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Coexpression cluster:C4742: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!1.45e-09!14
|ontology_enrichment_disease=DOID:2394!1.45e-09!14
|ontology_enrichment_uberon=UBERON:0007023!1.92e-20!115;UBERON:0004111!5.08e-16!241;UBERON:0000025!1.65e-15!194;UBERON:0000477!2.60e-15!286;UBERON:0000483!1.29e-12!309;UBERON:0004872!2.41e-12!84;UBERON:0000119!4.30e-12!312;UBERON:0001049!1.77e-11!57;UBERON:0005068!1.77e-11!57;UBERON:0006241!1.77e-11!57;UBERON:0007135!1.77e-11!57;UBERON:0000475!2.25e-11!365;UBERON:0007100!2.70e-11!27;UBERON:0000481!2.25e-10!347;UBERON:0002385!4.85e-10!63;UBERON:0001015!4.85e-10!63;UBERON:0000383!4.85e-10!63;UBERON:0004573!1.09e-09!33;UBERON:0004571!1.09e-09!33;UBERON:0001637!1.70e-09!42;UBERON:0003509!1.70e-09!42;UBERON:0004572!1.70e-09!42;UBERON:0003075!1.71e-09!86;UBERON:0007284!1.71e-09!86;UBERON:0001134!1.88e-09!61;UBERON:0002036!1.88e-09!61;UBERON:0003082!1.88e-09!61;UBERON:0002616!2.60e-09!59;UBERON:0000948!3.45e-09!24;UBERON:0005498!3.45e-09!24;UBERON:0004140!3.45e-09!24;UBERON:0009881!3.45e-09!24;UBERON:0004141!3.45e-09!24;UBERON:0003084!3.45e-09!24;UBERON:0007005!3.45e-09!24;UBERON:0004139!3.45e-09!24;UBERON:0004291!3.45e-09!24;UBERON:0000055!4.07e-09!69;UBERON:0002020!4.12e-09!34;UBERON:0003528!4.12e-09!34;UBERON:0003080!4.44e-09!42;UBERON:0001009!6.74e-09!113;UBERON:0002780!1.16e-08!41;UBERON:0001890!1.16e-08!41;UBERON:0006240!1.16e-08!41;UBERON:0000955!1.39e-08!69;UBERON:0006238!1.39e-08!69;UBERON:0003914!1.49e-08!118;UBERON:0001893!1.69e-08!34;UBERON:0002346!2.29e-08!90;UBERON:0001981!2.54e-08!60;UBERON:0007500!2.54e-08!60;UBERON:0004537!2.54e-08!60;UBERON:0006965!2.54e-08!60;UBERON:0000914!2.64e-08!83;UBERON:0002329!2.64e-08!83;UBERON:0003077!2.64e-08!83;UBERON:0003059!2.64e-08!83;UBERON:0007282!2.64e-08!83;UBERON:0009618!2.64e-08!83;UBERON:0007285!2.64e-08!83;UBERON:0000468!2.72e-08!659;UBERON:0002791!2.81e-08!33;UBERON:0000486!3.11e-08!82;UBERON:0004290!4.41e-08!70;UBERON:0000467!5.23e-08!625;UBERON:0000480!6.81e-08!626;UBERON:0002049!8.30e-08!79;UBERON:0007798!8.30e-08!79;UBERON:0001869!8.65e-08!32;UBERON:0004535!1.12e-07!110;UBERON:0000153!2.32e-07!129;UBERON:0007811!2.32e-07!129;UBERON:0000033!4.58e-07!123;UBERON:0001017!6.13e-07!82;UBERON:0002308!6.61e-07!9;UBERON:0000125!6.61e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.92e-20!115;UBERON:0004111!5.08e-16!241;UBERON:0000025!1.65e-15!194;UBERON:0000477!2.60e-15!286;UBERON:0000483!1.29e-12!309;UBERON:0004872!2.41e-12!84;UBERON:0000119!4.30e-12!312;UBERON:0001049!1.77e-11!57;UBERON:0005068!1.77e-11!57;UBERON:0006241!1.77e-11!57;UBERON:0007135!1.77e-11!57;UBERON:0000475!2.25e-11!365;UBERON:0007100!2.70e-11!27;UBERON:0000481!2.25e-10!347;UBERON:0002385!4.85e-10!63;UBERON:0001015!4.85e-10!63;UBERON:0000383!4.85e-10!63;UBERON:0004573!1.09e-09!33;UBERON:0004571!1.09e-09!33;UBERON:0001637!1.70e-09!42;UBERON:0003509!1.70e-09!42;UBERON:0004572!1.70e-09!42;UBERON:0003075!1.71e-09!86;UBERON:0007284!1.71e-09!86;UBERON:0001134!1.88e-09!61;UBERON:0002036!1.88e-09!61;UBERON:0003082!1.88e-09!61;UBERON:0002616!2.60e-09!59;UBERON:0000948!3.45e-09!24;UBERON:0005498!3.45e-09!24;UBERON:0004140!3.45e-09!24;UBERON:0009881!3.45e-09!24;UBERON:0004141!3.45e-09!24;UBERON:0003084!3.45e-09!24;UBERON:0007005!3.45e-09!24;UBERON:0004139!3.45e-09!24;UBERON:0004291!3.45e-09!24;UBERON:0000055!4.07e-09!69;UBERON:0002020!4.12e-09!34;UBERON:0003528!4.12e-09!34;UBERON:0003080!4.44e-09!42;UBERON:0001009!6.74e-09!113;UBERON:0002780!1.16e-08!41;UBERON:0001890!1.16e-08!41;UBERON:0006240!1.16e-08!41;UBERON:0000955!1.39e-08!69;UBERON:0006238!1.39e-08!69;UBERON:0003914!1.49e-08!118;UBERON:0001893!1.69e-08!34;UBERON:0002346!2.29e-08!90;UBERON:0001981!2.54e-08!60;UBERON:0007500!2.54e-08!60;UBERON:0004537!2.54e-08!60;UBERON:0006965!2.54e-08!60;UBERON:0000914!2.64e-08!83;UBERON:0002329!2.64e-08!83;UBERON:0003077!2.64e-08!83;UBERON:0003059!2.64e-08!83;UBERON:0007282!2.64e-08!83;UBERON:0009618!2.64e-08!83;UBERON:0007285!2.64e-08!83;UBERON:0000468!2.72e-08!659;UBERON:0002791!2.81e-08!33;UBERON:0000486!3.11e-08!82;UBERON:0004290!4.41e-08!70;UBERON:0000467!5.23e-08!625;UBERON:0000480!6.81e-08!626;UBERON:0002049!8.30e-08!79;UBERON:0007798!8.30e-08!79;UBERON:0001869!8.65e-08!32;UBERON:0004535!1.12e-07!110;UBERON:0000153!2.32e-07!129;UBERON:0007811!2.32e-07!129;UBERON:0000033!4.58e-07!123;UBERON:0001017!6.13e-07!82;UBERON:0002308!6.61e-07!9;UBERON:0000125!6.61e-07!9
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5
}}
}}

