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Coexpression cluster:C4699: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!3.99e-17!659;UBERON:0004872!2.55e-16!84;UBERON:0000475!3.28e-16!365;UBERON:0002100!9.61e-16!216;UBERON:0000055!4.99e-15!69;UBERON:0002049!2.38e-14!79;UBERON:0007798!2.38e-14!79;UBERON:0001981!2.96e-13!60;UBERON:0007500!2.96e-13!60;UBERON:0004537!2.96e-13!60;UBERON:0006965!2.96e-13!60;UBERON:0003104!5.01e-13!238;UBERON:0009142!5.01e-13!238;UBERON:0003914!5.97e-13!118;UBERON:0000467!3.72e-12!625;UBERON:0000480!5.61e-12!626;UBERON:0005256!6.18e-12!143;UBERON:0000490!1.81e-11!138;UBERON:0000483!6.89e-11!309;UBERON:0000481!7.59e-11!347;UBERON:0000119!1.47e-10!312;UBERON:0000486!1.69e-10!82;UBERON:0001009!2.18e-10!113;UBERON:0000477!2.39e-10!286;UBERON:0004111!3.42e-10!241;UBERON:0003102!1.01e-09!95;UBERON:0002385!1.18e-09!63;UBERON:0001015!1.18e-09!63;UBERON:0000383!1.18e-09!63;UBERON:0000914!1.30e-09!83;UBERON:0002329!1.30e-09!83;UBERON:0003077!1.30e-09!83;UBERON:0003059!1.30e-09!83;UBERON:0007282!1.30e-09!83;UBERON:0009618!1.30e-09!83;UBERON:0007285!1.30e-09!83;UBERON:0001134!2.22e-09!61;UBERON:0002036!2.22e-09!61;UBERON:0003082!2.22e-09!61;UBERON:0004535!2.42e-09!110;UBERON:0004290!2.57e-09!70;UBERON:0003103!4.23e-09!69;UBERON:0009569!1.70e-08!113;UBERON:0000926!4.45e-08!448;UBERON:0004120!4.45e-08!448;UBERON:0006603!4.45e-08!448;UBERON:0001637!5.26e-08!42;UBERON:0003509!5.26e-08!42;UBERON:0004572!5.26e-08!42;UBERON:0000487!1.70e-07!22;UBERON:0006914!3.91e-07!25;UBERON:0000922!4.57e-07!612;UBERON:0001986!4.62e-07!18;UBERON:0004638!4.62e-07!18;UBERON:0004852!4.62e-07!18;UBERON:0002050!6.13e-07!605;UBERON:0005423!6.13e-07!605
|ontology_enrichment_uberon=UBERON:0000468!3.99e-17!659;UBERON:0004872!2.55e-16!84;UBERON:0000475!3.28e-16!365;UBERON:0002100!9.61e-16!216;UBERON:0000055!4.99e-15!69;UBERON:0002049!2.38e-14!79;UBERON:0007798!2.38e-14!79;UBERON:0001981!2.96e-13!60;UBERON:0007500!2.96e-13!60;UBERON:0004537!2.96e-13!60;UBERON:0006965!2.96e-13!60;UBERON:0003104!5.01e-13!238;UBERON:0009142!5.01e-13!238;UBERON:0003914!5.97e-13!118;UBERON:0000467!3.72e-12!625;UBERON:0000480!5.61e-12!626;UBERON:0005256!6.18e-12!143;UBERON:0000490!1.81e-11!138;UBERON:0000483!6.89e-11!309;UBERON:0000481!7.59e-11!347;UBERON:0000119!1.47e-10!312;UBERON:0000486!1.69e-10!82;UBERON:0001009!2.18e-10!113;UBERON:0000477!2.39e-10!286;UBERON:0004111!3.42e-10!241;UBERON:0003102!1.01e-09!95;UBERON:0002385!1.18e-09!63;UBERON:0001015!1.18e-09!63;UBERON:0000383!1.18e-09!63;UBERON:0000914!1.30e-09!83;UBERON:0002329!1.30e-09!83;UBERON:0003077!1.30e-09!83;UBERON:0003059!1.30e-09!83;UBERON:0007282!1.30e-09!83;UBERON:0009618!1.30e-09!83;UBERON:0007285!1.30e-09!83;UBERON:0001134!2.22e-09!61;UBERON:0002036!2.22e-09!61;UBERON:0003082!2.22e-09!61;UBERON:0004535!2.42e-09!110;UBERON:0004290!2.57e-09!70;UBERON:0003103!4.23e-09!69;UBERON:0009569!1.70e-08!113;UBERON:0000926!4.45e-08!448;UBERON:0004120!4.45e-08!448;UBERON:0006603!4.45e-08!448;UBERON:0001637!5.26e-08!42;UBERON:0003509!5.26e-08!42;UBERON:0004572!5.26e-08!42;UBERON:0000487!1.70e-07!22;UBERON:0006914!3.91e-07!25;UBERON:0000922!4.57e-07!612;UBERON:0001986!4.62e-07!18;UBERON:0004638!4.62e-07!18;UBERON:0004852!4.62e-07!18;UBERON:0002050!6.13e-07!605;UBERON:0005423!6.13e-07!605
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460804059440161
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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C4699_Mesenchymal_Urothelial_vagina_Renal_MCF7_salivary_skeletal



