col.names = \"IFN\", dec = \",\")\n",
    "# ifn\n",
    "gene_set = as.list(ifn)\n",
    "gene_set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "# gene_set[[1]][2]\n",
    "# typeof(gene_set[[1]][2])\n",
    "# gene_set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<strong>$IFN</strong> = <style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>'IFIT1'</li><li>'IFIT4'</li><li>'IFIT3'</li><li>'MX2'</li><li>'OAS1'</li><li>'BST2'</li><li>'IFITM1'</li><li>'MX1'</li><li>'STAT1'</li><li>'IFI27'</li><li>'CXCL10'</li><li>'IFI16'</li><li>'IFI30'</li><li>'IFIH1'</li><li>'IFIT2'</li><li>'IFITM2'</li><li>'IRF1'</li><li>'IRF9'</li><li>'ISG15'</li><li>'OAS2'</li><li>'PSME1'</li><li>'SOCS1'</li><li>'STAT2'</li></ol>\n"
      ],
      "text/latex": [
       "\\textbf{\\$IFN} = \\begin{enumerate*}\n",
       "\\item 'IFIT1'\n",
       "\\item 'IFIT4'\n",
       "\\item 'IFIT3'\n",
       "\\item 'MX2'\n",
       "\\item 'OAS1'\n",
       "\\item 'BST2'\n",
       "\\item 'IFITM1'\n",
       "\\item 'MX1'\n",
       "\\item 'STAT1'\n",
       "\\item 'IFI27'\n",
       "\\item 'CXCL10'\n",
       "\\item 'IFI16'\n",
       "\\item 'IFI30'\n",
       "\\item 'IFIH1'\n",
       "\\item 'IFIT2'\n",
       "\\item 'IFITM2'\n",
       "\\item 'IRF1'\n",
       "\\item 'IRF9'\n",
       "\\item 'ISG15'\n",
       "\\item 'OAS2'\n",
       "\\item 'PSME1'\n",
       "\\item 'SOCS1'\n",
       "\\item 'STAT2'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "**$IFN** = 1. 'IFIT1'\n",
       "2. 'IFIT4'\n",
       "3. 'IFIT3'\n",
       "4. 'MX2'\n",
       "5. 'OAS1'\n",
       "6. 'BST2'\n",
       "7. 'IFITM1'\n",
       "8. 'MX1'\n",
       "9. 'STAT1'\n",
       "10. 'IFI27'\n",
       "11. 'CXCL10'\n",
       "12. 'IFI16'\n",
       "13. 'IFI30'\n",
       "14. 'IFIH1'\n",
       "15. 'IFIT2'\n",
       "16. 'IFITM2'\n",
       "17. 'IRF1'\n",
       "18. 'IRF9'\n",
       "19. 'ISG15'\n",
       "20. 'OAS2'\n",
       "21. 'PSME1'\n",
       "22. 'SOCS1'\n",
       "23. 'STAT2'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "$IFN\n",
       " [1] \"IFIT1\"  \"IFIT4\"  \"IFIT3\"  \"MX2\"    \"OAS1\"   \"BST2\"   \"IFITM1\" \"MX1\"   \n",
       " [9] \"STAT1\"  \"IFI27\"  \"CXCL10\" \"IFI16\"  \"IFI30\"  \"IFIH1\"  \"IFIT2\"  \"IFITM2\"\n",
       "[17] \"IRF1\"   \"IRF9\"   \"ISG15\"  \"OAS2\"   \"PSME1\"  \"SOCS1\"  \"STAT2\" \n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "# library(limma)\n",
    "geneSets <- list(IFN = c(\"IFIT1\", \"IFIT4\", \"IFIT3\", \"MX2\", \"OAS1\",\"BST2\", \"IFITM1\" , \"MX1\", \"STAT1\", \"IFI27\", \n",
    "                         \"CXCL10\", \"IFI16\", \"IFI30\", \"IFIH1\", \"IFIT2\", \"IFITM2\", \"IRF1\", \"IRF9\", \n",
    "                         \"ISG15\", \"OAS2\", \"PSME1\", \"SOCS1\", \"STAT2\"))\n",
    "geneSets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Estimating GSVA scores for 1 gene sets.\n",
      "Computing observed enrichment scores\n",
      "Estimating ECDFs with Gaussian kernels\n",
      "Using parallel with 4 cores\n",
      "  |======================================================================| 100%\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A matrix: 1 × 175 of type dbl</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>aab1.Primary.solid.Tumor</th><th scope=col>aab4.Primary.solid.Tumor</th><th scope=col>aab6.Primary.solid.Tumor</th><th scope=col>aab8.Primary.solid.Tumor</th><th scope=col>aab9.Primary.solid.Tumor</th><th scope=col>aaba.Primary.solid.Tumor</th><th scope=col>aabe.Primary.solid.Tumor</th><th scope=col>aabf.Primary.solid.Tumor</th><th scope=col>aabh.Primary.solid.Tumor</th><th scope=col>aabi.Primary.solid.Tumor</th><th scope=col>...