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Coexpression cluster:C3642: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115127657528216!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279156514553204!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032170730960707!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242790865122084!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066337307755597!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484151025904967!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308745011658662!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246219553531157!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247965361243155!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614962510691767!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196926657096514!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109295764377974
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115127657528216!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279156514553204!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032170730960707!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242790865122084!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066337307755597!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484151025904967!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308745011658662!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246219553531157!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247965361243155!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614962510691767!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196926657096514!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109295764377974
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}}
}}

Revision as of 16:15, 26 November 2012


Full id: C3642_colon_small_signet_choriocarcinoma_pancreatic_rectal_immature



Phase1 CAGE Peaks

Hg19::chr17:43502987..43503004,-p2@ARHGAP27
Hg19::chr17:43503012..43503035,-p4@ARHGAP27
Hg19::chr17:43503039..43503048,-p7@ARHGAP27


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell7.10e-33253
endodermal cell7.92e-1458
endo-epithelial cell3.29e-1242
epithelial cell of lung1.04e-0719
epithelial cell of alimentary canal1.29e-0720
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.42e-22160
endoderm6.42e-22160
presumptive endoderm6.42e-22160
subdivision of digestive tract3.34e-20118
digestive system5.70e-20145
digestive tract5.70e-20145
primitive gut5.70e-20145
trunk region element5.86e-19101
foregut2.43e-1387
organ1.15e-12503
renal system4.59e-1248
urinary system structure8.12e-1247
endo-epithelium1.40e-1182
anatomical space5.86e-1195
respiratory primordium6.22e-1138
endoderm of foregut6.22e-1138
immaterial anatomical entity7.44e-11117
respiratory system1.42e-1074
respiratory tract2.04e-1054
kidney4.36e-1026
kidney mesenchyme4.36e-1026
upper urinary tract4.36e-1026
kidney rudiment4.36e-1026
kidney field4.36e-1026
gastrointestinal system1.68e-0925
subdivision of trunk1.93e-09112
epithelial bud2.05e-0937
cavitated compound organ4.90e-0931
segment of respiratory tract1.05e-0847
abdomen element1.41e-0854
abdominal segment element1.41e-0854
lung1.78e-0822
respiratory tube1.78e-0822
respiration organ1.78e-0822
pair of lungs1.78e-0822
lung primordium1.78e-0822
lung bud1.78e-0822
viscus2.90e-0818
epithelial fold3.64e-0847
respiratory tract epithelium1.04e-0719
lung epithelium1.04e-0719
organ part1.91e-07218
thoracic cavity element3.01e-0734
thoracic cavity3.01e-0734
thoracic segment organ8.39e-0735
Disease
Ontology termp-valuen
carcinoma3.12e-40106
cell type cancer1.08e-33143
cancer1.27e-21235
disease of cellular proliferation3.52e-20239
adenocarcinoma4.90e-1225
squamous cell carcinoma2.50e-1014
disease of anatomical entity6.32e-0939
respiratory system cancer8.18e-0716


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105137.971147625824820.001974187055288560.0115127657528216
CTCF#1066435.360256373075030.0064925092527670.0279156514553204
E2F6#187635.017155731697390.00791769806886330.032170730960707
FOSL2#2355316.93020060456170.0002060162053171620.00242790865122084
RAD21#5885310.35503389545630.0009004912073565420.0066337307755597
RFX5#5993312.04791082719510.0005717246050312580.00484151025904967
SMC3#9126315.04493284493280.0002935825420371870.00308745011658662
SP1#666735.69838137814090.005403962701712170.0246219553531157
TFAP2A#7020316.5186343730450.0002218033880766340.00247965361243155
TFAP2C#7022310.80922860986020.0007916746575753130.00614962510691767
TRIM28#10155318.59052504526250.0001555969297255280.00196926657096514
ZNF263#1012738.221841637010680.001799043925565870.0109295764377974



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.