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Coexpression cluster:C1694: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.32e-12!106;DOID:1749!1.04e-11!14;DOID:0050687!1.73e-09!143
|ontology_enrichment_disease=DOID:305!4.32e-12!106;DOID:1749!1.04e-11!14;DOID:0050687!1.73e-09!143
|ontology_enrichment_uberon=UBERON:0005153!1.32e-13!37;UBERON:0005157!6.75e-12!51;UBERON:0005156!6.89e-09!59;UBERON:0000990!6.89e-09!59;UBERON:0002367!1.58e-08!11;UBERON:0010147!1.58e-08!11;UBERON:0009846!1.58e-08!11;UBERON:0003353!1.58e-08!11;UBERON:0004902!1.58e-08!11;UBERON:0003820!1.58e-08!11;UBERON:0009847!1.58e-08!11;UBERON:0005911!1.80e-08!82;UBERON:0006554!4.39e-08!44;UBERON:0007196!8.91e-08!14;UBERON:0001558!8.91e-08!14;UBERON:0001008!9.65e-08!45;UBERON:0000915!9.68e-08!52;UBERON:0003937!1.42e-07!12;UBERON:0005399!1.42e-07!12;UBERON:0000162!1.45e-07!14;UBERON:0001353!1.45e-07!14;UBERON:0000163!1.45e-07!14;UBERON:0006866!1.45e-07!14;UBERON:0000164!1.45e-07!14;UBERON:0000931!1.45e-07!14;UBERON:0003101!1.55e-07!22;UBERON:0000079!1.55e-07!22;UBERON:0004122!7.55e-07!15;UBERON:0000365!9.75e-07!5
|ontology_enrichment_uberon=UBERON:0005153!1.32e-13!37;UBERON:0005157!6.75e-12!51;UBERON:0005156!6.89e-09!59;UBERON:0000990!6.89e-09!59;UBERON:0002367!1.58e-08!11;UBERON:0010147!1.58e-08!11;UBERON:0009846!1.58e-08!11;UBERON:0003353!1.58e-08!11;UBERON:0004902!1.58e-08!11;UBERON:0003820!1.58e-08!11;UBERON:0009847!1.58e-08!11;UBERON:0005911!1.80e-08!82;UBERON:0006554!4.39e-08!44;UBERON:0007196!8.91e-08!14;UBERON:0001558!8.91e-08!14;UBERON:0001008!9.65e-08!45;UBERON:0000915!9.68e-08!52;UBERON:0003937!1.42e-07!12;UBERON:0005399!1.42e-07!12;UBERON:0000162!1.45e-07!14;UBERON:0001353!1.45e-07!14;UBERON:0000163!1.45e-07!14;UBERON:0006866!1.45e-07!14;UBERON:0000164!1.45e-07!14;UBERON:0000931!1.45e-07!14;UBERON:0003101!1.55e-07!22;UBERON:0000079!1.55e-07!22;UBERON:0004122!7.55e-07!15;UBERON:0000365!9.75e-07!5
|tf_chipseq_enrich=MEF2A#4205;3:11.2459385457864:0.00139936678741195:0.00910185388992442!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318894008403238!RFX5#5993;3:7.22874649631706:0.0050291827895866:0.0234651010258057!STAT3#6774;4:8.41557199772339:0.000377152721159863:0.00374175482523178
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}}
}}

Revision as of 14:16, 5 September 2012


Full id: C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial



Phase1 CAGE Peaks

Hg19::chr12:95510642..95510668,-p@chr12:95510642..95510668
-
Hg19::chr12:95510716..95510730,-p3@FGD6
Hg19::chr12:95510743..95510753,-p8@FGD6
Hg19::chr15:71389222..71389244,+p3@THSD4
Hg19::chr9:114908292..114908313,-p13@SUSD1


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


GO IDGO nameFDR corrected p-value
GO:0032488Cdc42 protein signal transduction0.0219815772092478
GO:0043088regulation of Cdc42 GTPase activity0.0219815772092478
GO:0032489regulation of Cdc42 protein signal transduction0.0219815772092478
GO:0032319regulation of Rho GTPase activity0.0219815772092478
GO:0046847filopodium formation0.028616528426325
GO:0030035microspike biogenesis0.028616528426325
GO:0030027lamellipodium0.028616528426325
GO:0022603regulation of anatomical structure morphogenesis0.028616528426325
GO:0008360regulation of cell shape0.028616528426325
GO:0022604regulation of cell morphogenesis0.028616528426325
GO:0001726ruffle0.028616528426325
GO:0030031cell projection biogenesis0.0304958262052178
GO:0031252leading edge0.0405097317596002
GO:0031267small GTPase binding0.0443909858229263
GO:0051020GTPase binding0.0472640384308379



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>


Uber Anatomy
Ontology termp-valuen
epithelial bud1.32e-1337
epithelial fold6.75e-1251
reproductive structure6.89e-0959
reproductive system6.89e-0959
prostate gland1.58e-0811
male accessory sex gland1.58e-0811
embryonic cloacal epithelium1.58e-0811
epithelium of hindgut1.58e-0811
urogenital sinus epithelium1.58e-0811
prostate bud1.58e-0811
prostate field1.58e-0811
endo-epithelium1.80e-0882
urinary system structure4.39e-0844
tracheobronchial tree8.91e-0814
lower respiratory tract8.91e-0814
renal system9.65e-0845
thoracic segment of trunk9.68e-0852
sex gland1.42e-0712
male reproductive gland1.42e-0712
cloaca1.45e-0714
anal region1.45e-0714
embryonic cloaca1.45e-0714
terminal part of digestive tract1.45e-0714
primitive urogenital sinus1.45e-0714
proctodeum1.45e-0714
male organism1.55e-0722
male reproductive system1.55e-0722
genitourinary system7.55e-0715
urothelium9.75e-075
Disease
Ontology termp-valuen
carcinoma4.32e-12106
squamous cell carcinoma1.04e-1114
cell type cancer1.73e-09143


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
MEF2A#4205311.24593854578640.001399366787411950.00910185388992442
RAD21#588536.21302033727380.007751055068811640.0318894008403238
RFX5#599337.228746496317060.00502918278958660.0234651010258057
STAT3#677448.415571997723390.0003771527211598630.00374175482523178



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.