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Coexpression cluster:C4551: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth
|full_id=C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth
|id=C4551
|id=C4551

Revision as of 17:39, 12 September 2012


Full id: C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth



Phase1 CAGE Peaks

Hg19::chr6:117803797..117803844,+p1@DCBLD1
Hg19::chr6:117803847..117803869,+p2@DCBLD1
Hg19::chr6:117803876..117803888,+p3@DCBLD1


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>

Uber Anatomy
Ontology termp-valuen
unilaminar epithelium9.96e-24138
trunk mesenchyme1.40e-18143
trunk3.26e-17216
epithelial tube2.04e-15118
multilaminar epithelium2.60e-1582
mesenchyme8.43e-15238
entire embryonic mesenchyme8.43e-15238
somite9.43e-1583
paraxial mesoderm9.43e-1583
presomitic mesoderm9.43e-1583
presumptive segmental plate9.43e-1583
trunk paraxial mesoderm9.43e-1583
presumptive paraxial mesoderm9.43e-1583
anatomical group1.30e-14626
multi-cellular organism1.35e-14659
dermomyotome2.11e-1470
anatomical system2.49e-14625
skeletal muscle tissue4.91e-1461
striated muscle tissue4.91e-1461
myotome4.91e-1461
blood vessel7.30e-1460
epithelial tube open at both ends7.30e-1460
blood vasculature7.30e-1460
vascular cord7.30e-1460
muscle tissue8.32e-1463
musculature8.32e-1463
musculature of body8.32e-1463
vasculature1.12e-1379
vascular system1.12e-1379
cell layer1.12e-13312
organism subdivision1.29e-13365
epithelium2.04e-13309
vessel3.80e-1369
splanchnic layer of lateral plate mesoderm1.17e-1284
multi-tissue structure6.78e-12347
artery7.85e-1142
arterial blood vessel7.85e-1142
arterial system7.85e-1142
mesoderm3.22e-10448
mesoderm-derived structure3.22e-10448
presumptive mesoderm3.22e-10448
embryonic structure3.36e-10605
developing anatomical structure3.36e-10605
germ layer4.96e-10604
embryonic tissue4.96e-10604
presumptive structure4.96e-10604
epiblast (generic)4.96e-10604
embryo2.25e-09612
endoderm-derived structure2.31e-09169
endoderm2.31e-09169
presumptive endoderm2.31e-09169
anatomical conduit4.17e-09241
systemic artery5.56e-0933
systemic arterial system5.56e-0933
anatomical cluster9.46e-09286
digestive system1.75e-07155
digestive tract1.75e-07155
primitive gut1.75e-07155
simple squamous epithelium2.30e-0722
tube7.14e-07194
cardiovascular system7.53e-07110


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#90536.336201576962630.003930750035764890.0190950092090446
CTCF#1066435.360256373075030.0064925092527670.0281007531641
CTCFL#140690319.74647435897440.0001298372005551160.0017223507416202
E2F1#186934.907389214879320.008460985347239390.0327328807482714
E2F6#187635.017155731697390.00791769806886330.0324001437432025
EBF1#187938.9064668465690.00141523283560980.00918560077796609
EGR1#195834.988179094810140.008056488137383440.0322170067228315
ELF1#199734.258097958807540.01295179875054610.0464580611934429
ESR1#2099330.76860329615453.43136389821584e-050.000678984869582728
ETS1#211339.728760922202340.001085840092584840.00764745117199189
GABPB1#255337.067683836182170.002832212825417420.0154719884545334
IRF1#365937.63716375356390.002244692747297240.0128639961498561
MYC#460935.22228187160940.007020843755740150.0295808415768011
PAX5#507936.669565531177830.003370290999677260.0173582119398014
SIN3A#2594235.408884726815140.006318961977991520.0278035924342541
SPI1#668838.204323508522730.001810593189410520.0109361252737751
THAP1#55145331.36914460285133.23800758564397e-050.000648713359365185
USF1#739136.361499277207960.00388404057290560.0191017759179548
YY1#752834.911170749853860.008441455341808260.0330974642205621
ZEB1#6935316.88843201754390.0002075486917327580.00243689463922175
ZNF263#1012738.221841637010680.001799043925565870.0109993179102081



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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