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Coexpression cluster:C2221: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!6.34e-14!118;UBERON:0004872!2.45e-12!84;UBERON:0001981!1.31e-11!60;UBERON:0007500!1.31e-11!60;UBERON:0004537!1.31e-11!60;UBERON:0006965!1.31e-11!60;UBERON:0002100!1.36e-11!216;UBERON:0000055!1.84e-11!69;UBERON:0001637!1.99e-11!42;UBERON:0003509!1.99e-11!42;UBERON:0004572!1.99e-11!42;UBERON:0000490!2.11e-11!138;UBERON:0002049!2.87e-11!79;UBERON:0007798!2.87e-11!79;UBERON:0005256!4.13e-09!143;UBERON:0004573!9.37e-09!33;UBERON:0004571!9.37e-09!33;UBERON:0003104!6.34e-08!238;UBERON:0009142!6.34e-08!238;UBERON:0000926!8.70e-08!448;UBERON:0004120!8.70e-08!448;UBERON:0006603!8.70e-08!448;UBERON:0000486!1.56e-07!82;UBERON:0000914!2.96e-07!83;UBERON:0002329!2.96e-07!83;UBERON:0003077!2.96e-07!83;UBERON:0003059!2.96e-07!83;UBERON:0007282!2.96e-07!83;UBERON:0009618!2.96e-07!83;UBERON:0007285!2.96e-07!83;UBERON:0004290!3.71e-07!70;UBERON:0004535!4.88e-07!110;UBERON:0001134!9.79e-07!61;UBERON:0002036!9.79e-07!61;UBERON:0003082!9.79e-07!61
|ontology_enrichment_uberon=UBERON:0003914!6.34e-14!118;UBERON:0004872!2.45e-12!84;UBERON:0001981!1.31e-11!60;UBERON:0007500!1.31e-11!60;UBERON:0004537!1.31e-11!60;UBERON:0006965!1.31e-11!60;UBERON:0002100!1.36e-11!216;UBERON:0000055!1.84e-11!69;UBERON:0001637!1.99e-11!42;UBERON:0003509!1.99e-11!42;UBERON:0004572!1.99e-11!42;UBERON:0000490!2.11e-11!138;UBERON:0002049!2.87e-11!79;UBERON:0007798!2.87e-11!79;UBERON:0005256!4.13e-09!143;UBERON:0004573!9.37e-09!33;UBERON:0004571!9.37e-09!33;UBERON:0003104!6.34e-08!238;UBERON:0009142!6.34e-08!238;UBERON:0000926!8.70e-08!448;UBERON:0004120!8.70e-08!448;UBERON:0006603!8.70e-08!448;UBERON:0000486!1.56e-07!82;UBERON:0000914!2.96e-07!83;UBERON:0002329!2.96e-07!83;UBERON:0003077!2.96e-07!83;UBERON:0003059!2.96e-07!83;UBERON:0007282!2.96e-07!83;UBERON:0009618!2.96e-07!83;UBERON:0007285!2.96e-07!83;UBERON:0004290!3.71e-07!70;UBERON:0004535!4.88e-07!110;UBERON:0001134!9.79e-07!61;UBERON:0002036!9.79e-07!61;UBERON:0003082!9.79e-07!61
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127178949231312!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267651097301478!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106315051358354!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995512128307635!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185650741131421!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391058019047554!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484721778820326!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142168219606154!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00886185248582272!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00766957295656022!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079480622609134!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321454685257786!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243634779157092!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326121841038268!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114404782598458!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507159788032826!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000680294296446535!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346097456141473
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}}
}}

Revision as of 12:28, 5 September 2012


Full id: C2221_Mesenchymal_Fibroblast_Keratocytes_Keratinocyte_Osteoblast_mesenchymal_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr12:57623876..57623891,+p5@SHMT2
Hg19::chr12:57623907..57623961,+p2@SHMT2
Hg19::chr12:57623963..57623989,+p4@SHMT2
Hg19::chr12:57623992..57624003,+p9@SHMT2


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
animal cell6.93e-34679
eukaryotic cell6.93e-34679
non-terminally differentiated cell1.26e-22180
somatic cell5.15e-22591
native cell1.80e-18722
embryonic cell1.51e-15248
fibroblast3.07e-1475
mesodermal cell1.21e-12119
epithelial cell7.55e-12254
vascular associated smooth muscle cell3.93e-0932
smooth muscle cell4.89e-0942
smooth muscle myoblast4.89e-0942
contractile cell1.14e-0859
muscle precursor cell1.15e-0857
myoblast1.15e-0857
multi-potent skeletal muscle stem cell1.15e-0857
muscle cell1.30e-0854
multi fate stem cell3.94e-07430
somatic stem cell4.94e-07436
Uber Anatomy
Ontology termp-valuen
epithelial tube6.34e-14118
splanchnic layer of lateral plate mesoderm2.45e-1284
blood vessel1.31e-1160
epithelial tube open at both ends1.31e-1160
blood vasculature1.31e-1160
vascular cord1.31e-1160
trunk1.36e-11216
vessel1.84e-1169
artery1.99e-1142
arterial blood vessel1.99e-1142
arterial system1.99e-1142
unilaminar epithelium2.11e-11138
vasculature2.87e-1179
vascular system2.87e-1179
trunk mesenchyme4.13e-09143
systemic artery9.37e-0933
systemic arterial system9.37e-0933
mesenchyme6.34e-08238
entire embryonic mesenchyme6.34e-08238
mesoderm8.70e-08448
mesoderm-derived structure8.70e-08448
presumptive mesoderm8.70e-08448
multilaminar epithelium1.56e-0782
somite2.96e-0783
paraxial mesoderm2.96e-0783
presomitic mesoderm2.96e-0783
presumptive segmental plate2.96e-0783
trunk paraxial mesoderm2.96e-0783
presumptive paraxial mesoderm2.96e-0783
dermomyotome3.71e-0770
cardiovascular system4.88e-07110
skeletal muscle tissue9.79e-0761
striated muscle tissue9.79e-0761
myotome9.79e-0761


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
ATF3#467422.46317452600873.92475754624726e-060.000127178949231312
CEBPB#105147.971147625824820.0002476385788090830.00267651097301478
E2F1#186944.907389214879320.001724022357361790.0106315051358354
E2F6#187645.017155731697390.00157802193473060.00995512128307635
HEY1#2346244.040111043105710.00375304636917980.0185650741131421
JUND#372746.994663941871030.000417684217818580.00391058019047554
MAX#414946.452555509007120.0005767613195645490.00484721778820326
MXI1#460149.96157162875930.0001015224754950450.00142168219606154
MYC#460945.22228187160940.001344309395272740.00886185248582272
NFKB1#479045.488063424193840.001102199566301980.00766957295656022
SIN3A#2594245.408884726815140.001168172384885160.0079480622609134
TAF1#687243.343046285745290.008005664898701650.0321454685257786
TBP#690843.706770687096390.005296377814784350.0243634779157092
TFAP2A#7020416.5186343730451.34240829060362e-050.000326121841038268
TFAP2C#7022410.80922860986027.32289634782688e-050.00114404782598458
USF1#739146.361499277207960.0006105011399140830.00507159788032826
USF2#7392412.99219738506963.50833029870167e-050.000680294296446535
ZBTB7A#5134147.35190930787590.000342223540015990.00346097456141473



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.