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Coexpression cluster:C725: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005148!prolactin receptor binding!0.012546365820773!8835$GO:0008269!JAK pathway signal transduction adaptor activity!0.012546365820773!8835$GO:0008268!receptor signaling protein tyrosine kinase signaling protein activity!0.012546365820773!8835$GO:0032868!response to insulin stimulus!0.012546365820773!1959$GO:0005131!growth hormone receptor binding!0.012546365820773!8835$GO:0005125!cytokine activity!0.012546365820773!7292;8835$GO:0007638!mechanosensory behavior!0.0154378789766626!1959$GO:0048168!regulation of neuronal synaptic plasticity!0.0202595321431702!1959$GO:0005159!insulin-like growth factor receptor binding!0.0220084121224001!8835$GO:0048167!regulation of synaptic plasticity!0.0249249009211236!1959$GO:0009612!response to mechanical stimulus!0.0249249009211236!1959$GO:0007267!cell-cell signaling!0.0249249009211236!7292;1959$GO:0050803!regulation of synapse structure and activity!0.0249249009211236!1959$GO:0043434!response to peptide hormone stimulus!0.0282827880332297!1959$GO:0007422!peripheral nervous system development!0.0287944772484493!1959$GO:0065008!regulation of biological quality!0.0388055118302518!1959;8835$GO:0005164!tumor necrosis factor receptor binding!0.0388055118302518!7292$GO:0007259!JAK-STAT cascade!0.0388055118302518!8835$GO:0032813!tumor necrosis factor receptor superfamily binding!0.0388055118302518!7292$GO:0007611!learning and/or memory!0.03905990040876!1959$GO:0005102!receptor binding!0.03905990040876!7292;8835$GO:0005070!SH3/SH2 adaptor activity!0.0400389898549058!8835$GO:0005126!hematopoietin/interferon-class (D200-domain) cytokine receptor binding!0.0449198938933818!8835$GO:0060090!molecular adaptor activity!0.0449198938933818!8835
|gostat_on_coexpression_clusters=GO:0005148!prolactin receptor binding!0.012546365820773!8835$GO:0008269!JAK pathway signal transduction adaptor activity!0.012546365820773!8835$GO:0008268!receptor signaling protein tyrosine kinase signaling protein activity!0.012546365820773!8835$GO:0032868!response to insulin stimulus!0.012546365820773!1959$GO:0005131!growth hormone receptor binding!0.012546365820773!8835$GO:0005125!cytokine activity!0.012546365820773!7292;8835$GO:0007638!mechanosensory behavior!0.0154378789766626!1959$GO:0048168!regulation of neuronal synaptic plasticity!0.0202595321431702!1959$GO:0005159!insulin-like growth factor receptor binding!0.0220084121224001!8835$GO:0048167!regulation of synaptic plasticity!0.0249249009211236!1959$GO:0009612!response to mechanical stimulus!0.0249249009211236!1959$GO:0007267!cell-cell signaling!0.0249249009211236!7292;1959$GO:0050803!regulation of synapse structure and activity!0.0249249009211236!1959$GO:0043434!response to peptide hormone stimulus!0.0282827880332297!1959$GO:0007422!peripheral nervous system development!0.0287944772484493!1959$GO:0065008!regulation of biological quality!0.0388055118302518!1959;8835$GO:0005164!tumor necrosis factor receptor binding!0.0388055118302518!7292$GO:0007259!JAK-STAT cascade!0.0388055118302518!8835$GO:0032813!tumor necrosis factor receptor superfamily binding!0.0388055118302518!7292$GO:0007611!learning and/or memory!0.03905990040876!1959$GO:0005102!receptor binding!0.03905990040876!7292;8835$GO:0005070!SH3/SH2 adaptor activity!0.0400389898549058!8835$GO:0005126!hematopoietin/interferon-class (D200-domain) cytokine receptor binding!0.0449198938933818!8835$GO:0060090!molecular adaptor activity!0.0449198938933818!8835
|id=C725
|id=C725
