<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd"> <html><head><title>Details for gene set VERHAAK_PN_2017[GSEA]</title><link href='xtools.css' rel='stylesheet'><link href='http://www.gsea-msigdb.org/gsea/images/XBench.gif' rel='shortcut icon'></head><body><div class='keyValTable'><table cols='2' border='0'><th class='keyValTable'></th><th class='keyValTable'></th><tr><td>Dataset</td><td>NF1_GRD_exprs.NF1_GRD_phenotype.cls<br>#GRD_versus_Ctrl.NF1_GRD_phenotype.cls<br>#GRD_versus_Ctrl_repos</td></tr><tr><td>Phenotype</td><td>NF1_GRD_phenotype.cls#GRD_versus_Ctrl_repos</td></tr><tr><td>Upregulated in class</td><td>GRD</td></tr><tr><td>GeneSet</td><td>VERHAAK_PN_2017</td></tr><tr><td>Enrichment Score (ES)</td><td>0.33894452</td></tr><tr><td>Normalized Enrichment Score (NES)</td><td>1.2055465</td></tr><tr><td>Nominal p-value</td><td>0.17330678</td></tr><tr><td>FDR q-value</td><td>0.12922944</td></tr><tr><td>FWER p-Value</td><td>0.558</td></tr><caption class='table'>Table: GSEA Results Summary</caption></table></div><br><div class='image'><img name='enplot_VERHAAK_PN_2017' src='enplot_VERHAAK_PN_2017_18.png'><br><br><caption>Fig 1: Enrichment plot: VERHAAK_PN_2017    <br> Profile of the Running ES Score & Positions of GeneSet Members on the Rank Ordered List</caption></div><br><div class='richTable'><table cols='9' border='1'><th class='richTable'></th><th class='richTable'>PROBE</th><th class='richTable'>DESCRIPTION<br>(from dataset)</th><th class='richTable'>GENE SYMBOL</th><th class='richTable'>GENE_TITLE</th><th class='richTable'>RANK IN GENE LIST</th><th class='richTable'>RANK METRIC SCORE</th><th class='richTable'>RUNNING ES</th><th class='richTable'>CORE ENRICHMENT</th><tr><td class='lessen'>1</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MTSS1'>MTSS1</a></td><td>MTSS1</td><td></td><td></td><td>362</td><td>0.085</td><td>0.0567</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>2</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PLCB4'>PLCB4</a></td><td>PLCB4</td><td></td><td></td><td>1109</td><td>0.058</td><td>0.0726</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>3</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MYB'>MYB</a></td><td>MYB</td><td></td><td></td><td>1166</td><td>0.057</td><td>0.1196</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>4</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=HN1'>HN1</a></td><td>HN1</td><td></td><td></td><td>1966</td><td>0.045</td><td>0.1214</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>5</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SOX10'>SOX10</a></td><td>SOX10</td><td></td><td></td><td>2218</td><td>0.042</td><td>0.1462</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>6</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=RAB33A'>RAB33A</a></td><td>RAB33A</td><td></td><td></td><td>2265</td><td>0.042</td><td>0.1801</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>7</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=DCTN3'>DCTN3</a></td><td>DCTN3</td><td></td><td></td><td>2342</td><td>0.041</td><td>0.2118</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>8</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NARF'>NARF</a></td><td>NARF</td><td></td><td></td><td>2394</td><td>0.040</td><td>0.2441</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>9</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MAST1'>MAST1</a></td><td>MAST1</td><td></td><td></td><td>2578</td><td>0.039</td><td>0.2691</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>10</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=KLRK1'>KLRK1</a></td><td>KLRK1</td><td></td><td></td><td>2943</td><td>0.036</td><td>0.2832</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>11</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=VIPR2'>VIPR2</a></td><td>VIPR2</td><td></td><td></td><td>2996</td><td>0.035</td><td>0.3113</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>12</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MYT1'>MYT1</a></td><td>MYT1</td><td></td><td></td><td>3053</td><td>0.035</td><td>0.3389</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>13</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CDKN1C'>CDKN1C</a></td><td>CDKN1C</td><td></td><td></td><td>4067</td><td>0.028</td><td>0.3160</td><td>No</td></tr><tr><td