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Coexpression cluster:C1326: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004232!interstitial collagenase activity!0.00412079823606691!4312$GO:0005615!extracellular space!0.00412079823606691!4312;85480$GO:0008133!collagenase activity!0.00412079823606691!4312$GO:0044421!extracellular region part!0.00432581913920992!4312;85480$GO:0030574!collagen catabolic process!0.00432581913920992!4312$GO:0044256!protein digestion!0.00432581913920992!4312$GO:0044254!multicellular organismal protein catabolic process!0.00432581913920992!4312$GO:0044266!multicellular organismal macromolecule catabolic process!0.00432581913920992!4312$GO:0044259!multicellular organismal macromolecule metabolic process!0.00432581913920992!4312$GO:0044268!multicellular organismal protein metabolic process!0.00432581913920992!4312$GO:0032963!collagen metabolic process!0.00432581913920992!4312$GO:0044243!multicellular organismal catabolic process!0.00432581913920992!4312$GO:0044236!multicellular organismal metabolic process!0.00437322683744746!4312$GO:0007586!digestion!0.0167553098487676!4312$GO:0004222!metalloendopeptidase activity!0.0325440067988259!4312$GO:0005125!cytokine activity!0.047689218626343!85480
|gostat_on_coexpression_clusters=GO:0004232!interstitial collagenase activity!0.00412079823606691!4312$GO:0005615!extracellular space!0.00412079823606691!4312;85480$GO:0008133!collagenase activity!0.00412079823606691!4312$GO:0044421!extracellular region part!0.00432581913920992!4312;85480$GO:0030574!collagen catabolic process!0.00432581913920992!4312$GO:0044256!protein digestion!0.00432581913920992!4312$GO:0044254!multicellular organismal protein catabolic process!0.00432581913920992!4312$GO:0044266!multicellular organismal macromolecule catabolic process!0.00432581913920992!4312$GO:0044259!multicellular organismal macromolecule metabolic process!0.00432581913920992!4312$GO:0044268!multicellular organismal protein metabolic process!0.00432581913920992!4312$GO:0032963!collagen metabolic process!0.00432581913920992!4312$GO:0044243!multicellular organismal catabolic process!0.00432581913920992!4312$GO:0044236!multicellular organismal metabolic process!0.00437322683744746!4312$GO:0007586!digestion!0.0167553098487676!4312$GO:0004222!metalloendopeptidase activity!0.0325440067988259!4312$GO:0005125!cytokine activity!0.047689218626343!85480
|id=C1326
|id=C1326
|ontology_enrichment_celltype=CL:0000359!3.20e-13!32;CL:0000680!1.42e-11!57;CL:0000056!1.42e-11!57;CL:0000355!1.42e-11!57;CL:0000055!8.37e-11!180;CL:0000192!1.06e-10!42;CL:0000514!1.06e-10!42;CL:0000048!1.78e-10!430;CL:0000187!1.85e-10!54;CL:0000183!5.51e-10!59;CL:0000723!5.83e-10!436;CL:0000393!1.27e-09!60;CL:0000211!1.27e-09!60;CL:0000034!2.65e-09!444;CL:0002494!4.65e-08!16;CL:0002371!8.11e-08!591;CL:0000569!1.90e-07!4;CL:0000011!1.90e-07!4;CL:0000144!9.40e-07!625
|ontology_enrichment_celltype=CL:0000569!5.16e-31!4;CL:0000011!5.16e-31!4;CL:0002494!8.81e-14!16;CL:0002596!3.82e-08!2;CL:0002593!6.58e-08!2;CL:0002583!8.60e-08!2;CL:0002589!9.19e-08!2;CL:0000359!6.96e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:2394!4.68e-09!14
|ontology_enrichment_uberon=UBERON:0001637!1.99e-23!42;UBERON:0003509!1.99e-23!42;UBERON:0004572!1.99e-23!42;UBERON:0001981!3.56e-18!60;UBERON:0007500!3.56e-18!60;UBERON:0004537!3.56e-18!60;UBERON:0006965!3.56e-18!60;UBERON:0004573!1.07e-17!33;UBERON:0004571!1.07e-17!33;UBERON:0004872!2.84e-17!84;UBERON:0000055!2.18e-15!69;UBERON:0002049!4.82e-14!79;UBERON:0007798!4.82e-14!79;UBERON:0003914!2.28e-13!118;UBERON:0004535!1.47e-12!110;UBERON:0004290!3.11e-12!70;UBERON:0001009!6.80e-12!113;UBERON:0000914!3.29e-11!83;UBERON:0002329!3.29e-11!83;UBERON:0003077!3.29e-11!83;UBERON:0003059!3.29e-11!83;UBERON:0007282!3.29e-11!83;UBERON:0009618!3.29e-11!83;UBERON:0007285!3.29e-11!83;UBERON:0003081!3.73e-11!216;UBERON:0001134!2.74e-10!61;UBERON:0002036!2.74e-10!61;UBERON:0003082!2.74e-10!61;UBERON:0000486!9.14e-10!82;UBERON:0002385!1.03e-09!63;UBERON:0001015!1.03e-09!63;UBERON:0000383!1.03e-09!63;UBERON:0002204!1.45e-09!167;UBERON:0000947!2.16e-09!21;UBERON:0010191!2.16e-09!21;UBERON:0000490!1.66e-08!138;UBERON:0000926!1.53e-07!448;UBERON:0004120!1.53e-07!448;UBERON:0006603!1.53e-07!448
|ontology_enrichment_uberon=UBERON:0004573!3.41e-14!33;UBERON:0004571!3.41e-14!33;UBERON:0004872!4.40e-12!83;UBERON:0002118!1.50e-11!5;UBERON:0001637!4.31e-11!42;UBERON:0003509!4.31e-11!42;UBERON:0004572!4.31e-11!42;UBERON:0000992!1.04e-09!13;UBERON:0000948!2.85e-09!24;UBERON:0005498!2.85e-09!24;UBERON:0004140!2.85e-09!24;UBERON:0009881!2.85e-09!24;UBERON:0004141!2.85e-09!24;UBERON:0003084!2.85e-09!24;UBERON:0007005!2.85e-09!24;UBERON:0004139!2.85e-09!24;UBERON:0004291!2.85e-09!24;UBERON:0004535!5.78e-09!109;UBERON:0001009!1.07e-08!112;UBERON:0003914!2.79e-08!117;UBERON:0007100!2.90e-08!27;UBERON:0005396!3.82e-08!2;UBERON:0002456!6.58e-08!2;UBERON:0007500!8.43e-08!59;UBERON:0001981!8.43e-08!59;UBERON:0004537!8.43e-08!59;UBERON:0006965!8.43e-08!59;UBERON:0001529!9.19e-08!2;UBERON:0007204!9.19e-08!2
|tf_chipseq_enrich=GATA2#2624;3:6.372465866777:0.00805882130874255:0.0318820879072602
|tf_chipseq_enrich=GATA2#2624;3:6.372465866777:0.00805882130874255:0.0318820879072602
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}}
}}

