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Coexpression cluster:C4667: Difference between revisions

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|full_id=C4667_left_heart_skeletal_Iris_mesothelioma_lung_extraskeletal
|full_id=C4667_left_heart_skeletal_Iris_mesothelioma_lung_extraskeletal
|id=C4667
|id=C4667
|ontology_enrichment_celltype=CL:0000055!4.41e-09!180
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!7.17e-16!659;UBERON:0000475!3.42e-15!365;UBERON:0000481!9.78e-15!347;UBERON:0000467!4.91e-13!625;UBERON:0000480!7.70e-13!626;UBERON:0000062!3.98e-12!511;UBERON:0003103!1.17e-10!69;UBERON:0000477!1.77e-10!286;UBERON:0000119!2.47e-10!312;UBERON:0000483!8.01e-10!309;UBERON:0002100!1.35e-09!216;UBERON:0003886!4.35e-09!63;UBERON:0002553!5.25e-09!70;UBERON:0000922!1.55e-08!612;UBERON:0002050!2.94e-08!605;UBERON:0005423!2.94e-08!605;UBERON:0000923!3.63e-08!604;UBERON:0005291!3.63e-08!604;UBERON:0006598!3.63e-08!604;UBERON:0002532!3.63e-08!604;UBERON:0007625!3.92e-08!11;UBERON:0004111!6.18e-08!241;UBERON:0003104!1.06e-07!238;UBERON:0009142!1.06e-07!238;UBERON:0005256!1.17e-07!143;UBERON:0000489!1.72e-07!32;UBERON:0000064!1.73e-07!219;UBERON:0000466!4.73e-07!126
|ontology_enrichment_uberon=UBERON:0000477!3.77e-10!373;UBERON:0000468!1.85e-09!656;UBERON:0000467!4.30e-08!624;UBERON:0007625!4.52e-08!11;UBERON:0000480!5.37e-08!625;UBERON:0003103!1.72e-07!68;UBERON:0000062!1.77e-07!503;UBERON:0000481!2.12e-07!342
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115793621176728!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281263967915104!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168455566862385!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000679113538309198!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901694983405501!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058412960522717!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446348722959833!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157653737558483!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187376697487036!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723243679710742!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486835271299303!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203962196812153!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.0031074761434906!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00198102983586546!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191143772214536!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423118500728879
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115793621176728!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281263967915104!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168455566862385!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000679113538309198!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901694983405501!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058412960522717!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446348722959833!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157653737558483!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187376697487036!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723243679710742!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486835271299303!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203962196812153!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.0031074761434906!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00198102983586546!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191143772214536!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423118500728879
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}}
}}

Revision as of 16:08, 19 October 2012


Full id: C4667_left_heart_skeletal_Iris_mesothelioma_lung_extraskeletal



Phase1 CAGE Peaks

Hg19::chr7:151433342..151433366,-p5@PRKAG2
Hg19::chr7:151433375..151433385,-p22@PRKAG2
Hg19::chr7:151433393..151433406,-p21@PRKAG2


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
anatomical cluster3.77e-10373
multi-cellular organism1.85e-09656
anatomical system4.30e-08624
pigment epithelium of eye4.52e-0811
anatomical group5.37e-08625
compound organ1.72e-0768
organ1.77e-07503
multi-tissue structure2.12e-07342


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#105137.971147625824820.001974187055288560.0115793621176728
CTCF#1066435.360256373075030.0064925092527670.0281263967915104
EP300#203336.77394172622320.003216880500103790.0168455566862385
ESR1#2099330.76860329615453.43136389821584e-050.000679113538309198
FOS#235338.99795530889440.001372499272417130.00901694983405501
FOXA1#3169311.08141974938550.000734755275698670.0058412960522717
JUN#3725312.51282919233630.0005103313992726250.00446348722959833
JUND#372736.994663941871030.002921845042734990.0157653737558483
MAX#414936.452555509007120.003721913834265510.0187376697487036
MXI1#460139.96157162875930.001011470541259020.00723243679710742
RFX5#5993312.04791082719510.0005717246050312580.00486835271299303
SMARCB1#6598318.25271578115740.000164397760679890.00203962196812153
SMC3#9126315.04493284493280.0002935825420371870.0031074761434906
TRIM28#10155318.59052504526250.0001555969297255280.00198102983586546
USF1#739136.361499277207960.00388404057290560.0191143772214536
USF2#7392312.99219738506960.0004558979393427810.00423118500728879



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.