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Coexpression cluster:C4084: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.84e-25!118;UBERON:0002049!1.03e-23!79;UBERON:0007798!1.03e-23!79;UBERON:0000055!2.44e-21!69;UBERON:0001981!6.34e-19!60;UBERON:0007500!6.34e-19!60;UBERON:0004537!6.34e-19!60;UBERON:0006965!6.34e-19!60;UBERON:0004872!2.25e-18!84;UBERON:0004535!1.52e-17!110;UBERON:0001009!2.61e-17!113;UBERON:0000468!1.37e-15!659;UBERON:0000490!1.83e-15!138;UBERON:0001637!1.83e-15!42;UBERON:0003509!1.83e-15!42;UBERON:0004572!1.83e-15!42;UBERON:0000467!7.96e-13!625;UBERON:0005256!1.20e-12!143;UBERON:0000480!1.60e-12!626;UBERON:0002100!6.90e-12!216;UBERON:0004573!1.06e-11!33;UBERON:0004571!1.06e-11!33;UBERON:0000926!1.10e-11!448;UBERON:0004120!1.10e-11!448;UBERON:0006603!1.10e-11!448;UBERON:0000487!2.21e-11!22;UBERON:0006914!2.65e-11!25;UBERON:0001986!1.21e-10!18;UBERON:0004638!1.21e-10!18;UBERON:0004852!1.21e-10!18;UBERON:0000119!1.67e-10!312;UBERON:0004111!5.95e-10!241;UBERON:0000483!8.55e-10!309;UBERON:0000477!3.77e-09!286;UBERON:0000025!3.98e-09!194;UBERON:0000923!1.22e-08!604;UBERON:0005291!1.22e-08!604;UBERON:0006598!1.22e-08!604;UBERON:0002532!1.22e-08!604;UBERON:0003081!1.24e-08!216;UBERON:0002050!1.39e-08!605;UBERON:0005423!1.39e-08!605;UBERON:0000922!7.20e-08!612;UBERON:0000947!1.28e-07!21;UBERON:0010191!1.28e-07!21;UBERON:0001134!5.85e-07!61;UBERON:0002036!5.85e-07!61;UBERON:0003082!5.85e-07!61;UBERON:0002385!6.47e-07!63;UBERON:0001015!6.47e-07!63;UBERON:0000383!6.47e-07!63;UBERON:0002417!8.99e-07!61;UBERON:0000916!8.99e-07!61
|ontology_enrichment_uberon=UBERON:0003914!1.84e-25!118;UBERON:0002049!1.03e-23!79;UBERON:0007798!1.03e-23!79;UBERON:0000055!2.44e-21!69;UBERON:0001981!6.34e-19!60;UBERON:0007500!6.34e-19!60;UBERON:0004537!6.34e-19!60;UBERON:0006965!6.34e-19!60;UBERON:0004872!2.25e-18!84;UBERON:0004535!1.52e-17!110;UBERON:0001009!2.61e-17!113;UBERON:0000468!1.37e-15!659;UBERON:0000490!1.83e-15!138;UBERON:0001637!1.83e-15!42;UBERON:0003509!1.83e-15!42;UBERON:0004572!1.83e-15!42;UBERON:0000467!7.96e-13!625;UBERON:0005256!1.20e-12!143;UBERON:0000480!1.60e-12!626;UBERON:0002100!6.90e-12!216;UBERON:0004573!1.06e-11!33;UBERON:0004571!1.06e-11!33;UBERON:0000926!1.10e-11!448;UBERON:0004120!1.10e-11!448;UBERON:0006603!1.10e-11!448;UBERON:0000487!2.21e-11!22;UBERON:0006914!2.65e-11!25;UBERON:0001986!1.21e-10!18;UBERON:0004638!1.21e-10!18;UBERON:0004852!1.21e-10!18;UBERON:0000119!1.67e-10!312;UBERON:0004111!5.95e-10!241;UBERON:0000483!8.55e-10!309;UBERON:0000477!3.77e-09!286;UBERON:0000025!3.98e-09!194;UBERON:0000923!1.22e-08!604;UBERON:0005291!1.22e-08!604;UBERON:0006598!1.22e-08!604;UBERON:0002532!1.22e-08!604;UBERON:0003081!1.24e-08!216;UBERON:0002050!1.39e-08!605;UBERON:0005423!1.39e-08!605;UBERON:0000922!7.20e-08!612;UBERON:0000947!1.28e-07!21;UBERON:0010191!1.28e-07!21;UBERON:0001134!5.85e-07!61;UBERON:0002036!5.85e-07!61;UBERON:0003082!5.85e-07!61;UBERON:0002385!6.47e-07!63;UBERON:0001015!6.47e-07!63;UBERON:0000383!6.47e-07!63;UBERON:0002417!8.99e-07!61;UBERON:0000916!8.99e-07!61
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}}
}}

