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Coexpression cluster:C3423: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.77e-10!106
|ontology_enrichment_disease=DOID:305!1.77e-10!106
|ontology_enrichment_uberon=UBERON:0007023!3.00e-27!115;UBERON:0001017!1.46e-15!82;UBERON:0005743!3.99e-15!86;UBERON:0001049!5.75e-14!57;UBERON:0005068!5.75e-14!57;UBERON:0006241!5.75e-14!57;UBERON:0007135!5.75e-14!57;UBERON:0000073!4.22e-13!94;UBERON:0001016!4.22e-13!94;UBERON:0003075!4.32e-13!86;UBERON:0007284!4.32e-13!86;UBERON:0000955!2.02e-12!69;UBERON:0006238!2.02e-12!69;UBERON:0002346!9.41e-12!90;UBERON:0002616!1.43e-10!59;UBERON:0002020!2.68e-10!34;UBERON:0003528!2.68e-10!34;UBERON:0001893!2.90e-10!34;UBERON:0003080!3.19e-10!42;UBERON:0002780!4.67e-10!41;UBERON:0001890!4.67e-10!41;UBERON:0006240!4.67e-10!41;UBERON:0002791!5.85e-10!33;UBERON:0001869!2.28e-09!32;UBERON:0004121!2.77e-09!169;UBERON:0000064!5.52e-09!219;UBERON:0000924!1.38e-08!173;UBERON:0006601!1.38e-08!173;UBERON:0003056!5.55e-08!61;UBERON:0000153!1.00e-07!129;UBERON:0007811!1.00e-07!129;UBERON:0000033!1.07e-07!123;UBERON:0000922!2.66e-07!612;UBERON:0000956!2.76e-07!25;UBERON:0000203!2.76e-07!25;UBERON:0002619!2.91e-07!22;UBERON:0000062!4.10e-07!511
|ontology_enrichment_uberon=UBERON:0007023!3.00e-27!115;UBERON:0001017!1.46e-15!82;UBERON:0005743!3.99e-15!86;UBERON:0001049!5.75e-14!57;UBERON:0005068!5.75e-14!57;UBERON:0006241!5.75e-14!57;UBERON:0007135!5.75e-14!57;UBERON:0000073!4.22e-13!94;UBERON:0001016!4.22e-13!94;UBERON:0003075!4.32e-13!86;UBERON:0007284!4.32e-13!86;UBERON:0000955!2.02e-12!69;UBERON:0006238!2.02e-12!69;UBERON:0002346!9.41e-12!90;UBERON:0002616!1.43e-10!59;UBERON:0002020!2.68e-10!34;UBERON:0003528!2.68e-10!34;UBERON:0001893!2.90e-10!34;UBERON:0003080!3.19e-10!42;UBERON:0002780!4.67e-10!41;UBERON:0001890!4.67e-10!41;UBERON:0006240!4.67e-10!41;UBERON:0002791!5.85e-10!33;UBERON:0001869!2.28e-09!32;UBERON:0004121!2.77e-09!169;UBERON:0000064!5.52e-09!219;UBERON:0000924!1.38e-08!173;UBERON:0006601!1.38e-08!173;UBERON:0003056!5.55e-08!61;UBERON:0000153!1.00e-07!129;UBERON:0007811!1.00e-07!129;UBERON:0000033!1.07e-07!123;UBERON:0000922!2.66e-07!612;UBERON:0000956!2.76e-07!25;UBERON:0000203!2.76e-07!25;UBERON:0002619!2.91e-07!22;UBERON:0000062!4.10e-07!511
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296143055502073!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401821621850167!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155764484728862!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268165596108032!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457236973609914!TAL1#6886;2:19.9124111182935:0.00328717660874055:0.0170098319298545
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}}
}}

Revision as of 13:17, 5 September 2012


Full id: C3423_chorionic_renal_amniotic_breast_Urothelial_heart_colon



Phase1 CAGE Peaks

Hg19::chr14:34394132..34394148,-p@chr14:34394132..34394148
-
Hg19::chr14:34420212..34420219,-p3@EGLN3
Hg19::chr14:34420259..34420291,-p1@EGLN3


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism3.00e-27115
central nervous system1.46e-1582
neural tube5.75e-1457
neural rod5.75e-1457
future spinal cord5.75e-1457
neural keel5.75e-1457
regional part of nervous system4.22e-1394
nervous system4.22e-1394
neural plate4.32e-1386
presumptive neural plate4.32e-1386
brain2.02e-1269
future brain2.02e-1269
neurectoderm9.41e-1290
regional part of brain1.43e-1059
gray matter2.68e-1034
brain grey matter2.68e-1034
telencephalon2.90e-1034
anterior neural tube3.19e-1042
regional part of forebrain4.67e-1041
forebrain4.67e-1041
future forebrain4.67e-1041
regional part of telencephalon5.85e-1033
cerebral hemisphere2.28e-0932
ectoderm-derived structure2.77e-09169
organ part5.52e-09219
ectoderm1.38e-08173
presumptive ectoderm1.38e-08173
pre-chordal neural plate5.55e-0861
anterior region of body1.00e-07129
craniocervical region1.00e-07129
head1.07e-07123
embryo2.66e-07612
cerebral cortex2.76e-0725
pallium2.76e-0725
regional part of cerebral cortex2.91e-0722
organ4.10e-07511
Disease
Ontology termp-valuen
carcinoma1.77e-10106


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
BRCA1#672213.45615376214920.007119807716084560.0296143055502073
ELK4#2005210.8237877723120.01091284719516480.0401821621850167
GTF2B#2959221.29588662288280.002878180589911410.0155764484728862
PBX3#5090214.60967512449610.006056122473217890.0268165596108032
SMC3#9126210.02995522995520.0126656379767470.0457236973609914
TAL1#6886219.91241111829350.003287176608740550.0170098319298545



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3423&oldid=2132099"