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{{Coexpression_clusters
 
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|full_id=C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus
 
|full_id=C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus
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|gostat_on_coexpression_clusters=GO:0010269!response to selenium ion!0.00356170431735566!2876$GO:0033598!mammary gland epithelial cell proliferation!0.00356170431735566!2876$GO:0033599!regulation of mammary gland epithelial cell proliferation!0.00356170431735566!2876$GO:0008539!proteasome inhibitor activity!0.00356170431735566!2876$GO:0043295!glutathione binding!0.00427398227263908!2876$GO:0008631!induction of apoptosis by oxidative stress!0.00474879929383486!2876$GO:0009650!UV protection!0.00610541935439425!2876$GO:0030503!regulation of cell redox homeostasis!0.00712267470585477!2876$GO:0043154!negative regulation of caspase activity!0.00712267470585477!2876$GO:0042744!hydrogen peroxide catabolic process!0.00771577659443147!2876$GO:0042743!hydrogen peroxide metabolic process!0.00771577659443147!2876$GO:0001836!release of cytochrome c from mitochondria!0.00771577659443147!2876$GO:0004602!glutathione peroxidase activity!0.0083782604577414!2876$GO:0006749!glutathione metabolic process!0.0083782604577414!2876$GO:0008637!apoptotic mitochondrial changes!0.0083782604577414!2876$GO:0017124!SH3 domain binding!0.0083782604577414!2876$GO:0042542!response to hydrogen peroxide!0.0083782604577414!2876$GO:0000302!response to reactive oxygen species!0.0106811811903355!2876$GO:0050678!regulation of epithelial cell proliferation!0.0111441033976822!2876$GO:0009411!response to UV!0.0111441033976822!2876$GO:0050673!epithelial cell proliferation!0.0111441033976822!2876$GO:0010038!response to metal ion!0.0111441033976822!2876$GO:0008629!induction of apoptosis by intracellular signals!0.0111441033976822!2876$GO:0010035!response to inorganic substance!0.0123917946099916!2876$GO:0006800!oxygen and reactive oxygen species metabolic process!0.0123917946099916!2876$GO:0060047!heart contraction!0.0123917946099916!2876$GO:0003015!heart process!0.0123917946099916!2876$GO:0008430!selenium binding!0.0127113856780267!2876$GO:0043281!regulation of caspase activity!0.0147255051928963!2876$GO:0040029!regulation of gene expression, epigenetic!0.0149003678103095!2876$GO:0004601!peroxidase activity!0.0149003678103095!2876$GO:0016684!oxidoreductase activity, acting on peroxide as acceptor!0.0149003678103095!2876$GO:0009416!response to light stimulus!0.0174643995027196!2876$GO:0006790!sulfur metabolic process!0.0175880982868606!2876$GO:0008632!apoptotic program!0.0175880982868606!2876$GO:0007005!mitochondrion organization and biogenesis!0.0175880982868606!2876$GO:0009314!response to radiation!0.0194166461393986!2876$GO:0045454!cell redox homeostasis!0.0202138906401953!2876$GO:0006979!response to oxidative stress!0.0218801128957829!2876$GO:0019904!protein domain specific binding!0.0225752112702164!2876$GO:0005681!spliceosome!0.0241013951022955!83443$GO:0008015!blood circulation!0.0264440662770201!2876$GO:0003013!circulatory system process!0.0264440662770201!2876$GO:0009628!response to abiotic stimulus!0.0266486946639436!2876$GO:0006916!anti-apoptosis!0.0268441119592487!2876$GO:0042277!peptide binding!0.0315119562790315!2876$GO:0006917!induction of apoptosis!0.0315119562790315!2876$GO:0012502!induction of programmed cell death!0.0315119562790315!2876$GO:0008380!RNA splicing!0.0320173688309457!83443$GO:0043066!negative regulation of apoptosis!0.0320173688309457!2876$GO:0043069!negative regulation of programmed cell death!0.0320173688309457!2876$GO:0043065!positive regulation of apoptosis!0.0345455564991135!2876$GO:0043068!positive regulation of programmed cell death!0.0345455564991135!2876$GO:0006397!mRNA processing!0.0358691419109499!83443$GO:0006732!coenzyme metabolic process!0.0371437391052508!2876$GO:0051336!regulation of hydrolase activity!0.0388762339987535!2876$GO:0016071!mRNA metabolic process!0.0419149300765837!83443$GO:0051186!cofactor metabolic process!0.0419149300765837!2876$GO:0019725!cellular homeostasis!0.0450273350297991!2876$GO:0004857!enzyme inhibitor activity!0.0473285241774172!2876
 