Revision as of 11:52, 5 September 2012


Full id: C4084_peripheral_osteoclastoma_mesenchymal_Preadipocyte_Adipocyte_melanoma_bone



Phase1 CAGE Peaks

Hg19::chr21:46293545..46293584,-p2@PTTG1IP
Hg19::chr21:46293586..46293641,-p1@PTTG1IP
Hg19::chr21:46293644..46293655,-p3@PTTG1IP


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
epithelial tube1.84e-25118
vasculature1.03e-2379
vascular system1.03e-2379
vessel2.44e-2169
blood vessel6.34e-1960
epithelial tube open at both ends6.34e-1960
blood vasculature6.34e-1960
vascular cord6.34e-1960
splanchnic layer of lateral plate mesoderm2.25e-1884
cardiovascular system1.52e-17110
circulatory system2.61e-17113
multi-cellular organism1.37e-15659
unilaminar epithelium1.83e-15138
artery1.83e-1542
arterial blood vessel1.83e-1542
arterial system1.83e-1542
anatomical system7.96e-13625
trunk mesenchyme1.20e-12143
anatomical group1.60e-12626
trunk6.90e-12216
systemic artery1.06e-1133
systemic arterial system1.06e-1133
mesoderm1.10e-11448
mesoderm-derived structure1.10e-11448
presumptive mesoderm1.10e-11448
simple squamous epithelium2.21e-1122
squamous epithelium2.65e-1125
endothelium1.21e-1018
blood vessel endothelium1.21e-1018
cardiovascular system endothelium1.21e-1018
cell layer1.67e-10312
anatomical conduit5.95e-10241
epithelium8.55e-10309
anatomical cluster3.77e-09286
tube3.98e-09194
germ layer1.22e-08604
embryonic tissue1.22e-08604
presumptive structure1.22e-08604
epiblast (generic)1.22e-08604
lateral plate mesoderm1.24e-08216
embryonic structure1.39e-08605
developing anatomical structure1.39e-08605
embryo7.20e-08612
aorta1.28e-0721
aortic system1.28e-0721
skeletal muscle tissue5.85e-0761
striated muscle tissue5.85e-0761
myotome5.85e-0761
muscle tissue6.47e-0763
musculature6.47e-0763
musculature of body6.47e-0763
abdominal segment of trunk8.99e-0761
abdomen8.99e-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
CCNT2#90536.336201576962630.003930750035764890.0190348033099295
E2F6#187635.017155731697390.00791769806886330.0322913335135119
ELF1#199734.258097958807540.01295179875054610.046318069774972
ELK4#2005316.2356816584680.0002336043955745990.00255979534880029
ESR1#2099330.76860329615453.43136389821584e-050.000677700858861127
GABPB1#255337.067683836182170.002832212825417420.015437267119345
HMGN3#932438.178547723350590.001827766942164210.0108868570590104
IRF1#365937.63716375356390.002244692747297240.0128316073253956
MXI1#460139.96157162875930.001011470541259020.00721071480263147
MYC#460935.22228187160940.007020843755740150.0295022894103865
NFKB1#479035.488063424193840.006049381815655430.0269996319421042
NRF1#4899312.21027944771090.0005492172401020010.00471746848745891
PAX5#507936.669565531177830.003370290999677260.017317220393353
SIN3A#2594235.408884726815140.006318961977991520.027727661443614
SP1#666735.69838137814090.005403962701712170.0246973770612689
USF1#739136.361499277207960.00388404057290560.0190649674951209
YY1#752834.911170749853860.008441455341808260.0329946539836494



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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