|ontology_enrichment_celltype=CL:0000048!1.25e-22!430;CL:0000723!1.37e-21!436;CL:0000034!1.58e-21!444;CL:0002139!1.11e-12!24;CL:0000988!1.29e-12!182;CL:0000134!3.08e-12!358;CL:0000037!3.12e-12!172;CL:0000566!3.12e-12!172;CL:0002371!3.96e-11!591;CL:0002032!7.25e-11!165;CL:0000837!7.25e-11!165;CL:0000738!7.45e-11!140;CL:0000144!8.43e-11!625;CL:0000071!1.17e-10!18;CL:0002546!1.17e-10!18;CL:0000222!1.51e-10!119;CL:0002320!2.13e-10!365;CL:0000219!5.28e-10!390;CL:0000763!3.04e-09!112;CL:0000049!3.04e-09!112;CL:0000192!4.02e-08!42;CL:0000514!4.02e-08!42;CL:0000680!7.06e-08!57;CL:0000056!7.06e-08!57;CL:0000355!7.06e-08!57;CL:0000115!1.07e-07!35;CL:0000187!1.18e-07!54;CL:0002031!1.73e-07!124;CL:0000183!2.09e-07!59;CL:0000766!2.94e-07!76;CL:0000359!4.79e-07!32;CL:0002087!5.23e-07!119
|ontology_enrichment_celltype=CL:0000080!1.50e-10!6;CL:1000413!9.27e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:2394!2.36e-09!14
|ontology_enrichment_uberon=UBERON:0004535!2.21e-26!110;UBERON:0001009!1.94e-24!113;UBERON:0003081!1.07e-21!216;UBERON:0000055!3.62e-20!69;UBERON:0004872!9.67e-19!84;UBERON:0001981!1.39e-17!60;UBERON:0007500!1.39e-17!60;UBERON:0004537!1.39e-17!60;UBERON:0006965!1.39e-17!60;UBERON:0002049!3.38e-17!79;UBERON:0007798!3.38e-17!79;UBERON:0002193!5.31e-14!112;UBERON:0001637!7.50e-12!42;UBERON:0003509!7.50e-12!42;UBERON:0004572!7.50e-12!42;UBERON:0002390!2.79e-11!102;UBERON:0003061!2.79e-11!102;UBERON:0001986!1.17e-10!18;UBERON:0004638!1.17e-10!18;UBERON:0004852!1.17e-10!18;UBERON:0002384!4.87e-10!375;UBERON:0000178!9.33e-10!15;UBERON:0000179!9.33e-10!15;UBERON:0000463!9.33e-10!15;UBERON:0003914!9.89e-10!118;UBERON:0000487!2.36e-09!22;UBERON:0000490!3.52e-09!138;UBERON:0004573!2.37e-08!33;UBERON:0004571!2.37e-08!33;UBERON:0002405!2.98e-08!115;UBERON:0006914!1.50e-07!25;UBERON:0001134!5.13e-07!61;UBERON:0002036!5.13e-07!61;UBERON:0003082!5.13e-07!61;UBERON:0002204!5.44e-07!167;UBERON:0000947!9.53e-07!21;UBERON:0010191!9.53e-07!21
|ontology_enrichment_uberon=UBERON:0000178!8.34e-22!15;UBERON:0000179!8.34e-22!15;UBERON:0000463!8.34e-22!15;UBERON:0004535!4.96e-15!109;UBERON:0001009!2.56e-14!112;UBERON:0003081!9.05e-07!203;UBERON:0003915!9.27e-07!9;UBERON:0004700!9.27e-07!9;UBERON:0001917!9.27e-07!9
|tf_chipseq_enrich=CEBPB#1051;6:4.34789870499535:0.00102243427262561:0.00724584467657907!EP300#2033;6:3.69487730521265:0.00244128806655223:0.0137462629061165!FOXA1#3169;7:7.05181256779074:1.15697264990643e-05:0.000294571103324177!FOXA2#3170;6:13.4347984105447:1.73076139279195e-06:6.52324031403099e-05!HDAC2#3066;6:7.31761103815978:5.69712326977083e-05:0.000950330389988174!HEY1#23462;7:2.57097975470363:0.00712682984021317:0.0296340718112045!HNF4A#3172;6:12.6176129252475:2.49318000901648e-06:8.78196380983718e-05!HNF4G#3174;6:15.6836850144255:7.0138286269284e-07:3.1438508496471e-05!SP1#6667;6:3.10820802444049:0.00601132120248979:0.0269483785494626!USF1#7391;7:4.0482268127687:0.000433910736700334:0.0040508807929066
|tf_chipseq_enrich=CEBPB#1051;6:4.34789870499535:0.00102243427262561:0.00724584467657907!EP300#2033;6:3.69487730521265:0.00244128806655223:0.0137462629061165!FOXA1#3169;7:7.05181256779074:1.15697264990643e-05:0.000294571103324177!FOXA2#3170;6:13.4347984105447:1.73076139279195e-06:6.52324031403099e-05!HDAC2#3066;6:7.31761103815978:5.69712326977083e-05:0.000950330389988174!HEY1#23462;7:2.57097975470363:0.00712682984021317:0.0296340718112045!HNF4A#3172;6:12.6176129252475:2.49318000901648e-06:8.78196380983718e-05!HNF4G#3174;6:15.6836850144255:7.0138286269284e-07:3.1438508496471e-05!SP1#6667;6:3.10820802444049:0.00601132120248979:0.0269483785494626!USF1#7391;7:4.0482268127687:0.000433910736700334:0.0040508807929066
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}}
}}

