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Coexpression cluster:C1357: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.45e-07!235;DOID:14566!4.34e-07!239;DOID:2531!6.14e-07!51;DOID:0060083!6.14e-07!51
|ontology_enrichment_disease=DOID:162!1.45e-07!235;DOID:14566!4.34e-07!239;DOID:2531!6.14e-07!51;DOID:0060083!6.14e-07!51
|ontology_enrichment_uberon=UBERON:0003914!2.70e-13!118;UBERON:0000490!4.00e-12!138;UBERON:0002049!3.55e-11!79;UBERON:0007798!3.55e-11!79;UBERON:0000486!6.41e-11!82;UBERON:0000055!1.13e-10!69;UBERON:0001981!1.68e-10!60;UBERON:0007500!1.68e-10!60;UBERON:0004537!1.68e-10!60;UBERON:0006965!1.68e-10!60;UBERON:0004290!1.94e-10!70;UBERON:0001637!4.81e-10!42;UBERON:0003509!4.81e-10!42;UBERON:0004572!4.81e-10!42;UBERON:0003104!4.83e-10!238;UBERON:0009142!4.83e-10!238;UBERON:0004872!7.98e-10!84;UBERON:0005256!2.30e-09!143;UBERON:0000914!1.72e-08!83;UBERON:0002329!1.72e-08!83;UBERON:0003077!1.72e-08!83;UBERON:0003059!1.72e-08!83;UBERON:0007282!1.72e-08!83;UBERON:0009618!1.72e-08!83;UBERON:0007285!1.72e-08!83;UBERON:0002100!4.92e-08!216;UBERON:0001986!5.25e-08!18;UBERON:0004638!5.25e-08!18;UBERON:0004852!5.25e-08!18;UBERON:0004211!5.54e-08!16;UBERON:0001285!5.54e-08!16;UBERON:0007684!5.54e-08!16;UBERON:0003220!5.54e-08!16;UBERON:0004208!5.54e-08!16;UBERON:0000119!7.46e-08!312;UBERON:0001134!9.34e-08!61;UBERON:0002036!9.34e-08!61;UBERON:0003082!9.34e-08!61;UBERON:0000487!1.13e-07!22;UBERON:0000483!1.63e-07!309;UBERON:0006914!2.93e-07!25;UBERON:0006555!3.82e-07!17;UBERON:0005103!3.82e-07!17;UBERON:0000083!3.82e-07!17;UBERON:0009201!3.82e-07!17;UBERON:0004819!3.82e-07!17;UBERON:0006553!3.82e-07!17;UBERON:0003074!3.82e-07!17;UBERON:0003060!3.82e-07!17;UBERON:0002385!6.46e-07!63;UBERON:0001015!6.46e-07!63;UBERON:0000383!6.46e-07!63;UBERON:0001225!7.23e-07!13;UBERON:0008987!7.23e-07!13
|ontology_enrichment_uberon=UBERON:0003914!2.70e-13!118;UBERON:0000490!4.00e-12!138;UBERON:0002049!3.55e-11!79;UBERON:0007798!3.55e-11!79;UBERON:0000486!6.41e-11!82;UBERON:0000055!1.13e-10!69;UBERON:0001981!1.68e-10!60;UBERON:0007500!1.68e-10!60;UBERON:0004537!1.68e-10!60;UBERON:0006965!1.68e-10!60;UBERON:0004290!1.94e-10!70;UBERON:0001637!4.81e-10!42;UBERON:0003509!4.81e-10!42;UBERON:0004572!4.81e-10!42;UBERON:0003104!4.83e-10!238;UBERON:0009142!4.83e-10!238;UBERON:0004872!7.98e-10!84;UBERON:0005256!2.30e-09!143;UBERON:0000914!1.72e-08!83;UBERON:0002329!1.72e-08!83;UBERON:0003077!1.72e-08!83;UBERON:0003059!1.72e-08!83;UBERON:0007282!1.72e-08!83;UBERON:0009618!1.72e-08!83;UBERON:0007285!1.72e-08!83;UBERON:0002100!4.92e-08!216;UBERON:0001986!5.25e-08!18;UBERON:0004638!5.25e-08!18;UBERON:0004852!5.25e-08!18;UBERON:0004211!5.54e-08!16;UBERON:0001285!5.54e-08!16;UBERON:0007684!5.54e-08!16;UBERON:0003220!5.54e-08!16;UBERON:0004208!5.54e-08!16;UBERON:0000119!7.46e-08!312;UBERON:0001134!9.34e-08!61;UBERON:0002036!9.34e-08!61;UBERON:0003082!9.34e-08!61;UBERON:0000487!1.13e-07!22;UBERON:0000483!1.63e-07!309;UBERON:0006914!2.93e-07!25;UBERON:0006555!3.82e-07!17;UBERON:0005103!3.82e-07!17;UBERON:0000083!3.82e-07!17;UBERON:0009201!3.82e-07!17;UBERON:0004819!3.82e-07!17;UBERON:0006553!3.82e-07!17;UBERON:0003074!3.82e-07!17;UBERON:0003060!3.82e-07!17;UBERON:0002385!6.46e-07!63;UBERON:0001015!6.46e-07!63;UBERON:0000383!6.46e-07!63;UBERON:0001225!7.23e-07!13;UBERON:0008987!7.23e-07!13
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}}
}}