Phase1 CAGE Peaks

Hg19::chr7:75931982..75932005,+p1@HSPB1
Hg19::chr7:75932326..75932393,-p@chr7:75932326..75932393
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Hg19::chrX:49090623..49090648,-p2@HSPB1P2


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

GO IDGO nameFDR corrected p-value
GO:0006446regulation of translational initiation0.0362062875309078
GO:0006986response to unfolded protein0.0362062875309078
GO:0051789response to protein stimulus0.0362062875309078
GO:0006413translational initiation0.0362062875309078
GO:0022618protein-RNA complex assembly0.0362062875309078
GO:0009986cell surface0.0362062875309078
GO:0006916anti-apoptosis0.0362062875309078
GO:0006417regulation of translation0.0362062875309078
GO:0031326regulation of cellular biosynthetic process0.0362062875309078
GO:0009889regulation of biosynthetic process0.0362062875309078
GO:0043066negative regulation of apoptosis0.0362062875309078
GO:0043069negative regulation of programmed cell death0.0362062875309078
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0362062875309078
GO:0009607response to biotic stimulus0.0394968125010513
GO:0051674localization of cell0.0458005857765218
GO:0006928cell motility0.0458005857765218
GO:0051246regulation of protein metabolic process0.0474958616438451



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
multi-cellular organism3.99e-17659
splanchnic layer of lateral plate mesoderm2.55e-1684
organism subdivision3.28e-16365
trunk9.61e-16216
vessel4.99e-1569
vasculature2.38e-1479
vascular system2.38e-1479
blood vessel2.96e-1360
epithelial tube open at both ends2.96e-1360
blood vasculature2.96e-1360
vascular cord2.96e-1360
mesenchyme5.01e-13238
entire embryonic mesenchyme5.01e-13238
epithelial tube5.97e-13118
anatomical system3.72e-12625
anatomical group5.61e-12626
trunk mesenchyme6.18e-12143
unilaminar epithelium1.81e-11138
epithelium6.89e-11309
multi-tissue structure7.59e-11347
cell layer1.47e-10312
multilaminar epithelium1.69e-1082
circulatory system2.18e-10113
anatomical cluster2.39e-10286
anatomical conduit3.42e-10241
surface structure1.01e-0995
muscle tissue1.18e-0963
musculature1.18e-0963
musculature of body1.18e-0963
somite1.30e-0983
paraxial mesoderm1.30e-0983
presomitic mesoderm1.30e-0983
presumptive segmental plate1.30e-0983
trunk paraxial mesoderm1.30e-0983
presumptive paraxial mesoderm1.30e-0983
skeletal muscle tissue2.22e-0961
striated muscle tissue2.22e-0961
myotome2.22e-0961
cardiovascular system2.42e-09110
dermomyotome2.57e-0970
compound organ4.23e-0969
subdivision of trunk1.70e-08113
mesoderm4.45e-08448
mesoderm-derived structure4.45e-08448
presumptive mesoderm4.45e-08448
artery5.26e-0842
arterial blood vessel5.26e-0842
arterial system5.26e-0842
simple squamous epithelium1.70e-0722
squamous epithelium3.91e-0725
embryo4.57e-07612
endothelium4.62e-0718
blood vessel endothelium4.62e-0718
cardiovascular system endothelium4.62e-0718
embryonic structure6.13e-07605
developing anatomical structure6.13e-07605


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
NR3C1#290829.982015554115360.01278474365547170.0460804059440161



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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