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Coexpression cluster:C4248: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190542401014272!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280322119082944!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172082073461622!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326409887958161!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163147664451062!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392393593902266!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123093016148231!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000758568580693047!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721465454572811!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277591515949969!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.0015510092924093!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615541830490779!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248817658940232!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.0061721192566817!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019081109807314!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140569802509772
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190542401014272!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280322119082944!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172082073461622!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326409887958161!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163147664451062!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392393593902266!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123093016148231!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000758568580693047!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721465454572811!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277591515949969!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.0015510092924093!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615541830490779!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248817658940232!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.0061721192566817!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019081109807314!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140569802509772
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}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4248_Mesenchymal_salivary_Osteoblast_breast_Pericytes_Hair_parotid



Phase1 CAGE Peaks

Hg19::chr2:85829422..85829431,-p6@TMEM150A
Hg19::chr2:85829444..85829455,-p5@TMEM150A
Hg19::chr2:85829477..85829493,-p4@TMEM150A


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


No GOStat results

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
fibroblast4.27e-0776
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.09e-18656
anatomical system1.09e-15624
anatomical group2.29e-15625
organ2.00e-13503
multi-tissue structure1.74e-11342
organism subdivision1.79e-11264
anatomical cluster9.42e-10373
trunk1.21e-09199
mesenchyme1.81e-09160
entire embryonic mesenchyme1.81e-09160
embryo4.71e-09592
developing anatomical structure5.62e-09581
anatomical conduit1.37e-08240
germ layer1.79e-08560
germ layer / neural crest1.79e-08560
embryonic tissue1.79e-08560
presumptive structure1.79e-08560
germ layer / neural crest derived structure1.79e-08560
epiblast (generic)1.79e-08560
embryonic structure3.88e-08564
trunk mesenchyme2.38e-07122
epithelium2.96e-07306
cell layer3.29e-07309
subdivision of trunk7.67e-07112
immaterial anatomical entity9.82e-07117


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
CCNT2#90536.336201576962630.003930750035764890.0190542401014272
CTCF#1066435.360256373075030.0064925092527670.0280322119082944
CTCFL#140690319.74647435897440.0001298372005551160.00172082073461622
E2F1#186934.907389214879320.008460985347239390.0326409887958161
ESR1#2099220.51240219743630.003099741577095180.0163147664451062
HDAC2#3066313.41562023662630.0004140761399857210.00392393593902266
HNF4A#3172323.13229036295378.07584663437677e-050.00123093016148231
HNF4G#3174328.75342252644684.20470658818262e-050.000758568580693047
MXI1#460139.96157162875930.001011470541259020.00721465454572811
SIN3A#2594235.408884726815140.006318961977991520.0277591515949969
STAT1#6772320.70658749719920.0001125992441046670.0015510092924093
TCF7L2#6934310.77017656313730.0008003181298398380.00615541830490779
TFAP2A#7020316.5186343730450.0002218033880766340.00248817658940232
TFAP2C#7022310.80922860986020.0007916746575753130.0061721192566817
USF1#739136.361499277207960.00388404057290560.019081109807314
ZBTB7A#5134137.35190930787590.002516255860282270.0140569802509772



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.