</th><th scope=col>aauh.Primary.solid.Tumor</th><th scope=col>aaui.Primary.solid.Tumor</th><th scope=col>aaul.Primary.solid.Tumor</th><th scope=col>a8t3.Primary.solid.Tumor</th><th scope=col>a8t5.Primary.solid.Tumor</th><th scope=col>a89d.Solid.Tissue.Normal</th><th scope=col>a89d.Primary.solid.Tumor</th><th scope=col>a8sy.Primary.solid.Tumor</th><th scope=col>a8lh.Primary.solid.Tumor</th><th scope=col>aapl.Primary.solid.Tumor</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>IFN</th><td>0.3890645</td><td>0.665666</td><td>0.6975262</td><td>0.5517719</td><td>-0.5680738</td><td>-0.6733197</td><td>0.06648113</td><td>0.754224</td><td>-0.4082518</td><td>-0.5363576</td><td>...</td><td>-0.6569772</td><td>-0.5892199</td><td>0.09721354</td><td>-0.3979062</td><td>-0.2104749</td><td>0.1162344</td><td>0.3577832</td><td>0.5274399</td><td>0.5898278</td><td>0.5303184</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A matrix: 1 × 175 of type dbl\n",
       "\\begin{tabular}{r|lllllllllllllllllllll}\n",
       "  & aab1.Primary.solid.Tumor & aab4.Primary.solid.Tumor & aab6.Primary.solid.Tumor & aab8.Primary.solid.Tumor & aab9.Primary.solid.Tumor & aaba.Primary.solid.Tumor & aabe.Primary.solid.Tumor & aabf.Primary.solid.Tumor & aabh.Primary.solid.Tumor & aabi.Primary.solid.Tumor & ... & aauh.Primary.solid.Tumor & aaui.Primary.solid.Tumor & aaul.Primary.solid.Tumor & a8t3.Primary.solid.Tumor & a8t5.Primary.solid.Tumor & a89d.Solid.Tissue.Normal & a89d.Primary.solid.Tumor & a8sy.Primary.solid.Tumor & a8lh.Primary.solid.Tumor & aapl.Primary.solid.Tumor\\\\\n",
       "\\hline\n",
       "\tIFN & 0.3890645 & 0.665666 & 0.6975262 & 0.5517719 & -0.5680738 & -0.6733197 & 0.06648113 & 0.754224 & -0.4082518 & -0.5363576 & ... & -0.6569772 & -0.5892199 & 0.09721354 & -0.3979062 & -0.2104749 & 0.1162344 & 0.3577832 & 0.5274399 & 0.5898278 & 0.5303184\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A matrix: 1 × 175 of type dbl\n",
       "\n",
       "| <!--/--> | aab1.Primary.solid.Tumor | aab4.Primary.solid.Tumor | aab6.Primary.solid.Tumor | aab8.Primary.solid.Tumor | aab9.Primary.solid.Tumor | aaba.Primary.solid.Tumor | aabe.Primary.solid.Tumor | aabf.Primary.solid.Tumor | aabh.Primary.solid.Tumor | aabi.Primary.solid.Tumor | ... | aauh.Primary.solid.Tumor | aaui.Primary.solid.Tumor | aaul.Primary.solid.Tumor | a8t3.Primary.solid.Tumor | a8t5.Primary.solid.Tumor | a89d.Solid.Tissue.Normal | a89d.Primary.solid.Tumor | a8sy.Primary.solid.Tumor | a8lh.Primary.solid.Tumor | aapl.Primary.solid.Tumor |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| IFN | 0.3890645 | 0.665666 | 0.6975262 | 0.5517719 | -0.5680738 | -0.6733197 | 0.06648113 | 0.754224 | -0.4082518 | -0.5363576 | ... | -0.6569772 | -0.5892199 | 0.09721354 | -0.3979062 | -0.2104749 | 0.1162344 | 0.3577832 | 0.5274399 | 0.5898278 | 0.5303184 |\n",
       "\n"
      ],
      "text/plain": [
       "    aab1.Primary.solid.Tumor aab4.Primary.solid.Tumor aab6.Primary.solid.Tumor\n",
       "IFN 0.3890645                0.665666                 0.6975262               \n",
       "    aab8.Primary.solid.Tumor aab9.Primary.solid.Tumor aaba.Primary.solid.Tumor\n",
       "IFN 0.5517719                -0.5680738               -0.6733197              \n",
       "    aabe.Primary.solid.Tumor aabf.Primary.solid.Tumor aabh.Primary.solid.Tumor\n",
       "IFN 0.06648113               0.754224                 -0.4082518              \n",
       "    aabi.Primary.solid.Tumor ... aauh.Primary.solid.Tumor\n",
