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Coexpression cluster:C4422: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.68e-40!115;UBERON:0001049!8.25e-25!57;UBERON:0005068!8.25e-25!57;UBERON:0006241!8.25e-25!57;UBERON:0007135!8.25e-25!57;UBERON:0002616!9.30e-22!59;UBERON:0003075!1.93e-21!86;UBERON:0007284!1.93e-21!86;UBERON:0001017!1.63e-20!82;UBERON:0005743!3.15e-20!86;UBERON:0002780!1.26e-19!41;UBERON:0001890!1.26e-19!41;UBERON:0006240!1.26e-19!41;UBERON:0003080!1.83e-19!42;UBERON:0002346!5.51e-19!90;UBERON:0001893!6.59e-19!34;UBERON:0002020!6.80e-19!34;UBERON:0003528!6.80e-19!34;UBERON:0001869!2.87e-18!32;UBERON:0002791!2.89e-18!33;UBERON:0000153!2.94e-18!129;UBERON:0007811!2.94e-18!129;UBERON:0003056!3.35e-18!61;UBERON:0000073!1.89e-17!94;UBERON:0001016!1.89e-17!94;UBERON:0000955!2.27e-17!69;UBERON:0006238!2.27e-17!69;UBERON:0000033!1.05e-16!123;UBERON:0000956!4.57e-15!25;UBERON:0000203!4.57e-15!25;UBERON:0004121!9.53e-14!169;UBERON:0002619!2.37e-13!22;UBERON:0000924!1.61e-12!173;UBERON:0006601!1.61e-12!173;UBERON:0001950!2.63e-12!20;UBERON:0000178!3.20e-08!15;UBERON:0000179!3.20e-08!15;UBERON:0000463!3.20e-08!15;UBERON:0000064!4.07e-07!219
|ontology_enrichment_uberon=UBERON:0007023!5.68e-40!115;UBERON:0001049!8.25e-25!57;UBERON:0005068!8.25e-25!57;UBERON:0006241!8.25e-25!57;UBERON:0007135!8.25e-25!57;UBERON:0002616!9.30e-22!59;UBERON:0003075!1.93e-21!86;UBERON:0007284!1.93e-21!86;UBERON:0001017!1.63e-20!82;UBERON:0005743!3.15e-20!86;UBERON:0002780!1.26e-19!41;UBERON:0001890!1.26e-19!41;UBERON:0006240!1.26e-19!41;UBERON:0003080!1.83e-19!42;UBERON:0002346!5.51e-19!90;UBERON:0001893!6.59e-19!34;UBERON:0002020!6.80e-19!34;UBERON:0003528!6.80e-19!34;UBERON:0001869!2.87e-18!32;UBERON:0002791!2.89e-18!33;UBERON:0000153!2.94e-18!129;UBERON:0007811!2.94e-18!129;UBERON:0003056!3.35e-18!61;UBERON:0000073!1.89e-17!94;UBERON:0001016!1.89e-17!94;UBERON:0000955!2.27e-17!69;UBERON:0006238!2.27e-17!69;UBERON:0000033!1.05e-16!123;UBERON:0000956!4.57e-15!25;UBERON:0000203!4.57e-15!25;UBERON:0004121!9.53e-14!169;UBERON:0002619!2.37e-13!22;UBERON:0000924!1.61e-12!173;UBERON:0006601!1.61e-12!173;UBERON:0001950!2.63e-12!20;UBERON:0000178!3.20e-08!15;UBERON:0000179!3.20e-08!15;UBERON:0000463!3.20e-08!15;UBERON:0000064!4.07e-07!219
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280728315744694!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666948451919083!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109832436161907
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}}
}}

Revision as of 13:33, 5 September 2012


Full id: C4422_Osteoblast_CD4_CD34_acute_CD133_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr4:57522598..57522664,-p3@HOPX
Hg19::chr4:57522674..57522699,-p5@HOPX
Hg19::chr4:57522701..57522712,-p10@HOPX


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>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell7.70e-1018
alpha-beta T cell7.70e-1018
immature T cell7.70e-1018
mature T cell7.70e-1018
immature alpha-beta T cell7.70e-1018
CD8-positive, alpha-beta T cell5.07e-0911
Uber Anatomy
Ontology termp-valuen
adult organism5.68e-40115
neural tube8.25e-2557
neural rod8.25e-2557
future spinal cord8.25e-2557
neural keel8.25e-2557
regional part of brain9.30e-2259
neural plate1.93e-2186
presumptive neural plate1.93e-2186
central nervous system1.63e-2082
regional part of forebrain1.26e-1941
forebrain1.26e-1941
future forebrain1.26e-1941
anterior neural tube1.83e-1942
neurectoderm5.51e-1990
telencephalon6.59e-1934
gray matter6.80e-1934
brain grey matter6.80e-1934
cerebral hemisphere2.87e-1832
regional part of telencephalon2.89e-1833
anterior region of body2.94e-18129
craniocervical region2.94e-18129
pre-chordal neural plate3.35e-1861
regional part of nervous system1.89e-1794
nervous system1.89e-1794
brain2.27e-1769
future brain2.27e-1769
head1.05e-16123
cerebral cortex4.57e-1525
pallium4.57e-1525
ectoderm-derived structure9.53e-14169
regional part of cerebral cortex2.37e-1322
ectoderm1.61e-12173
presumptive ectoderm1.61e-12173
neocortex2.63e-1220
blood3.20e-0815
haemolymphatic fluid3.20e-0815
organism substance3.20e-0815
organ part4.07e-07219


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
CTCF#1066435.360256373075030.0064925092527670.0280728315744694
RAD21#5885310.35503389545630.0009004912073565420.00666948451919083
ZNF263#1012738.221841637010680.001799043925565870.0109832436161907



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:C4422&oldid=2132317"