<!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_CL_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_CL_2017</td></tr><tr><td>Enrichment Score (ES)</td><td>0.44006732</td></tr><tr><td>Normalized Enrichment Score (NES)</td><td>1.5842261</td></tr><tr><td>Nominal p-value</td><td>0.009746589</td></tr><tr><td>FDR q-value</td><td>0.01330119</td></tr><tr><td>FWER p-Value</td><td>0.024</td></tr><caption class='table'>Table: GSEA Results Summary</caption></table></div><br><div class='image'><img name='enplot_VERHAAK_CL_2017' src='enplot_VERHAAK_CL_2017_6.png'><br><br><caption>Fig 1: Enrichment plot: VERHAAK_CL_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=GATM'>GATM</a></td><td>GATM</td><td></td><td></td><td>24</td><td>0.183</td><td>0.1322</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>2</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=LHFP'>LHFP</a></td><td>LHFP</td><td></td><td></td><td>243</td><td>0.095</td><td>0.1911</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>3</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=DTNA'>DTNA</a></td><td>DTNA</td><td></td><td></td><td>290</td><td>0.091</td><td>0.2556</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>4</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PLCE1'>PLCE1</a></td><td>PLCE1</td><td></td><td></td><td>500</td><td>0.078</td><td>0.3028</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>5</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PHKB'>PHKB</a></td><td>PHKB</td><td></td><td></td><td>1025</td><td>0.060</td><td>0.3222</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>6</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ABLIM1'>ABLIM1</a></td><td>ABLIM1</td><td></td><td></td><td>1755</td><td>0.048</td><td>0.3231</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>7</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NCOA1'>NCOA1</a></td><td>NCOA1</td><td></td><td></td><td>1844</td><td>0.046</td><td>0.3529</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>8</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ZFHX4'>ZFHX4</a></td><td>ZFHX4</td><td></td><td></td><td>1942</td><td>0.045</td><td>0.3815</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>9</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SOX9'>SOX9</a></td><td>SOX9</td><td></td><td></td><td>2323</td><td>0.041</td><td>0.3937</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>10</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=VAV3'>VAV3</a></td><td>VAV3</td><td></td><td></td><td>3218</td><td>0.034</td><td>0.3767</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>11</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=KIAA0494'>KIAA0494</a></td><td>KIAA0494</td><td></td><td></td><td>3309</td><td>0.033</td><td>0.3965</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>12</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ACSL3'>ACSL3</a></td><td>ACSL3</td><td></td><td></td><td>3718</td><td>0.030</td><td>0.3994</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>13</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=TYK2'>TYK2</a></td><td>TYK2</td><td></td><td></td><td>3910</td><td>0.029</td><td>0.4115</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>14</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CDH4'>CDH4</a></td><td>CDH4</td><td></td><td></td><td>3939</td><td>0.029</td><td>0.4310</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>15</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=FGFR3'>FGFR3</a></td><td>FGFR3</td><td></td><td></td><td>4501</td><td>0.025</td><td>0.4234</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>16</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SLC4A4'>SLC4A4</a></td><td>SLC4A4</td><td></td><td></td><td>4538</td><td>0.025</td><td>0.4401</td><td bgcolor='#CCFFCC'>Yes</td></tr><tr><td class='lessen'>17</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ZNF45'>ZNF45</a></td><td>ZNF45</td><td></td><td></td><td>4974</td><td>0.023</td><td>0.4364</td><td>No</td></tr><tr><td class='lessen'>18</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PTPRA'>PTPRA</a></td><td>PTPRA</td><td></td><td></td><td>5269</td><td>0.021</td><td>0.4382</td><td>No</td></tr><tr><td class='lessen'>19</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SLC3A2'>SLC3A2</a></td><td>SLC3A2</td><td></td><td></td><td>6265</td><td>0.017</td><td>0.4041</td><td>No</td></tr><tr><td class='lessen'>20</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PLCG1'>PLCG1</a></td><td>PLCG1</td><td></td><td></td><td>6810</td><td>0.014</td><td>0.3892</td><td>No</td></tr><tr><td class='lessen'>21</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MEOX2'>MEOX2</a></td><td>MEOX2</td><td></td><td></td><td>6835</td><td>0.014</td><td>0.3984</td><td>No</td></tr><tr><td class='lessen'>22</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=STXBP3'>STXBP3</a></td><td>STXBP3</td><td></td><td></td><td>8077</td><td>0.009</td><td>0.3475</td><td>No</td></tr><tr><td class='lessen'>23</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=BBS1'>BBS1</a></td><td>BBS1</td><td></td><td></td><td>8334</td><td>0.008</td><td>0.3418</td><td>No</td></tr><tr><td class='lessen'>24</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=RBCK1'>RBCK1</a></td><td>RBCK1</td><td></td><td></td><td>8828</td><td>0.007</td><td>0.3236</td><td>No</td></tr><tr><td