       "IFN -0.5363576               ... -0.6569772              \n",
       "    aaui.Primary.solid.Tumor aaul.Primary.solid.Tumor a8t3.Primary.solid.Tumor\n",
       "IFN -0.5892199               0.09721354               -0.3979062              \n",
       "    a8t5.Primary.solid.Tumor a89d.Solid.Tissue.Normal a89d.Primary.solid.Tumor\n",
       "IFN -0.2104749               0.1162344                0.3577832               \n",
       "    a8sy.Primary.solid.Tumor a8lh.Primary.solid.Tumor aapl.Primary.solid.Tumor\n",
       "IFN 0.5274399                0.5898278                0.5303184               "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## emestimate GSVA enrichment scores for IFN \n",
    "library(GSVA)  ## import GSVA library \n",
    "\n",
    "\n",
    "gsva_es <- gsva(exp_set, gene_set)\n",
    "gsva_es\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Part 3 \n",
    "\n",
    "Check distribution of GSVA scores for samples. Do the GSVA scores segregate samples into subtypes?\n",
    "\n",
    "Here, we have plotted the density estimation of the GSVA score. By looking at it we can conclude that the sample of Adenocarcinoma separates into 3 subtypes.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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G44DzciTcZ5ZnPD+SUpIk3FeWLzw3e8EWkqvvOaIb4DjkhT8Z3XDPEdcESaiu+8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\njNLaAAAAAElFTkSuQmCC",
      "text/plain": [
       "Plot with title \" Density estimate\""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      },
      "text/plain": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot(density(as.vector(gsva_es)), main=\" Density estimate\",\n",
    "     xlab=\"GSVA score\", lwd=3, las=2, col = \"purple\", xaxt=\"n\", xlim = c(-1.5, 1.5), cex.axis=1.5)\n",
    "axis(1, at=seq(-1.5, 1.5, by=0.25), labels = seq(-1.5, 1.5, by=0.25), cex.axis= 1.5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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T+mcAUi+aK2eiPii1YfH8hTuAKRfFFb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\nEAlAACIBCEAkAAGIBCAAkQAEIBKAgP8Bixnu1GQiK2sAAAAASUVORK5CYII=",
      "text/plain": [
       "Plot with title \"Histogram plot of GSVA Score \""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      },
      "text/plain": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Create the histogram.\n",
    "v = as.vector(gsva_es)\n",
    "hist(v, main=\"Histogram plot of GSVA Score \", xlab = \"Weight\",col = \"cyan\",border = \"black\", xlim = c(-1,1), ylim = c(0, 15), breaks = 50)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Rreferences:\n",
    "**(Not in order)**\n",
    "\n",
    "1. https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.pdf\n",
    "2. https://clincancerres.aacrjournals.org/content/23/12/3129\n",
    "3. https://bioconductor.org/packages/release/bioc/manuals/GSVA/man/GSVA.pdf\n",
    "4. https://towardsdatascience.com/decoding-gene-set-variation-analysis-8193a0cfda3\n",
    "5. https://artyomovlab.wustl.edu/phantasus/\n",
    "6. https://en.wikipedia.org/wiki/Pancreatic_cancer\n",
    "7. https://en.wikipedia.org/wiki/RNA\n",
    "8. https://bitesizebio.com/13542/what-everyone-should-know-about-rna-seq/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "R",
   "language": "R",
   "name": "ir"
  },
  "language_info": {
   "codemirror_mode": "r",
   "file_extension": ".r",
   "mimetype": "text/x-r-source",
   "name": "R",
   "pygments_lexer": "r",
   "version": "3.6.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}