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Coexpression cluster:C2155: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!4.84e-23!79;UBERON:0007798!4.84e-23!79;UBERON:0003081!6.81e-21!216;UBERON:0000055!1.96e-20!69;UBERON:0001981!8.69e-19!60;UBERON:0007500!8.69e-19!60;UBERON:0004537!8.69e-19!60;UBERON:0006965!8.69e-19!60;UBERON:0004535!2.08e-18!110;UBERON:0004872!2.58e-18!84;UBERON:0001637!2.06e-17!42;UBERON:0003509!2.06e-17!42;UBERON:0004572!2.06e-17!42;UBERON:0001009!4.37e-17!113;UBERON:0003914!7.51e-16!118;UBERON:0000914!7.95e-16!83;UBERON:0002329!7.95e-16!83;UBERON:0003077!7.95e-16!83;UBERON:0003059!7.95e-16!83;UBERON:0007282!7.95e-16!83;UBERON:0009618!7.95e-16!83;UBERON:0007285!7.95e-16!83;UBERON:0000486!7.72e-15!82;UBERON:0004290!1.21e-14!70;UBERON:0005256!9.77e-14!143;UBERON:0002204!5.33e-13!167;UBERON:0001134!1.46e-12!61;UBERON:0002036!1.46e-12!61;UBERON:0003082!1.46e-12!61;UBERON:0004573!1.67e-12!33;UBERON:0004571!1.67e-12!33;UBERON:0002385!2.53e-12!63;UBERON:0001015!2.53e-12!63;UBERON:0000383!2.53e-12!63;UBERON:0000490!4.19e-12!138;UBERON:0000926!5.09e-10!448;UBERON:0004120!5.09e-10!448;UBERON:0006603!5.09e-10!448;UBERON:0001986!1.16e-08!18;UBERON:0004638!1.16e-08!18;UBERON:0004852!1.16e-08!18;UBERON:0000487!2.40e-08!22;UBERON:0004211!5.57e-08!16;UBERON:0001285!5.57e-08!16;UBERON:0007684!5.57e-08!16;UBERON:0003220!5.57e-08!16;UBERON:0004208!5.57e-08!16;UBERON:0002100!8.98e-08!216;UBERON:0000947!2.87e-07!21;UBERON:0010191!2.87e-07!21;UBERON:0000353!3.69e-07!17;UBERON:0006555!4.87e-07!17;UBERON:0005103!4.87e-07!17;UBERON:0000083!4.87e-07!17;UBERON:0009201!4.87e-07!17;UBERON:0004819!4.87e-07!17;UBERON:0006553!4.87e-07!17;UBERON:0003074!4.87e-07!17;UBERON:0003060!4.87e-07!17;UBERON:0001225!9.74e-07!13;UBERON:0008987!9.74e-07!13
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}}
}}

Revision as of 18:02, 8 August 2012


Full id: C2155_Alveolar_Mesenchymal_Renal_Hair_Smooth_Fibroblast_Bronchial



Phase1 CAGE Peaks

Hg19::chr11:65625643..65625659,-p1@CFL1
Hg19::chr11:66036082..66036125,+p1@RAB1B
Hg19::chr17:79829190..79829260,-p1@ARHGDIA
Hg19::chr7:5570229..5570234,-p1@ACTB


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:0007264small GTPase mediated signal transduction0.00561280380812922
GO:0006916anti-apoptosis0.00561280380812922
GO:0007266Rho protein signal transduction0.00561280380812922
GO:0043066negative regulation of apoptosis0.00561280380812922
GO:0043069negative regulation of programmed cell death0.00561280380812922
GO:0005856cytoskeleton0.00561280380812922
GO:0035267NuA4 histone acetyltransferase complex0.00898898000577465
GO:0007242intracellular signaling cascade0.00898898000577465
GO:0051674localization of cell0.00898898000577465
GO:0006928cell motility0.00898898000577465
GO:0043189H4/H2A histone acetyltransferase complex0.00898898000577465
GO:0007265Ras protein signal transduction0.00951756176553976
GO:0000123histone acetyltransferase complex0.0134669426856117
GO:0042981regulation of apoptosis0.0134669426856117
GO:0043067regulation of programmed cell death0.0134669426856117
GO:0005094Rho GDP-dissociation inhibitor activity0.0144325718247894
GO:0005737cytoplasm0.0144325718247894
GO:0043232intracellular non-membrane-bound organelle0.0144325718247894
GO:0043228non-membrane-bound organelle0.0144325718247894
GO:0031981nuclear lumen0.0144325718247894
GO:0007162negative regulation of cell adhesion0.017474096358452
GO:0005092GDP-dissociation inhibitor activity0.0179612957941699
GO:0006915apoptosis0.0186480408191993
GO:0012501programmed cell death0.0186480408191993
GO:0016265death0.0190659149538056
GO:0008219cell death0.0190659149538056
GO:0031974membrane-enclosed lumen0.0201966507970214
GO:0043233organelle lumen0.0201966507970214
GO:0005515protein binding0.0204183646101707
GO:0016363nuclear matrix0.0220909551404238
GO:0044428nuclear part0.0236262360421581
GO:0048523negative regulation of cellular process0.0240742996074799
GO:0048519negative regulation of biological process0.0251846368767134
GO:0048468cell development0.0265674164750137
GO:0030155regulation of cell adhesion0.0265674164750137
GO:0051179localization0.0275572213624321
GO:0005200structural constituent of cytoskeleton0.0310461000661591
GO:0043229intracellular organelle0.0310461000661591
GO:0043226organelle0.0310461000661591
GO:0007165signal transduction0.0368719025886468
GO:0007154cell communication0.0422377920115624
GO:0050954sensory perception of mechanical stimulus0.0422377920115624
GO:0007605sensory perception of sound0.0422377920115624
GO:0048869cellular developmental process0.0422377920115624
GO:0030154cell differentiation0.0422377920115624
GO:0050794regulation of cellular process0.0431562287345324