class='lessen'>14</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PKMYT1'>PKMYT1</a></td><td>PKMYT1</td><td></td><td></td><td>4615</td><td>0.025</td><td>0.3119</td><td>No</td></tr><tr><td class='lessen'>15</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=DACH1'>DACH1</a></td><td>DACH1</td><td></td><td></td><td>4922</td><td>0.023</td><td>0.3174</td><td>No</td></tr><tr><td class='lessen'>16</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=JPH3'>JPH3</a></td><td>JPH3</td><td></td><td></td><td>5411</td><td>0.020</td><td>0.3125</td><td>No</td></tr><tr><td class='lessen'>17</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=GPR17'>GPR17</a></td><td>GPR17</td><td></td><td></td><td>7361</td><td>0.012</td><td>0.2325</td><td>No</td></tr><tr><td class='lessen'>18</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NPPA'>NPPA</a></td><td>NPPA</td><td></td><td></td><td>7771</td><td>0.011</td><td>0.2226</td><td>No</td></tr><tr><td class='lessen'>19</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PCDHA9'>PCDHA9</a></td><td>PCDHA9</td><td></td><td></td><td>7977</td><td>0.010</td><td>0.2215</td><td>No</td></tr><tr><td class='lessen'>20</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=RASL11B'>RASL11B</a></td><td>RASL11B</td><td></td><td></td><td>8153</td><td>0.009</td><td>0.2211</td><td>No</td></tr><tr><td class='lessen'>21</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=KLRC4'>KLRC4</a></td><td>KLRC4</td><td></td><td></td><td>8265</td><td>0.009</td><td>0.2234</td><td>No</td></tr><tr><td class='lessen'>22</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=KCNK3'>KCNK3</a></td><td>KCNK3</td><td></td><td></td><td>8406</td><td>0.008</td><td>0.2239</td><td>No</td></tr><tr><td class='lessen'>23</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SMPD3'>SMPD3</a></td><td>SMPD3</td><td></td><td></td><td>9100</td><td>0.006</td><td>0.1966</td><td>No</td></tr><tr><td class='lessen'>24</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PFDN2'>PFDN2</a></td><td>PFDN2</td><td></td><td></td><td>9401</td><td>0.005</td><td>0.1866</td><td>No</td></tr><tr><td class='lessen'>25</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=TCP1'>TCP1</a></td><td>TCP1</td><td></td><td></td><td>9442</td><td>0.004</td><td>0.1886</td><td>No</td></tr><tr><td class='lessen'>26</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=BAMBI'>BAMBI</a></td><td>BAMBI</td><td></td><td></td><td>9481</td><td>0.004</td><td>0.1904</td><td>No</td></tr><tr><td class='lessen'>27</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=GRID2'>GRID2</a></td><td>GRID2</td><td></td><td></td><td>9539</td><td>0.004</td><td>0.1912</td><td>No</td></tr><tr><td class='lessen'>28</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NHLH1'>NHLH1</a></td><td>NHLH1</td><td></td><td></td><td>10113</td><td>0.002</td><td>0.1663</td><td>No</td></tr><tr><td class='lessen'>29</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=EPHB1'>EPHB1</a></td><td>EPHB1</td><td></td><td></td><td>10273</td><td>0.001</td><td>0.1601</td><td>No</td></tr><tr><td class='lessen'>30</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ZNF643'>ZNF643</a></td><td>ZNF643</td><td></td><td></td><td>10518</td><td>0.001</td><td>0.1492</td><td>No</td></tr><tr><td class='lessen'>31</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=HRASLS'>HRASLS</a></td><td>HRASLS</td><td></td><td></td><td>10626</td><td>0.000</td><td>0.1443</td><td>No</td></tr><tr><td class='lessen'>32</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PDGFRA'>PDGFRA</a></td><td>PDGFRA</td><td></td><td></td><td>11054</td><td>-0.001</td><td>0.1257</td><td>No</td></tr><tr><td