Revision as of 16:38, 19 October 2012


Full id: C725_Mast_cord_mycosis_mesenchymal_Endothelial_hepatic_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:64576035..64576046,-p2@EGR2
Hg19::chr12:93966545..93966557,+p25@SOCS2
Hg19::chr16:72128270..72128282,-p5@TXNL4B
Hg19::chr1:173174598..173174624,-p4@TNFSF4
Hg19::chr1:173174630..173174644,-p7@TNFSF4
Hg19::chr1:173174664..173174677,-p6@TNFSF4
Hg19::chr1:173174681..173174702,-p5@TNFSF4
Hg19::chr1:173174706..173174733,-p3@TNFSF4
Hg19::chr1:173174759..173174799,-p2@TNFSF4
Hg19::chr1:173176462..173176477,-p1@TNFSF4
Hg19::chr2:191185566..191185602,-p@chr2:191185566..191185602
-


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:0005148prolactin receptor binding0.012546365820773
GO:0008269JAK pathway signal transduction adaptor activity0.012546365820773
GO:0008268receptor signaling protein tyrosine kinase signaling protein activity0.012546365820773
GO:0032868response to insulin stimulus0.012546365820773
GO:0005131growth hormone receptor binding0.012546365820773
GO:0005125cytokine activity0.012546365820773
GO:0007638mechanosensory behavior0.0154378789766626
GO:0048168regulation of neuronal synaptic plasticity0.0202595321431702
GO:0005159insulin-like growth factor receptor binding0.0220084121224001
GO:0048167regulation of synaptic plasticity0.0249249009211236
GO:0009612response to mechanical stimulus0.0249249009211236
GO:0007267cell-cell signaling0.0249249009211236
GO:0050803regulation of synapse structure and activity0.0249249009211236
GO:0043434response to peptide hormone stimulus0.0282827880332297
GO:0007422peripheral nervous system development0.0287944772484493
GO:0065008regulation of biological quality0.0388055118302518
GO:0005164tumor necrosis factor receptor binding0.0388055118302518
GO:0007259JAK-STAT cascade0.0388055118302518
GO:0032813tumor necrosis factor receptor superfamily binding0.0388055118302518
GO:0007611learning and/or memory0.03905990040876
GO:0005102receptor binding0.03905990040876
GO:0005070SH3/SH2 adaptor activity0.0400389898549058
GO:0005126hematopoietin/interferon-class (D200-domain) cytokine receptor binding0.0449198938933818
GO:0060090molecular adaptor activity0.0449198938933818



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
circulating cell1.50e-106
endothelial cell of artery9.27e-079
Uber Anatomy
Ontology termp-valuen
blood8.34e-2215
haemolymphatic fluid8.34e-2215
organism substance8.34e-2215
cardiovascular system4.96e-15109
circulatory system2.56e-14112
lateral plate mesoderm9.05e-07203
endothelial tube9.27e-079
arterial system endothelium9.27e-079
endothelium of artery9.27e-079
Disease
Ontology termp-valuen
ovarian cancer2.36e-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
CEBPB#105164.347898704995350.001022434272625610.00724584467657907
EP300#203363.694877305212650.002441288066552230.0137462629061165
FOXA1#316977.051812567790741.15697264990643e-050.000294571103324177
FOXA2#3170613.43479841054471.73076139279195e-066.52324031403099e-05
HDAC2#306667.317611038159785.69712326977083e-050.000950330389988174
HEY1#2346272.570979754703630.007126829840213170.0296340718112045
HNF4A#3172612.61761292524752.49318000901648e-068.78196380983718e-05
HNF4G#3174615.68368501442557.0138286269284e-073.1438508496471e-05
SP1#666763.108208024440490.006011321202489790.0269483785494626
USF1#739174.04822681276870.0004339107367003340.0040508807929066



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.