|id=C1437
 
|id=C1437
 
}}
 
}}

Revision as of 08:34, 18 May 2012


Full id: C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus



Phase1 CAGE Peaks

  Short description
Hg19::chr17:79791135..79791175,- p1@FAM195B
Hg19::chr19:507487..507508,+ p1@TPGS1
Hg19::chr1:36789194..36789256,- p1@FAM176B
Hg19::chr1:36789257..36789268,- p2@FAM176B
Hg19::chr3:49395753..49395769,- p3@GPX1
Hg19::chr6:144416737..144416766,- p2@SF3B5


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0010269response to selenium ion0.00356170431735566
GO:0033598mammary gland epithelial cell proliferation0.00356170431735566
GO:0033599regulation of mammary gland epithelial cell proliferation0.00356170431735566
GO:0008539proteasome inhibitor activity0.00356170431735566
GO:0043295glutathione binding0.00427398227263908
GO:0008631induction of apoptosis by oxidative stress0.00474879929383486
GO:0009650UV protection0.00610541935439425
GO:0030503regulation of cell redox homeostasis0.00712267470585477
GO:0043154negative regulation of caspase activity0.00712267470585477
GO:0042744hydrogen peroxide catabolic process0.00771577659443147
GO:0042743hydrogen peroxide metabolic process0.00771577659443147
GO:0001836release of cytochrome c from mitochondria0.00771577659443147
GO:0004602glutathione peroxidase activity0.0083782604577414
GO:0006749glutathione metabolic process0.0083782604577414
GO:0008637apoptotic mitochondrial changes0.0083782604577414
GO:0017124SH3 domain binding0.0083782604577414
GO:0042542response to hydrogen peroxide0.0083782604577414
GO:0000302response to reactive oxygen species0.0106811811903355
GO:0050678regulation of epithelial cell proliferation0.0111441033976822
GO:0009411response to UV0.0111441033976822
GO:0050673epithelial cell proliferation0.0111441033976822
GO:0010038response to metal ion0.0111441033976822
GO:0008629induction of apoptosis by intracellular signals0.0111441033976822
GO:0010035response to inorganic substance0.0123917946099916
GO:0006800oxygen and reactive oxygen species metabolic process0.0123917946099916
GO:0060047heart contraction0.0123917946099916
GO:0003015heart process0.0123917946099916
GO:0008430selenium binding0.0127113856780267
GO:0043281regulation of caspase activity0.0147255051928963
GO:0040029regulation of gene expression, epigenetic0.0149003678103095
GO:0004601peroxidase activity0.0149003678103095
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0149003678103095
GO:0009416response to light stimulus0.0174643995027196
GO:0006790sulfur metabolic process0.0175880982868606
GO:0008632apoptotic program0.0175880982868606
GO:0007005mitochondrion organization and biogenesis0.0175880982868606
GO:0009314response to radiation0.0194166461393986
GO:0045454cell redox homeostasis0.0202138906401953
GO:0006979response to oxidative stress0.0218801128957829
GO:0019904protein domain specific binding0.0225752112702164
GO:0005681spliceosome0.0241013951022955
GO:0008015blood circulation0.0264440662770201
GO:0003013circulatory system process0.0264440662770201
GO:0009628response to abiotic stimulus0.0266486946639436
GO:0006916anti-apoptosis0.0268441119592487
GO:0042277peptide binding0.0315119562790315
GO:0006917induction of apoptosis0.0315119562790315
GO:0012502induction of programmed cell death0.0315119562790315
GO:0008380RNA splicing0.0320173688309457
GO:0043066negative regulation of apoptosis0.0320173688309457
GO:0043069negative regulation of programmed cell death0.0320173688309457
GO:0043065positive regulation of apoptosis0.0345455564991135
GO:0043068positive regulation of programmed cell death0.0345455564991135
GO:0006397mRNA processing0.0358691419109499
GO:0006732coenzyme metabolic process0.0371437391052508
GO:0051336regulation of hydrolase activity0.0388762339987535
GO:0016071mRNA metabolic process0.0419149300765837
GO:0051186cofactor metabolic process0.0419149300765837
GO:0019725cellular homeostasis0.0450273350297991
GO:0004857enzyme inhibitor activity0.0473285241774172



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.