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 cell5.26e-50591
animal cell5.43e-38679
eukaryotic cell5.43e-38679
native cell9.39e-31722
mesodermal cell7.78e-24119
non-terminally differentiated cell5.94e-21180
somatic stem cell3.29e-19436
multi fate stem cell1.12e-18430
embryonic cell2.52e-18248
stem cell1.47e-17444
contractile cell1.84e-1759
smooth muscle cell6.93e-1742
smooth muscle myoblast6.93e-1742
muscle precursor cell1.29e-1557
myoblast1.29e-1557
multi-potent skeletal muscle stem cell1.29e-1557
muscle cell3.62e-1554
vascular associated smooth muscle cell7.55e-1532
electrically responsive cell6.51e-1360
electrically active cell6.51e-1360
endothelial cell4.20e-1235
meso-epithelial cell1.92e-1044
endothelial cell of vascular tree1.43e-0924
fibroblast7.09e-0975
blood vessel endothelial cell1.16e-0818
embryonic blood vessel endothelial progenitor cell1.16e-0818
lining cell1.71e-0857
barrier cell1.71e-0857
epithelial cell of nephron5.57e-0816
connective tissue cell2.72e-07365
mesenchymal cell5.96e-07358
kidney cortical cell9.74e-0713
renal cortical epithelial cell9.74e-0713
Uber Anatomy
Ontology termp-valuen
vasculature4.84e-2379
vascular system4.84e-2379
lateral plate mesoderm6.81e-21216
vessel1.96e-2069
blood vessel8.69e-1960
epithelial tube open at both ends8.69e-1960
blood vasculature8.69e-1960
vascular cord8.69e-1960
cardiovascular system2.08e-18110
splanchnic layer of lateral plate mesoderm2.58e-1884
artery2.06e-1742
arterial blood vessel2.06e-1742
arterial system2.06e-1742
circulatory system4.37e-17113
epithelial tube7.51e-16118
somite7.95e-1683
paraxial mesoderm7.95e-1683
presomitic mesoderm7.95e-1683
presumptive segmental plate7.95e-1683
trunk paraxial mesoderm7.95e-1683
presumptive paraxial mesoderm7.95e-1683
multilaminar epithelium7.72e-1582
dermomyotome1.21e-1470
trunk mesenchyme9.77e-14143
musculoskeletal system5.33e-13167
skeletal muscle tissue1.46e-1261
striated muscle tissue1.46e-1261
myotome1.46e-1261
systemic artery1.67e-1233
systemic arterial system1.67e-1233
muscle tissue2.53e-1263
musculature2.53e-1263
musculature of body2.53e-1263
unilaminar epithelium4.19e-12138
mesoderm5.09e-10448
mesoderm-derived structure5.09e-10448
presumptive mesoderm5.09e-10448
endothelium1.16e-0818
blood vessel endothelium1.16e-0818
cardiovascular system endothelium1.16e-0818
simple squamous epithelium2.40e-0822
nephron epithelium5.57e-0816
nephron5.57e-0816
uriniferous tubule5.57e-0816
metanephric mesenchyme5.57e-0816
nephrogenic mesenchyme5.57e-0816
trunk8.98e-08216
aorta2.87e-0721
aortic system2.87e-0721
parenchyma3.69e-0717
excretory tube4.87e-0717
mesonephric epithelium4.87e-0717
mesonephric tubule4.87e-0717
nephric duct4.87e-0717
kidney epithelium4.87e-0717
renal duct4.87e-0717
mesonephric duct4.87e-0717
pronephric duct4.87e-0717
cortex of kidney9.74e-0713
renal parenchyma9.74e-0713


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

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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