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Coexpression cluster:C3530: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!1.04e-21!216;UBERON:0000475!5.51e-19!365;UBERON:0000481!8.77e-19!347;UBERON:0000119!1.60e-18!312;UBERON:0000483!2.45e-17!309;UBERON:0000477!3.02e-17!286;UBERON:0004111!1.08e-16!241;UBERON:0003914!4.26e-15!118;UBERON:0009569!2.36e-14!113;UBERON:0000490!2.64e-14!138;UBERON:0003104!7.89e-14!238;UBERON:0009142!7.89e-14!238;UBERON:0000468!2.28e-13!659;UBERON:0000466!4.72e-13!126;UBERON:0005256!1.20e-12!143;UBERON:0000025!1.78e-12!194;UBERON:0002049!2.23e-12!79;UBERON:0007798!2.23e-12!79;UBERON:0005177!6.70e-11!107;UBERON:0003886!2.15e-10!63;UBERON:0000464!2.23e-10!104;UBERON:0002417!3.40e-10!61;UBERON:0000916!3.40e-10!61;UBERON:0004872!5.25e-10!84;UBERON:0003103!7.31e-10!69;UBERON:0000055!7.77e-10!69;UBERON:0002553!3.75e-09!70;UBERON:0000467!2.33e-08!625;UBERON:0005172!3.19e-08!55;UBERON:0005173!3.19e-08!55;UBERON:0000480!4.14e-08!626;UBERON:0000487!1.12e-07!22;UBERON:0001008!1.17e-07!45;UBERON:0001981!1.63e-07!60;UBERON:0007500!1.63e-07!60;UBERON:0004537!1.63e-07!60;UBERON:0006965!1.63e-07!60;UBERON:0001986!1.98e-07!18;UBERON:0004638!1.98e-07!18;UBERON:0004852!1.98e-07!18;UBERON:0000489!2.85e-07!32;UBERON:0006554!3.03e-07!44;UBERON:0001048!3.34e-07!168;UBERON:0003064!3.78e-07!37;UBERON:0001009!4.00e-07!113;UBERON:0006914!4.25e-07!25;UBERON:0004535!6.26e-07!110;UBERON:0000058!8.03e-07!26;UBERON:0002050!9.51e-07!605;UBERON:0005423!9.51e-07!605;UBERON:0002323!9.86e-07!46
|ontology_enrichment_uberon=UBERON:0002100!1.04e-21!216;UBERON:0000475!5.51e-19!365;UBERON:0000481!8.77e-19!347;UBERON:0000119!1.60e-18!312;UBERON:0000483!2.45e-17!309;UBERON:0000477!3.02e-17!286;UBERON:0004111!1.08e-16!241;UBERON:0003914!4.26e-15!118;UBERON:0009569!2.36e-14!113;UBERON:0000490!2.64e-14!138;UBERON:0003104!7.89e-14!238;UBERON:0009142!7.89e-14!238;UBERON:0000468!2.28e-13!659;UBERON:0000466!4.72e-13!126;UBERON:0005256!1.20e-12!143;UBERON:0000025!1.78e-12!194;UBERON:0002049!2.23e-12!79;UBERON:0007798!2.23e-12!79;UBERON:0005177!6.70e-11!107;UBERON:0003886!2.15e-10!63;UBERON:0000464!2.23e-10!104;UBERON:0002417!3.40e-10!61;UBERON:0000916!3.40e-10!61;UBERON:0004872!5.25e-10!84;UBERON:0003103!7.31e-10!69;UBERON:0000055!7.77e-10!69;UBERON:0002553!3.75e-09!70;UBERON:0000467!2.33e-08!625;UBERON:0005172!3.19e-08!55;UBERON:0005173!3.19e-08!55;UBERON:0000480!4.14e-08!626;UBERON:0000487!1.12e-07!22;UBERON:0001008!1.17e-07!45;UBERON:0001981!1.63e-07!60;UBERON:0007500!1.63e-07!60;UBERON:0004537!1.63e-07!60;UBERON:0006965!1.63e-07!60;UBERON:0001986!1.98e-07!18;UBERON:0004638!1.98e-07!18;UBERON:0004852!1.98e-07!18;UBERON:0000489!2.85e-07!32;UBERON:0006554!3.03e-07!44;UBERON:0001048!3.34e-07!168;UBERON:0003064!3.78e-07!37;UBERON:0001009!4.00e-07!113;UBERON:0006914!4.25e-07!25;UBERON:0004535!6.26e-07!110;UBERON:0000058!8.03e-07!26;UBERON:0002050!9.51e-07!605;UBERON:0005423!9.51e-07!605;UBERON:0002323!9.86e-07!46
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}}
}}

