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Coexpression cluster:C2443: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512090445204501!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00996776538292784!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016087814057464!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418904907853015!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186003136596958!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0282942118517359!JUND#3727;3:5.24599795640327:0.0104343275174842:0.038687543723322!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434917092686171!RXRA#6256;3:15.05596285435:0.000475830799730358:0.0043390633801658!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796154761844302!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00923773366438045!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322135864517627!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140323139116104!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244140178575391!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483025400891027!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346399343823706
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512090445204501!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00996776538292784!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016087814057464!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418904907853015!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186003136596958!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0282942118517359!JUND#3727;3:5.24599795640327:0.0104343275174842:0.038687543723322!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434917092686171!RXRA#6256;3:15.05596285435:0.000475830799730358:0.0043390633801658!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796154761844302!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00923773366438045!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322135864517627!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140323139116104!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244140178575391!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483025400891027!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346399343823706
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}}
}}

Revision as of 15:30, 26 November 2012


Full id: C2443_Mesenchymal_Hepatic_Alveolar_Smooth_Astrocyte_Renal_Hair



Phase1 CAGE Peaks

Hg19::chr17:79479822..79479830,-p1@ACTG1
Hg19::chr19:1026566..1026648,+p1@CNN2
Hg19::chr19:2096259..2096342,-p1@MOB3A
Hg19::chr7:143078379..143078454,+p1@ZYX


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


p.valueFDRnGenesnPathwayName
0.0001458532098643570.03077502728137932200Focal adhesion (KEGG):04510
8.75676438203826e-050.03077502728137932155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.0001288708350416320.03077502728137932188Focal Adhesion (Wikipathways):WP306



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:0005911intercellular junction0.00105713136868672
GO:0030054cell junction0.00326156077542858
GO:0005913cell-cell adherens junction0.0104577467891468
GO:0031032actomyosin structure organization and biogenesis0.0126684703362576
GO:0005856cytoskeleton0.0142566507029949
GO:0005912adherens junction0.0217068263005428
GO:0044459plasma membrane part0.0264873599816309
GO:0043232intracellular non-membrane-bound organelle0.0336456441217229
GO:0043228non-membrane-bound organelle0.0336456441217229
GO:0005516calmodulin binding0.0339637806473224
GO:0005886plasma membrane0.0470180521288173
GO:0030036actin cytoskeleton organization and biogenesis0.048091021929576
GO:0030029actin filament-based process0.048091021929576



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
somatic cell7.15e-44588
animal cell2.50e-28679
eukaryotic cell2.50e-28679
mesodermal cell2.09e-24121
native cell5.32e-24722
contractile cell4.80e-1959
embryonic cell3.20e-18250
muscle precursor cell5.50e-1758
myoblast5.50e-1758
multi-potent skeletal muscle stem cell5.50e-1758
muscle cell8.88e-1755
smooth muscle cell1.40e-1543
smooth muscle myoblast1.40e-1543
somatic stem cell1.43e-15433
multi fate stem cell1.87e-15427
stem cell7.20e-15441
electrically responsive cell1.80e-1461
electrically active cell1.80e-1461
non-terminally differentiated cell1.00e-12106
vascular associated smooth muscle cell2.64e-1232
fibroblast2.97e-1276
meso-epithelial cell5.36e-0945
endothelial cell7.01e-0936
lining cell8.67e-0858
barrier cell8.67e-0858
blood vessel endothelial cell2.25e-0718
embryonic blood vessel endothelial progenitor cell2.25e-0718
endothelial cell of vascular tree4.03e-0724
Uber Anatomy
Ontology termp-valuen
cardiovascular system2.58e-22109
mesoderm1.20e-21315
mesoderm-derived structure1.20e-21315
presumptive mesoderm1.20e-21315
vasculature2.02e-2178
vascular system2.02e-2178
circulatory system1.43e-20112
epithelial vesicle4.83e-1978
multilaminar epithelium2.80e-1783
vessel1.95e-1668
epithelial tube open at both ends3.62e-1659
blood vessel3.62e-1659
blood vasculature3.62e-1659
vascular cord3.62e-1659
somite4.22e-1671
presomitic mesoderm4.22e-1671
presumptive segmental plate4.22e-1671
dermomyotome4.22e-1671
trunk paraxial mesoderm4.22e-1671
lateral plate mesoderm4.88e-16203
splanchnic layer of lateral plate mesoderm1.46e-1583
dense mesenchyme tissue1.91e-1573
paraxial mesoderm2.74e-1572
presumptive paraxial mesoderm2.74e-1572
unilaminar epithelium1.84e-14148
skeletal muscle tissue2.55e-1462
striated muscle tissue2.55e-1462
myotome2.55e-1462
artery5.41e-1442
arterial blood vessel5.41e-1442
arterial system5.41e-1442
epithelial tube1.40e-13117
muscle tissue1.48e-1364
musculature1.48e-1364
musculature of body1.48e-1364
musculoskeletal system2.82e-13167
trunk mesenchyme1.63e-11122
mesenchyme4.57e-11160
entire embryonic mesenchyme4.57e-11160
organism subdivision8.97e-10264
systemic artery1.32e-0933
systemic arterial system1.32e-0933
trunk2.66e-08199
blood vessel endothelium2.25e-0718
endothelium2.25e-0718
cardiovascular system endothelium2.25e-0718
ectodermal placode3.20e-0731
surface structure5.17e-0799
simple squamous epithelium9.02e-0722


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#90546.336201576962630.0006203100587215640.00512090445204501
E2F6#187645.017155731697390.00157802193473060.00996776538292784
ELF1#199744.258097958807540.003041525565781240.016087814057464
EP300#203335.08045629466740.01144298405398240.0418904907853015
HEY1#2346244.040111043105710.00375304636917980.0186003136596958
HMGN3#932436.133910792512940.006640696683324720.0282942118517359
JUND#372735.245997956403270.01043432751748420.038687543723322
PAX5#507935.002174148383370.01196533174786410.0434917092686171
RXRA#6256315.055962854350.0004758307997303580.0043390633801658
SIN3A#2594245.408884726815140.001168172384885160.00796154761844302
SRF#6722310.34788369662590.001439893778401260.00923773366438045
TAF1#687243.343046285745290.008005664898701650.0322135864517627
TAF7#687938.574802053692940.00250055433515240.0140323139116104
TBP#690843.706770687096390.005296377814784350.0244140178575391
USF1#739134.771124457905970.01370465887188020.0483025400891027
ZBTB7A#5134147.35190930787590.000342223540015990.00346399343823706



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.