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Coexpression cluster:C2348: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!8.05e-10!22;DOID:2994!8.05e-10!22;DOID:0050687!1.75e-07!143
|ontology_enrichment_disease=DOID:3095!8.05e-10!22;DOID:2994!8.05e-10!22;DOID:0050687!1.75e-07!143
|ontology_enrichment_uberon=UBERON:0001032!1.40e-11!24;UBERON:0004456!1.40e-11!24;UBERON:0000020!2.28e-11!23;UBERON:0002104!8.11e-11!21;UBERON:0000970!1.30e-10!20;UBERON:0000019!5.48e-10!19;UBERON:0000047!5.48e-10!19;UBERON:0004088!5.48e-10!19;UBERON:0003072!5.48e-10!19;UBERON:0003071!5.48e-10!19;UBERON:0004128!5.48e-10!19;UBERON:0000924!3.06e-09!173;UBERON:0006601!3.06e-09!173;UBERON:0004121!3.22e-09!169;UBERON:0001456!3.97e-09!21;UBERON:0002200!2.32e-08!11;UBERON:0006876!2.32e-08!11;UBERON:0005631!5.28e-08!14;UBERON:0000158!5.28e-08!14;UBERON:0007625!5.82e-08!11;UBERON:0000073!6.53e-08!94;UBERON:0001016!6.53e-08!94;UBERON:0005085!8.75e-07!29;UBERON:0000481!9.07e-07!347
|ontology_enrichment_uberon=UBERON:0001032!1.40e-11!24;UBERON:0004456!1.40e-11!24;UBERON:0000020!2.28e-11!23;UBERON:0002104!8.11e-11!21;UBERON:0000970!1.30e-10!20;UBERON:0000019!5.48e-10!19;UBERON:0000047!5.48e-10!19;UBERON:0004088!5.48e-10!19;UBERON:0003072!5.48e-10!19;UBERON:0003071!5.48e-10!19;UBERON:0004128!5.48e-10!19;UBERON:0000924!3.06e-09!173;UBERON:0006601!3.06e-09!173;UBERON:0004121!3.22e-09!169;UBERON:0001456!3.97e-09!21;UBERON:0002200!2.32e-08!11;UBERON:0006876!2.32e-08!11;UBERON:0005631!5.28e-08!14;UBERON:0000158!5.28e-08!14;UBERON:0007625!5.82e-08!11;UBERON:0000073!6.53e-08!94;UBERON:0001016!6.53e-08!94;UBERON:0005085!8.75e-07!29;UBERON:0000481!9.07e-07!347
|tf_chipseq_enrich=CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.95117937055607e-06!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.0081654388040461!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101364294505074!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433803704768761!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000721127555643346!GATA3#2625;2:13.618258178603:0.0076966520809334:0.0316892945943627!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391233381387934!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129209055584107!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683521219447454!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321801107057002!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243871088351231!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119942293887139!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115262902369231!USF1#7391;4:6.36149927720796:0.000610501139914083:0.0050748271690136!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106712578887534
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}}
}}

Revision as of 12:49, 5 September 2012


Full id: C2348_gastric_Iris_retina_papillotubular_neuroblastoma_Ciliary_embryonic



Phase1 CAGE Peaks

Hg19::chr15:74495084..74495137,-p1@STRA6
Hg19::chr15:74495188..74495220,-p5@STRA6
Hg19::chr15:74495324..74495347,+p2@ENST00000558645
Hg19::chr15:74495350..74495381,+p1@ENST00000558645


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
neurectodermal cell8.30e-1059
neural cell9.03e-0725
Uber Anatomy
Ontology termp-valuen
sensory system1.40e-1124
entire sense organ system1.40e-1124
sense organ2.28e-1123
visual system8.11e-1121
eye1.30e-1020
camera-type eye5.48e-1019
simple eye5.48e-1019
ocular region5.48e-1019
optic cup5.48e-1019
eye primordium5.48e-1019
optic vesicle5.48e-1019
ectoderm3.06e-09173
presumptive ectoderm3.06e-09173
ectoderm-derived structure3.22e-09169
face3.97e-0921
vasculature of head2.32e-0811
vasculature of organ2.32e-0811
extraembryonic membrane5.28e-0814
membranous layer5.28e-0814
pigment epithelium of eye5.82e-0811
regional part of nervous system6.53e-0894
nervous system6.53e-0894
ectodermal placode8.75e-0729
multi-tissue structure9.07e-07347
Disease
Ontology termp-valuen
germ cell and embryonal cancer8.05e-1022
germ cell cancer8.05e-1022
cell type cancer1.75e-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
CTBP2#1488462.71700033932816.45042639894877e-083.95117937055607e-06
CTCF#1066445.360256373075030.001211145381643620.0081654388040461
EGR1#195844.988179094810140.001615011500076050.0101364294505074
EP300#203346.77394172622320.0004748459821442640.00433803704768761
GATA2#2624412.7449317335543.78864877853583e-050.000721127555643346
GATA3#2625213.6182581786030.00769665208093340.0316892945943627
JUND#372746.994663941871030.000417684217818580.00391233381387934
RAD21#5885410.35503389545638.6948481184721e-050.00129209055584107
SP1#666745.69838137814090.0009482606065333980.00683521219447454
TAF1#687243.343046285745290.008005664898701650.0321801107057002
TBP#690843.706770687096390.005296377814784350.0243871088351231
TCF12#6938410.63446490218647.8163066689251e-050.00119942293887139
TCF7L2#6934410.77017656313737.42969445082454e-050.00115262902369231
USF1#739146.361499277207960.0006105011399140830.0050748271690136
YY1#752844.911170749853860.00171871838055440.0106712578887534



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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