class='lessen'>25</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MLC1'>MLC1</a></td><td>MLC1</td><td></td><td></td><td>9469</td><td>0.004</td><td>0.2971</td><td>No</td></tr><tr><td class='lessen'>26</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=GRIK1'>GRIK1</a></td><td>GRIK1</td><td></td><td></td><td>9586</td><td>0.004</td><td>0.2944</td><td>No</td></tr><tr><td class='lessen'>27</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=DENND2A'>DENND2A</a></td><td>DENND2A</td><td></td><td></td><td>9891</td><td>0.003</td><td>0.2823</td><td>No</td></tr><tr><td class='lessen'>28</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CTNND1'>CTNND1</a></td><td>CTNND1</td><td></td><td></td><td>10035</td><td>0.002</td><td>0.2773</td><td>No</td></tr><tr><td class='lessen'>29</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PNPLA6'>PNPLA6</a></td><td>PNPLA6</td><td></td><td></td><td>10054</td><td>0.002</td><td>0.2781</td><td>No</td></tr><tr><td class='lessen'>30</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=TJP1'>TJP1</a></td><td>TJP1</td><td></td><td></td><td>10109</td><td>0.002</td><td>0.2770</td><td>No</td></tr><tr><td class='lessen'>31</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ELOVL2'>ELOVL2</a></td><td>ELOVL2</td><td></td><td></td><td>10475</td><td>0.001</td><td>0.2605</td><td>No</td></tr><tr><td class='lessen'>32</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=USP8'>USP8</a></td><td>USP8</td><td></td><td></td><td>10618</td><td>0.000</td><td>0.2540</td><td>No</td></tr><tr><td class='lessen'>33</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=NPEPL1'>NPEPL1</a></td><td>NPEPL1</td><td></td><td></td><td>11036</td><td>-0.001</td><td>0.2356</td><td>No</td></tr><tr><td class='lessen'>34</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=EYA2'>EYA2</a></td><td>EYA2</td><td></td><td></td><td>11213</td><td>-0.002</td><td>0.2288</td><td>No</td></tr><tr><td class='lessen'>35</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SALL1'>SALL1</a></td><td>SALL1</td><td></td><td></td><td>11657</td><td>-0.003</td><td>0.2108</td><td>No</td></tr><tr><td class='lessen'>36</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PAX6'>PAX6</a></td><td>PAX6</td><td></td><td></td><td>11825</td><td>-0.004</td><td>0.2060</td><td>No</td></tr><tr><td class='lessen'>37</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=BCKDHB'>BCKDHB</a></td><td>BCKDHB</td><td></td><td></td><td>11836</td><td>-0.004</td><td>0.2085</td><td>No</td></tr><tr><td class='lessen'>38</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ACSBG1'>ACSBG1</a></td><td>ACSBG1</td><td></td><td></td><td>12021</td><td>-0.005</td><td>0.2034</td><td>No</td></tr><tr><td class='lessen'>39</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=POLRMT'>POLRMT</a></td><td>POLRMT</td><td></td><td></td><td>12094</td><td>-0.005</td><td>0.2037</td><td>No</td></tr><tr><td class='lessen'>40</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=MYO5C'>MYO5C</a></td><td>MYO5C</td><td></td><td></td><td>12276</td><td>-0.006</td><td>0.1994</td><td>No</td></tr><tr><td class='lessen'>41</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ARNTL'>ARNTL</a></td><td>ARNTL</td><td></td><td></td><td>12633</td><td>-0.007</td><td>0.1879</td><td>No</td></tr><tr><td class='lessen'>42</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=UPF1'>UPF1</a></td><td>UPF1</td><td></td><td></td><td>13825</td><td>-0.011</td><td>0.1408</td><td>No</td></tr><tr><td class='lessen'>43</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=CST3'>CST3</a></td><td>CST3</td><td></td><td></td><td>14040</td><td>-0.012</td><td>0.1398</td><td>No</td></tr><tr><td class='lessen'>44</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SPRY2'>SPRY2</a></td><td>SPRY2</td><td></td><td></td><td>16493</td><td>-0.023</td><td>0.0426</td><td>No</td></tr><tr><td class='lessen'>45</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=C14orf159'>C14orf159</a></td><td>C14orf159</td><td></td><td></td><td>16777</td><td>-0.024</td><td>0.0471</td><td>No</td></tr><tr><td class='lessen'>46</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=RASGRP1'>RASGRP1</a></td><td>RASGRP1</td><td></td><td></td><td>17827</td><td>-0.030</td><td>0.0202</td><td>No</td></tr><tr><td class='lessen'>47</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=PPARGC1A'>PPARGC1A</a></td><td>PPARGC1A</td><td></td><td></td><td>19659</td><td>-0.045</td><td>-0.0317</td><td>No</td></tr><tr><td class='lessen'>48</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=SLC20A2'>SLC20A2</a></td><td>SLC20A2</td><td></td><td></td><td>21135</td><td>-0.079</td><td>-0.0426</td><td>No</td></tr><tr><td class='lessen'>49</td><td><a href='https://www.affymetrix.com/LinkServlet?probeset=ZHX3'>ZHX3</a></td><td>ZHX3</td><td></td><td></td><td>21264</td><td>-0.088</td><td>0.0154</td><td>No</td></tr><caption class='table'>Table: GSEA details <a href='VERHAAK_CL_2017.xls'>[plain text format]</a></caption></table></div><br><div class='image'><img name='VERHAAK_CL_2017' src='VERHAAK_CL_2017_7.png'><br><br><caption>Fig 2: VERHAAK_CL_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_8.png'><br><br><caption>Fig 3: VERHAAK_CL_2017: Random ES distribution    <br> Gene set null distribution of ES for <b>VERHAAK_CL_2017</b></caption></div><br></body></html>