class='lessen'>33</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=HOXD3'>HOXD3</a></td><td>HOXD3</td><td></td><td></td><td>11340</td><td>-0.002</td><td>0.1145</td><td>No</td></tr><tr><td class='lessen'>34</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ERBB3'>ERBB3</a></td><td>ERBB3</td><td></td><td></td><td>11564</td><td>-0.003</td><td>0.1068</td><td>No</td></tr><tr><td class='lessen'>35</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=IL1RAPL1'>IL1RAPL1</a></td><td>IL1RAPL1</td><td></td><td></td><td>11783</td><td>-0.004</td><td>0.1001</td><td>No</td></tr><tr><td class='lessen'>36</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=KLRC3'>KLRC3</a></td><td>KLRC3</td><td></td><td></td><td>13100</td><td>-0.009</td><td>0.0464</td><td>No</td></tr><tr><td class='lessen'>37</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CLGN'>CLGN</a></td><td>CLGN</td><td></td><td></td><td>13156</td><td>-0.009</td><td>0.0515</td><td>No</td></tr><tr><td class='lessen'>38</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CA10'>CA10</a></td><td>CA10</td><td></td><td></td><td>13883</td><td>-0.012</td><td>0.0278</td><td>No</td></tr><tr><td class='lessen'>39</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SIM2'>SIM2</a></td><td>SIM2</td><td></td><td></td><td>14181</td><td>-0.013</td><td>0.0251</td><td>No</td></tr><tr><td class='lessen'>40</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=GABRB3'>GABRB3</a></td><td>GABRB3</td><td></td><td></td><td>14334</td><td>-0.013</td><td>0.0295</td><td>No</td></tr><tr><td class='lessen'>41</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=BCL11A'>BCL11A</a></td><td>BCL11A</td><td></td><td></td><td>14923</td><td>-0.016</td><td>0.0158</td><td>No</td></tr><tr><td class='lessen'>42</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=HDAC2'>HDAC2</a></td><td>HDAC2</td><td></td><td></td><td>15049</td><td>-0.016</td><td>0.0241</td><td>No</td></tr><tr><td class='lessen'>43</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=UGT8'>UGT8</a></td><td>UGT8</td><td></td><td></td><td>15565</td><td>-0.018</td><td>0.0162</td><td>No</td></tr><tr><td class='lessen'>44</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SLC17A6'>SLC17A6</a></td><td>SLC17A6</td><td></td><td></td><td>16364</td><td>-0.022</td><td>-0.0018</td><td>No</td></tr><tr><td class='lessen'>45</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PAK7'>PAK7</a></td><td>PAK7</td><td></td><td></td><td>18244</td><td>-0.033</td><td>-0.0608</td><td>No</td></tr><tr><td class='lessen'>46</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PTTG1'>PTTG1</a></td><td>PTTG1</td><td></td><td></td><td>18617</td><td>-0.035</td><td>-0.0475</td><td>No</td></tr><tr><td class='lessen'>47</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CENPJ'>CENPJ</a></td><td>CENPJ</td><td></td><td></td><td>18780</td><td>-0.037</td><td>-0.0233</td><td>No</td></tr><tr><td class='lessen'>48</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SLC1A1'>SLC1A1</a></td><td>SLC1A1</td><td></td><td></td><td>19759</td><td>-0.047</td><td>-0.0284</td><td>No</td></tr><tr><td class='lessen'>49</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ZNF804A'>ZNF804A</a></td><td>ZNF804A</td><td></td><td></td><td>20595</td><td>-0.060</td><td>-0.0150</td><td>No</td></tr><tr><td class='lessen'>50</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NMU'>NMU</a></td><td>NMU</td><td></td><td></td><td>20948</td><td>-0.071</td><td>0.0300</td><td>No</td></tr><caption class='table'>Table: GSEA details <a href='VERHAAK_PN_2017.xls'>[plain text format]</a></caption></table></div><br><div class='image'><img name='VERHAAK_PN_2017' src='VERHAAK_PN_2017_19.png'><br><br><caption>Fig 2: VERHAAK_PN_2017    <br> Blue-Pink O' Gram in the Space of the Analyzed GeneSet</caption></div><br><div class='image'><img name='gset_rnd_es_dist' src='gset_rnd_es_dist_20.png'><br><br><caption>Fig 3: VERHAAK_PN_2017: Random ES distribution    <br> Gene set null distribution of ES for <b>VERHAAK_PN_2017</b></caption></div><br></body></html>