Revision as of 13:55, 5 September 2012


Full id: C4742_skeletal_Mesothelial_heart_mature_mesenchymal_caudate_left



Phase1 CAGE Peaks

Hg19::chr8:22250334..22250354,+p7@SLC39A14
Hg19::chr8:22250363..22250385,+p5@SLC39A14
Hg19::chr8:22250390..22250405,+p6@SLC39A14


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>


Uber Anatomy
Ontology termp-valuen
adult organism1.92e-20115
anatomical conduit5.08e-16241
tube1.65e-15194
anatomical cluster2.60e-15286
epithelium1.29e-12309
splanchnic layer of lateral plate mesoderm2.41e-1284
cell layer4.30e-12312
neural tube1.77e-1157
neural rod1.77e-1157
future spinal cord1.77e-1157
neural keel1.77e-1157
organism subdivision2.25e-11365
primary circulatory organ2.70e-1127
multi-tissue structure2.25e-10347
muscle tissue4.85e-1063
musculature4.85e-1063
musculature of body4.85e-1063
systemic artery1.09e-0933
systemic arterial system1.09e-0933
artery1.70e-0942
arterial blood vessel1.70e-0942
arterial system1.70e-0942
neural plate1.71e-0986
presumptive neural plate1.71e-0986
skeletal muscle tissue1.88e-0961
striated muscle tissue1.88e-0961
myotome1.88e-0961
regional part of brain2.60e-0959
heart3.45e-0924
primitive heart tube3.45e-0924
primary heart field3.45e-0924
anterior lateral plate mesoderm3.45e-0924
heart tube3.45e-0924
heart primordium3.45e-0924
cardiac mesoderm3.45e-0924
cardiogenic plate3.45e-0924
heart rudiment3.45e-0924
vessel4.07e-0969
gray matter4.12e-0934
brain grey matter4.12e-0934
anterior neural tube4.44e-0942
circulatory system6.74e-09113
regional part of forebrain1.16e-0841
forebrain1.16e-0841
future forebrain1.16e-0841
brain1.39e-0869
future brain1.39e-0869
epithelial tube1.49e-08118
telencephalon1.69e-0834
neurectoderm2.29e-0890
blood vessel2.54e-0860
epithelial tube open at both ends2.54e-0860
blood vasculature2.54e-0860
vascular cord2.54e-0860
somite2.64e-0883
paraxial mesoderm2.64e-0883
presomitic mesoderm2.64e-0883
presumptive segmental plate2.64e-0883
trunk paraxial mesoderm2.64e-0883
presumptive paraxial mesoderm2.64e-0883
multi-cellular organism2.72e-08659
regional part of telencephalon2.81e-0833
multilaminar epithelium3.11e-0882
dermomyotome4.41e-0870
anatomical system5.23e-08625
anatomical group6.81e-08626
vasculature8.30e-0879
vascular system8.30e-0879
cerebral hemisphere8.65e-0832
cardiovascular system1.12e-07110
anterior region of body2.32e-07129
craniocervical region2.32e-07129
head4.58e-07123
central nervous system6.13e-0782
nucleus of brain6.61e-079
neural nucleus6.61e-079
Disease
Ontology termp-valuen
ovarian cancer1.45e-0914


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
STAT3#6774310.51946499715420.0008589184530415310.00646007376618209
ZNF263#1012738.221841637010680.001799043925565870.0110180231362326



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.