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Coexpression cluster:C2269: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.45e-31!115;UBERON:0005743!1.96e-21!86;UBERON:0000073!3.19e-20!94;UBERON:0001016!3.19e-20!94;UBERON:0001017!5.52e-20!82;UBERON:0001049!8.15e-20!57;UBERON:0005068!8.15e-20!57;UBERON:0006241!8.15e-20!57;UBERON:0007135!8.15e-20!57;UBERON:0003075!1.08e-19!86;UBERON:0007284!1.08e-19!86;UBERON:0002346!3.02e-18!90;UBERON:0002616!2.14e-17!59;UBERON:0000955!1.20e-16!69;UBERON:0006238!1.20e-16!69;UBERON:0003056!3.65e-16!61;UBERON:0003080!1.24e-14!42;UBERON:0002780!3.82e-14!41;UBERON:0001890!3.82e-14!41;UBERON:0006240!3.82e-14!41;UBERON:0002020!1.81e-11!34;UBERON:0003528!1.81e-11!34;UBERON:0001893!6.60e-11!34;UBERON:0001869!7.17e-11!32;UBERON:0002791!9.74e-11!33;UBERON:0000153!1.27e-10!129;UBERON:0007811!1.27e-10!129;UBERON:0004121!2.29e-10!169;UBERON:0000033!4.93e-10!123;UBERON:0000924!8.15e-10!173;UBERON:0006601!8.15e-10!173;UBERON:0000922!4.90e-09!612;UBERON:0000468!2.86e-08!659;UBERON:0000062!3.11e-08!511;UBERON:0000467!4.41e-08!625;UBERON:0000956!5.41e-08!25;UBERON:0000203!5.41e-08!25;UBERON:0000480!6.85e-08!626;UBERON:0002050!1.05e-07!605;UBERON:0005423!1.05e-07!605;UBERON:0000923!2.02e-07!604;UBERON:0005291!2.02e-07!604;UBERON:0006598!2.02e-07!604;UBERON:0002532!2.02e-07!604
|ontology_enrichment_uberon=UBERON:0007023!5.45e-31!115;UBERON:0005743!1.96e-21!86;UBERON:0000073!3.19e-20!94;UBERON:0001016!3.19e-20!94;UBERON:0001017!5.52e-20!82;UBERON:0001049!8.15e-20!57;UBERON:0005068!8.15e-20!57;UBERON:0006241!8.15e-20!57;UBERON:0007135!8.15e-20!57;UBERON:0003075!1.08e-19!86;UBERON:0007284!1.08e-19!86;UBERON:0002346!3.02e-18!90;UBERON:0002616!2.14e-17!59;UBERON:0000955!1.20e-16!69;UBERON:0006238!1.20e-16!69;UBERON:0003056!3.65e-16!61;UBERON:0003080!1.24e-14!42;UBERON:0002780!3.82e-14!41;UBERON:0001890!3.82e-14!41;UBERON:0006240!3.82e-14!41;UBERON:0002020!1.81e-11!34;UBERON:0003528!1.81e-11!34;UBERON:0001893!6.60e-11!34;UBERON:0001869!7.17e-11!32;UBERON:0002791!9.74e-11!33;UBERON:0000153!1.27e-10!129;UBERON:0007811!1.27e-10!129;UBERON:0004121!2.29e-10!169;UBERON:0000033!4.93e-10!123;UBERON:0000924!8.15e-10!173;UBERON:0006601!8.15e-10!173;UBERON:0000922!4.90e-09!612;UBERON:0000468!2.86e-08!659;UBERON:0000062!3.11e-08!511;UBERON:0000467!4.41e-08!625;UBERON:0000956!5.41e-08!25;UBERON:0000203!5.41e-08!25;UBERON:0000480!6.85e-08!626;UBERON:0002050!1.05e-07!605;UBERON:0005423!1.05e-07!605;UBERON:0000923!2.02e-07!604;UBERON:0005291!2.02e-07!604;UBERON:0006598!2.02e-07!604;UBERON:0002532!2.02e-07!604
|tf_chipseq_enrich=MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484799802446696!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229845465881214!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507240481714295!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248206689407024
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}}
}}

Revision as of 12:24, 5 September 2012


Full id: C2269_merkel_small_Mast_anaplastic_acute_colon_pineal



Phase1 CAGE Peaks

Hg19::chr13:72441074..72441172,-p2@DACH1
Hg19::chr13:72441259..72441268,-p8@DACH1
Hg19::chr13:72441289..72441300,-p13@DACH1
Hg19::chr13:72441315..72441454,-p1@DACH1


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
adult organism5.45e-31115
regional part of nervous system3.19e-2094
nervous system3.19e-2094
central nervous system5.52e-2082
neural tube8.15e-2057
neural rod8.15e-2057
future spinal cord8.15e-2057
neural keel8.15e-2057
neural plate1.08e-1986
presumptive neural plate1.08e-1986
neurectoderm3.02e-1890
regional part of brain2.14e-1759
brain1.20e-1669
future brain1.20e-1669
pre-chordal neural plate3.65e-1661
anterior neural tube1.24e-1442
regional part of forebrain3.82e-1441
forebrain3.82e-1441
future forebrain3.82e-1441
gray matter1.81e-1134
brain grey matter1.81e-1134
telencephalon6.60e-1134
cerebral hemisphere7.17e-1132
regional part of telencephalon9.74e-1133
anterior region of body1.27e-10129
craniocervical region1.27e-10129
ectoderm-derived structure2.29e-10169
head4.93e-10123
ectoderm8.15e-10173
presumptive ectoderm8.15e-10173
embryo4.90e-09612
multi-cellular organism2.86e-08659
organ3.11e-08511
anatomical system4.41e-08625
cerebral cortex5.41e-0825
pallium5.41e-0825
anatomical group6.85e-08626
embryonic structure1.05e-07605
developing anatomical structure1.05e-07605
germ layer2.02e-07604
embryonic tissue2.02e-07604
presumptive structure2.02e-07604
epiblast (generic)2.02e-07604


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
MAX#414946.452555509007120.0005767613195645490.00484799802446696
TRIM28#10155418.59052504526258.36730015875654e-060.000229845465881214
USF1#739146.361499277207960.0006105011399140830.00507240481714295
ZNF263#1012748.221841637010680.0002187871180958320.00248206689407024



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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