Revision as of 17:11, 8 August 2012


Full id: C1357_Mesenchymal_Alveolar_Renal_Placental_acantholytic_Tracheal_Bronchial



Phase1 CAGE Peaks

Hg19::chr12:132628963..132629027,+p1@NOC4L
Hg19::chr12:53895052..53895143,+p1@TARBP2
Hg19::chr16:2022036..2022112,+p1@TBL3
Hg19::chr16:88772866..88772947,+p1@CTU2
Hg19::chr19:59055814..59055835,+p1@TRIM28
Hg19::chr19:984313..984357,+p1@WDR18


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:0007199G-protein signaling, coupled to cGMP nucleotide second messenger0.011538404895764
GO:0019934cGMP-mediated signaling0.011538404895764
GO:0006357regulation of transcription from RNA polymerase II promoter0.0172999664284364
GO:0030515snoRNA binding0.0172999664284364
GO:0005634nucleus0.0172999664284364
GO:0043193positive regulation of gene-specific transcription0.0172999664284364
GO:0001837epithelial to mesenchymal transition0.0172999664284364
GO:0032583regulation of gene-specific transcription0.0172999664284364
GO:0005732small nucleolar ribonucleoprotein complex0.0192196385985799
GO:0006366transcription from RNA polymerase II promoter0.0203185721744452
GO:0048762mesenchymal cell differentiation0.0230544017185297
GO:0014031mesenchymal cell development0.0230544017185297
GO:0043231intracellular membrane-bound organelle0.0295162839166376
GO:0043227membrane-bound organelle0.0295162839166376
GO:0003723RNA binding0.0295162839166376
GO:0044452nucleolar part0.0295162839166376
GO:0003725double-stranded RNA binding0.0358917455404646



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>

Cell Type
Ontology termp-valuen
embryonic cell1.64e-27248
animal cell4.13e-26679
eukaryotic cell4.13e-26679
epithelial cell1.59e-22254
mesodermal cell6.84e-16119
native cell1.22e-15722
non-terminally differentiated cell3.81e-15180
somatic cell5.69e-12591
electrically responsive cell1.11e-1160
electrically active cell1.11e-1160
contractile cell1.48e-1159
muscle cell2.38e-0954
muscle precursor cell1.14e-0857
myoblast1.14e-0857
multi-potent skeletal muscle stem cell1.14e-0857
blood vessel endothelial cell5.25e-0818
embryonic blood vessel endothelial progenitor cell5.25e-0818
endothelial cell5.33e-0835
meso-epithelial cell5.45e-0844
epithelial cell of nephron5.54e-0816
smooth muscle cell1.23e-0742
smooth muscle myoblast1.23e-0742
ectodermal cell1.26e-0771
lining cell1.58e-0757
barrier cell1.58e-0757
squamous epithelial cell1.82e-0762
kidney cortical cell7.23e-0713
renal cortical epithelial cell7.23e-0713
endothelial cell of vascular tree9.19e-0724
Uber Anatomy
Ontology termp-valuen
epithelial tube2.70e-13118
unilaminar epithelium4.00e-12138
vasculature3.55e-1179
vascular system3.55e-1179
multilaminar epithelium6.41e-1182
vessel1.13e-1069
blood vessel1.68e-1060
epithelial tube open at both ends1.68e-1060
blood vasculature1.68e-1060
vascular cord1.68e-1060
dermomyotome1.94e-1070
artery4.81e-1042
arterial blood vessel4.81e-1042
arterial system4.81e-1042
mesenchyme4.83e-10238
entire embryonic mesenchyme4.83e-10238
splanchnic layer of lateral plate mesoderm7.98e-1084
trunk mesenchyme2.30e-09143
somite1.72e-0883
paraxial mesoderm1.72e-0883
presomitic mesoderm1.72e-0883
presumptive segmental plate1.72e-0883
trunk paraxial mesoderm1.72e-0883
presumptive paraxial mesoderm1.72e-0883
trunk4.92e-08216
endothelium5.25e-0818
blood vessel endothelium5.25e-0818
cardiovascular system endothelium5.25e-0818
nephron epithelium5.54e-0816
nephron5.54e-0816
uriniferous tubule5.54e-0816
metanephric mesenchyme5.54e-0816
nephrogenic mesenchyme5.54e-0816
cell layer7.46e-08312
skeletal muscle tissue9.34e-0861
striated muscle tissue9.34e-0861
myotome9.34e-0861
simple squamous epithelium1.13e-0722
epithelium1.63e-07309
squamous epithelium2.93e-0725
excretory tube3.82e-0717
mesonephric epithelium3.82e-0717
mesonephric tubule3.82e-0717
nephric duct3.82e-0717
kidney epithelium3.82e-0717
renal duct3.82e-0717
mesonephric duct3.82e-0717
pronephric duct3.82e-0717
muscle tissue6.46e-0763
musculature6.46e-0763
musculature of body6.46e-0763
cortex of kidney7.23e-0713
renal parenchyma7.23e-0713
Disease
Ontology termp-valuen
cancer1.45e-07235
disease of cellular proliferation4.34e-07239
hematologic cancer6.14e-0751
immune system cancer6.14e-0751


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)

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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

No analysis results for this cluster

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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