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Coexpression cluster:C4703: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019115459256158!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662875507250602!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.03243191232749!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00919359968391194!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322491113633126!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464963876566851!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090203543837375!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154825163713044!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109217388529974!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128745931042329!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270852862661939!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200225137116847!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246682098030397!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473499251601559!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137360645088644!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247895840736205!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000942461143618049!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191206841100018!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140924091480062!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110141478716322
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019115459256158!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662875507250602!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.03243191232749!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00919359968391194!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322491113633126!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464963876566851!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090203543837375!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154825163713044!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109217388529974!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128745931042329!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270852862661939!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200225137116847!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246682098030397!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473499251601559!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137360645088644!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247895840736205!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000942461143618049!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191206841100018!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140924091480062!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110141478716322
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}}
}}

Revision as of 16:54, 26 November 2012


Full id: C4703_amniotic_mesenchymal_cervical_seminal_chorionic_Fibroblast_glioblastoma



Phase1 CAGE Peaks

Hg19::chr7:86975001..86975019,+p2@CROT
Hg19::chr7:86975021..86975036,+p3@CROT
Hg19::chr7:86975045..86975051,+p4@CROT


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><br>


Cell Type
Ontology termp-valuen
epithelial cell of alimentary canal5.48e-0820
Uber Anatomy
Ontology termp-valuen
organ system subdivision6.47e-11223
orifice6.88e-1036
ectoderm-derived structure3.11e-09171
ectoderm3.11e-09171
presumptive ectoderm3.11e-09171
endoderm-derived structure8.16e-09160
endoderm8.16e-09160
presumptive endoderm8.16e-09160
extraembryonic membrane2.20e-0814
membranous layer2.20e-0814
organ component layer6.06e-0866
organ part1.66e-07218
digestive system2.06e-07145
digestive tract2.06e-07145
primitive gut2.06e-07145
reproductive structure6.38e-0759
reproductive system6.38e-0759
mucosa8.66e-0720


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
CCNT2#90536.336201576962630.003930750035764890.019115459256158
CHD2#1106310.34402283411690.0009033701102746880.00662875507250602
E2F6#187635.017155731697390.00791769806886330.03243191232749
EBF1#187938.9064668465690.00141523283560980.00919359968391194
EGR1#195834.988179094810140.008056488137383440.0322491113633126
ELF1#199734.258097958807540.01295179875054610.0464963876566851
FOS#235338.99795530889440.001372499272417130.0090203543837375
GABPB1#255337.067683836182170.002832212825417420.0154825163713044
HMGN3#932438.178547723350590.001827766942164210.0109217388529974
IRF1#365937.63716375356390.002244692747297240.0128745931042329
NFKB1#479035.488063424193840.006049381815655430.0270852862661939
NFYA#4800318.42558069983050.0001598135507814160.00200225137116847
NFYB#4801316.75979325353650.0002123649923296180.00246682098030397
NRF1#4899312.21027944771090.0005492172401020010.00473499251601559
PBX3#5090321.91451268674419.49854535978121e-050.00137360645088644
SP1#666735.69838137814090.005403962701712170.0247895840736205
SP2#6668326.15353049384465.58768218891694e-050.000942461143618049
USF1#739136.361499277207960.00388404057290560.0191206841100018
ZBTB7A#5134137.35190930787590.002516255860282270.0140924091480062
ZNF263#1012738.221841637010680.001799043925565870.0110141478716322



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.