Revision as of 12:54, 5 September 2012


Full id: C3530_Myoblast_ovary_extraskeletal_Fibroblast_kidney_breast_cervix



Phase1 CAGE Peaks

Hg19::chr15:96873921..96873946,+p1@NR2F2
Hg19::chr15:96873984..96873999,+p3@NR2F2
Hg19::chr15:96874012..96874042,+p2@NR2F2


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
trunk1.04e-21216
organism subdivision5.51e-19365
multi-tissue structure8.77e-19347
cell layer1.60e-18312
epithelium2.45e-17309
anatomical cluster3.02e-17286
anatomical conduit1.08e-16241
epithelial tube4.26e-15118
subdivision of trunk2.36e-14113
unilaminar epithelium2.64e-14138
mesenchyme7.89e-14238
entire embryonic mesenchyme7.89e-14238
multi-cellular organism2.28e-13659
immaterial anatomical entity4.72e-13126
trunk mesenchyme1.20e-12143
tube1.78e-12194
vasculature2.23e-1279
vascular system2.23e-1279
trunk region element6.70e-11107
body cavity precursor2.15e-1063
anatomical space2.23e-10104
abdominal segment of trunk3.40e-1061
abdomen3.40e-1061
splanchnic layer of lateral plate mesoderm5.25e-1084
compound organ7.31e-1069
vessel7.77e-1069
anatomical cavity3.75e-0970
anatomical system2.33e-08625
abdomen element3.19e-0855
abdominal segment element3.19e-0855
anatomical group4.14e-08626
simple squamous epithelium1.12e-0722
renal system1.17e-0745
blood vessel1.63e-0760
epithelial tube open at both ends1.63e-0760
blood vasculature1.63e-0760
vascular cord1.63e-0760
endothelium1.98e-0718
blood vessel endothelium1.98e-0718
cardiovascular system endothelium1.98e-0718
cavitated compound organ2.85e-0732
urinary system structure3.03e-0744
primordium3.34e-07168
intermediate mesoderm3.78e-0737
circulatory system4.00e-07113
squamous epithelium4.25e-0725
cardiovascular system6.26e-07110
duct8.03e-0726
embryonic structure9.51e-07605
developing anatomical structure9.51e-07605
body cavity9.86e-0746


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#90536.336201576962630.003930750035764890.0189705916351779
CEBPB#105137.971147625824820.001974187055288560.0115095524096953
E2F1#186934.907389214879320.008460985347239390.0324658993563206
E2F4#1874312.66806031528440.0004917987006298980.00436500080692496
E2F6#187635.017155731697390.00791769806886330.0321494680849895
EGR1#195834.988179094810140.008056488137383440.0319964849442974
FOSL1#8061339.7135797163731.59554825631833e-050.0003707998761496
GATA3#2625327.2365163572064.94721007899563e-050.000850364834496749
GTF2B#2959331.94382993432423.06634405746243e-050.00062719527422115
GTF2F1#2962312.73966087675770.0004835525047438590.00433379730910014
HMGN3#932438.178547723350590.001827766942164210.0108565177542335
HNF4A#3172323.13229036295378.07584663437677e-050.00122681214057844
HNF4G#3174328.75342252644684.20470658818262e-050.000755956879606137
IRF1#365937.63716375356390.002244692747297240.0127861175803096
MAX#414936.452555509007120.003721913834265510.0186254412523649
MXI1#460139.96157162875930.001011470541259020.007194508741984
MYC#460935.22228187160940.007020843755740150.0293981998639141
NFYA#4800318.42558069983050.0001598135507814160.00199340349099013
NFYB#4801316.75979325353650.0002123649923296180.00245480768499314
NR2C2#7182332.61461090524092.88098172333076e-050.000604433206514547
NRF1#4899312.21027944771090.0005492172401020010.00470508566475374
RXRA#6256320.07461713913330.0001235730348432220.00165057477759193
SIN3A#2594235.408884726815140.006318961977991520.0276081856601178
SP1#666735.69838137814090.005403962701712170.0246047807395639
SREBF1#6720347.00584944048839.62099323994382e-060.00025451036296517
SRF#6722313.79717826216780.0003806615025800190.00374561020048564
TCF7L2#6934310.77017656313730.0008003181298398380.0061278904077964
YY1#752834.911170749853860.008441455341808260.0328704058179454
ZBTB7A#5134137.35190930787590.002516255860282270.0139911220674024
ZNF143#7702313.50087655222790.0004062804962997170.00388495960016903
ZNF263#1012738.221841637010680.001799043925565870.0109200481542586



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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