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Coexpression cluster:C2083: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!4.51e-18!169;UBERON:0000925!4.51e-18!169;UBERON:0006595!4.51e-18!169;UBERON:0003914!1.26e-16!118;UBERON:0001007!3.08e-14!155;UBERON:0001555!3.08e-14!155;UBERON:0007026!3.08e-14!155;UBERON:0001009!7.67e-14!113;UBERON:0004872!8.90e-13!84;UBERON:0004535!1.06e-12!110;UBERON:0002049!2.53e-12!79;UBERON:0007798!2.53e-12!79;UBERON:0003104!4.10e-12!238;UBERON:0009142!4.10e-12!238;UBERON:0000490!5.32e-12!138;UBERON:0000477!6.57e-12!286;UBERON:0003102!4.67e-11!95;UBERON:0004921!8.69e-11!129;UBERON:0004185!8.69e-11!129;UBERON:0000055!2.47e-10!69;UBERON:0000077!2.96e-10!130;UBERON:0004111!6.43e-10!241;UBERON:0000481!8.06e-10!347;UBERON:0005256!1.38e-09!143;UBERON:0001048!2.88e-09!168;UBERON:0002100!4.78e-09!216;UBERON:0005911!1.08e-08!82;UBERON:0000161!1.89e-08!35;UBERON:0000119!2.28e-08!312;UBERON:0003103!2.68e-08!69;UBERON:0000483!5.78e-08!309;UBERON:0001981!7.05e-08!60;UBERON:0007500!7.05e-08!60;UBERON:0004537!7.05e-08!60;UBERON:0006965!7.05e-08!60;UBERON:0009569!7.75e-08!113;UBERON:0007100!2.49e-07!27;UBERON:0003929!3.26e-07!54;UBERON:0000487!3.69e-07!22;UBERON:0002365!4.06e-07!31;UBERON:0002330!4.06e-07!31;UBERON:0001986!5.17e-07!18;UBERON:0004638!5.17e-07!18;UBERON:0004852!5.17e-07!18
|ontology_enrichment_uberon=UBERON:0004119!4.51e-18!169;UBERON:0000925!4.51e-18!169;UBERON:0006595!4.51e-18!169;UBERON:0003914!1.26e-16!118;UBERON:0001007!3.08e-14!155;UBERON:0001555!3.08e-14!155;UBERON:0007026!3.08e-14!155;UBERON:0001009!7.67e-14!113;UBERON:0004872!8.90e-13!84;UBERON:0004535!1.06e-12!110;UBERON:0002049!2.53e-12!79;UBERON:0007798!2.53e-12!79;UBERON:0003104!4.10e-12!238;UBERON:0009142!4.10e-12!238;UBERON:0000490!5.32e-12!138;UBERON:0000477!6.57e-12!286;UBERON:0003102!4.67e-11!95;UBERON:0004921!8.69e-11!129;UBERON:0004185!8.69e-11!129;UBERON:0000055!2.47e-10!69;UBERON:0000077!2.96e-10!130;UBERON:0004111!6.43e-10!241;UBERON:0000481!8.06e-10!347;UBERON:0005256!1.38e-09!143;UBERON:0001048!2.88e-09!168;UBERON:0002100!4.78e-09!216;UBERON:0005911!1.08e-08!82;UBERON:0000161!1.89e-08!35;UBERON:0000119!2.28e-08!312;UBERON:0003103!2.68e-08!69;UBERON:0000483!5.78e-08!309;UBERON:0001981!7.05e-08!60;UBERON:0007500!7.05e-08!60;UBERON:0004537!7.05e-08!60;UBERON:0006965!7.05e-08!60;UBERON:0009569!7.75e-08!113;UBERON:0007100!2.49e-07!27;UBERON:0003929!3.26e-07!54;UBERON:0000487!3.69e-07!22;UBERON:0002365!4.06e-07!31;UBERON:0002330!4.06e-07!31;UBERON:0001986!5.17e-07!18;UBERON:0004638!5.17e-07!18;UBERON:0004852!5.17e-07!18
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511161134786346!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.0081543845096363!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106233506980062!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00994851097677949!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101254764111204!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160512323680963!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185466267507698!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484409935295552!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443041458724424!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321146009739006!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243431062182926!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106598508787173!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00345896489845446
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}}
}}

Revision as of 13:38, 5 September 2012


Full id: C2083_Placental_acantholytic_Amniotic_Endothelial_Tracheal_Urothelial_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:97050727..97050740,-p3@PDLIM1
Hg19::chr10:97050749..97050772,-p1@PDLIM1
Hg19::chr10:97050777..97050806,-p2@PDLIM1
Hg19::chr10:97050816..97050825,-p4@PDLIM1


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.51e-18169
endoderm4.51e-18169
presumptive endoderm4.51e-18169
epithelial tube1.26e-16118
digestive system3.08e-14155
digestive tract3.08e-14155
primitive gut3.08e-14155
circulatory system7.67e-14113
splanchnic layer of lateral plate mesoderm8.90e-1384
cardiovascular system1.06e-12110
vasculature2.53e-1279
vascular system2.53e-1279
mesenchyme4.10e-12238
entire embryonic mesenchyme4.10e-12238
unilaminar epithelium5.32e-12138
anatomical cluster6.57e-12286
surface structure4.67e-1195
subdivision of digestive tract8.69e-11129
endodermal part of digestive tract8.69e-11129
vessel2.47e-1069
mixed endoderm/mesoderm-derived structure2.96e-10130
anatomical conduit6.43e-10241
multi-tissue structure8.06e-10347
trunk mesenchyme1.38e-09143
primordium2.88e-09168
trunk4.78e-09216
endo-epithelium1.08e-0882
orifice1.89e-0835
cell layer2.28e-08312
compound organ2.68e-0869
epithelium5.78e-08309
blood vessel7.05e-0860
epithelial tube open at both ends7.05e-0860
blood vasculature7.05e-0860
vascular cord7.05e-0860
subdivision of trunk7.75e-08113
primary circulatory organ2.49e-0727
gut epithelium3.26e-0754
simple squamous epithelium3.69e-0722
exocrine gland4.06e-0731
exocrine system4.06e-0731
endothelium5.17e-0718
blood vessel endothelium5.17e-0718
cardiovascular system endothelium5.17e-0718


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#90546.336201576962630.0006203100587215640.00511161134786346
CTCF#1066445.360256373075030.001211145381643620.0081543845096363
E2F1#186944.907389214879320.001724022357361790.0106233506980062
E2F6#187645.017155731697390.00157802193473060.00994851097677949
EGR1#195844.988179094810140.001615011500076050.0101254764111204
ELF1#199744.258097958807540.003041525565781240.0160512323680963
HEY1#2346244.040111043105710.00375304636917980.0185466267507698
MAX#414946.452555509007120.0005767613195645490.00484409935295552
PAX5#507946.669565531177830.0005052774169483260.00443041458724424
TAF1#687243.343046285745290.008005664898701650.0321146009739006
TBP#690843.706770687096390.005296377814784350.0243431062182926
YY1#752844.911170749853860.00171871838055440.0106598508787173
ZBTB7A#5134147.35190930787590.000342223540015990.00345896489845446



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.

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