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Coexpression cluster:C2865: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2865_cervix_uterus_lung_rectum_rectal_Prostate_stomach
|full_id=C2865_cervix_uterus_lung_rectum_rectal_Prostate_stomach
|gostat_on_coexpression_clusters=GO:0045104!intermediate filament cytoskeleton organization and biogenesis!0.00772695160720593!667$GO:0045103!intermediate filament-based process!0.00772695160720593!667$GO:0005200!structural constituent of cytoskeleton!0.0260140704109266!667$GO:0007050!cell cycle arrest!0.0260140704109266!667$GO:0045786!negative regulation of progression through cell cycle!0.0463617096432356!667
|gostat_on_coexpression_clusters=GO:0045104!intermediate filament cytoskeleton organization and biogenesis!0.00772695160720593!667$GO:0045103!intermediate filament-based process!0.00772695160720593!667$GO:0005200!structural constituent of cytoskeleton!0.0260140704109266!667$GO:0007050!cell cycle arrest!0.0260140704109266!667$GO:0045786!negative regulation of progression through cell cycle!0.0463617096432356!667

Revision as of 15:39, 12 September 2012


Full id: C2865_cervix_uterus_lung_rectum_rectal_Prostate_stomach



Phase1 CAGE Peaks

Hg19::chr6:56407223..56407227,-p1@BC038763
Hg19::chr6:56407600..56407638,-p11@DST
Hg19::chr6:56407645..56407662,-p25@DST
Hg19::chr6:56407665..56407745,-p7@DST


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:0045104intermediate filament cytoskeleton organization and biogenesis0.00772695160720593
GO:0045103intermediate filament-based process0.00772695160720593
GO:0005200structural constituent of cytoskeleton0.0260140704109266
GO:0007050cell cycle arrest0.0260140704109266
GO:0045786negative regulation of progression through cell cycle0.0463617096432356



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism2.15e-17115
multi-cellular organism2.23e-11659
organ1.16e-10511
subdivision of digestive tract8.24e-10129
endodermal part of digestive tract8.24e-10129
anatomical cluster1.09e-09286
digestive system2.11e-09155
digestive tract2.11e-09155
primitive gut2.11e-09155
anatomical group3.19e-09626
anatomical system4.68e-09625
multi-tissue structure6.27e-09347
anatomical conduit3.58e-08241
endoderm-derived structure1.44e-07169
endoderm1.44e-07169
presumptive endoderm1.44e-07169
mixed endoderm/mesoderm-derived structure5.09e-07130
embryo7.21e-07612
Disease
Ontology termp-valuen
cell type cancer5.34e-07143


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
BHLHE40#8553333.65386016023314.35025573591721e-050.00077545034784683
CCNT2#90546.336201576962630.0006203100587215640.00513470414700971
CEBPB#105147.971147625824820.0002476385788090830.00268624070754485
CTCF#1066445.360256373075030.001211145381643620.00819718829067969
E2F1#186944.907389214879320.001724022357361790.0106775289675922
E2F4#187439.501045236463330.001850751034728270.0109321071950673
ELF1#199744.258097958807540.003041525565781240.0161237444071177
EP300#203335.08045629466740.01144298405398240.0419198783406596
FOS#235348.99795530889440.0001525147711168630.00195393647947425
FOXA1#3169411.08141974938556.62943068949433e-050.00107327718459169
FOXA2#3170318.47284781449890.0002594484187437260.00278227060326276
GATA1#2623413.56030814380042.95627390049268e-050.000615040418114651
GTF2F1#296239.554745657568240.001820362319304780.0109049455240262
HDAC2#3066413.41562023662633.0859005065161e-050.000628487447347962
HEY1#2346244.040111043105710.00375304636917980.0186569760460169
HMGN3#932448.178547723350590.0002234570284440470.00248589993541413
IRF1#365935.727872815172930.008097114790333330.0320202412566309
JUN#372539.384621894252250.001918994502030470.0112898753265863
JUNB#3726322.95797449486590.0001359772504018780.00177983808180496
JUND#372735.245997956403270.01043432751748420.0387177834007864
MAX#414946.452555509007120.0005767613195645490.00486365566847008
MYC#460945.22228187160940.001344309395272740.00889666871129139
NANOG#79923321.93358386075950.0001557535816382770.00196600777286923
PAX5#507935.002174148383370.01196533174786410.0435250350881257
RAD21#5885410.35503389545638.6948481184721e-050.00129892896959678
REST#597849.650028716128020.0001152825614219170.00157529706036158
SIN3A#2594245.408884726815140.001168172384885160.00797977341258557
SMARCB1#6598418.25271578115749.00423392720929e-060.000242119770114266
SMC3#9126311.28369963369960.001115802366868050.00766011196958738
TAF1#687243.343046285745290.008005664898701650.0323256770290161
TBP#690843.706770687096390.005296377814784350.0244983569953613
TCF12#6938410.63446490218647.8163066689251e-050.00120260349469044
TCF7L2#693438.077632422353010.002978381685834620.0158727971060306
TFAP2C#7022410.80922860986027.32289634782688e-050.00114851474946793
TRIM28#10155418.59052504526258.36730015875654e-060.000230938811120606
USF1#739134.771124457905970.01370465887188020.0483400610598228
USF2#739239.74414803880220.001718341848410070.0107269518413688
YY1#752844.911170749853860.00171871838055440.0107056258690715
ZNF263#1012748.221841637010680.0002187871180958320.00249862305377918



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.

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