Revision as of 11:08, 19 October 2012


Full id: C1326_mesenchymal_CD14_Fibroblast_Smooth_Preadipocyte_Endothelial_Renal



Phase1 CAGE Peaks

Hg19::chr11:102668601..102668604,-p14@MMP1
Hg19::chr13:43938419..43938424,-p@chr13:43938419..43938424
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Hg19::chr13:43938433..43938456,-p@chr13:43938433..43938456
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Hg19::chr5:110407337..110407343,+p9@TSLP
Hg19::chr5:110407408..110407415,+p3@TSLP
Hg19::chr5:99385675..99385684,-p@chr5:99385675..99385684
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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:0004232interstitial collagenase activity0.00412079823606691
GO:0005615extracellular space0.00412079823606691
GO:0008133collagenase activity0.00412079823606691
GO:0044421extracellular region part0.00432581913920992
GO:0030574collagen catabolic process0.00432581913920992
GO:0044256protein digestion0.00432581913920992
GO:0044254multicellular organismal protein catabolic process0.00432581913920992
GO:0044266multicellular organismal macromolecule catabolic process0.00432581913920992
GO:0044259multicellular organismal macromolecule metabolic process0.00432581913920992
GO:0044268multicellular organismal protein metabolic process0.00432581913920992
GO:0032963collagen metabolic process0.00432581913920992
GO:0044243multicellular organismal catabolic process0.00432581913920992
GO:0044236multicellular organismal metabolic process0.00437322683744746
GO:0007586digestion0.0167553098487676
GO:0004222metalloendopeptidase activity0.0325440067988259
GO:0005125cytokine activity0.047689218626343



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
systemic artery3.41e-1433
systemic arterial system3.41e-1433
splanchnic layer of lateral plate mesoderm4.40e-1283
right ovary1.50e-115
artery4.31e-1142
arterial blood vessel4.31e-1142
arterial system4.31e-1142
female gonad1.04e-0913
heart2.85e-0924
primitive heart tube2.85e-0924
primary heart field2.85e-0924
anterior lateral plate mesoderm2.85e-0924
heart tube2.85e-0924
heart primordium2.85e-0924
cardiac mesoderm2.85e-0924
cardiogenic plate2.85e-0924
heart rudiment2.85e-0924
cardiovascular system5.78e-09109
circulatory system1.07e-08112
epithelial tube2.79e-08117
primary circulatory organ2.90e-0827
carotid artery segment3.82e-082
internal thoracic artery6.58e-082
epithelial tube open at both ends8.43e-0859
blood vessel8.43e-0859
blood vasculature8.43e-0859
vascular cord8.43e-0859
brachiocephalic artery9.19e-082
brachiocephalic vasculature9.19e-082
Disease
Ontology termp-valuen
ovarian cancer4.68e-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
GATA2#262436.3724658667770.008058821308742550.0318820879072602



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.