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Coexpression cluster:C3262: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00138942465350452!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320846028252052!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319418253959528!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387095841783596!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436135792397488!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000849665636310187!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185960368816369!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293464300410528!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268813082349163!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136247572974892!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010887013766414
|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00138942465350452!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320846028252052!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319418253959528!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00387095841783596!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436135792397488!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000849665636310187!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185960368816369!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293464300410528!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268813082349163!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136247572974892!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010887013766414
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3262_splenic_myeloma_Gingival_Mallassezderived_Corneal_B_Macrophage



Phase1 CAGE Peaks

Hg19::chr12:15114658..15114684,-p4@ARHGDIB
Hg19::chr12:15114685..15114697,-p8@ARHGDIB
Hg19::chr12:15114705..15114712,-p9@ARHGDIB


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.16e-29168
angioblastic mesenchymal cell2.16e-29168
hematopoietic cell1.57e-28177
hematopoietic oligopotent progenitor cell1.65e-26161
hematopoietic multipotent progenitor cell1.65e-26161
leukocyte6.07e-24136
hematopoietic lineage restricted progenitor cell2.62e-21120
nongranular leukocyte2.72e-20115
nucleate cell3.76e-1655
lymphocyte4.76e-1553
common lymphoid progenitor4.76e-1553
lymphoid lineage restricted progenitor cell1.62e-1452
myeloid cell3.15e-12108
common myeloid progenitor3.15e-12108
lymphocyte of B lineage1.03e-1024
pro-B cell1.03e-1024
dendritic cell2.14e-0810
endothelial cell of artery9.98e-089
myeloid lineage restricted progenitor cell2.31e-0766
conventional dendritic cell3.47e-078
granulocyte monocyte progenitor cell4.19e-0767
macrophage dendritic cell progenitor5.86e-0761
blood vessel endothelial cell5.95e-0718
embryonic blood vessel endothelial progenitor cell5.95e-0718
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.49e-13203
hematopoietic system3.88e-1298
blood island3.88e-1298
hemolymphoid system3.29e-11108
blood8.57e-0815
haemolymphatic fluid8.57e-0815
organism substance8.57e-0815
endothelial tube9.98e-089
arterial system endothelium9.98e-089
endothelium of artery9.98e-089
blood vessel endothelium5.95e-0718
endothelium5.95e-0718
cardiovascular system endothelium5.95e-0718
immune system8.98e-0793
Disease
Ontology termp-valuen
hematologic cancer1.59e-1251
immune system cancer1.59e-1251
leukemia8.23e-0939


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00138942465350452
E2F6#187635.017155731697390.00791769806886330.0320846028252052
EGR1#195834.988179094810140.008056488137383440.0319418253959528
GATA1#2623313.56030814380040.0004009615963782630.00387095841783596
GATA2#2624312.7449317335540.0004829527704283790.00436135792397488
GATA3#2625327.2365163572064.94721007899563e-050.000849665636310187
MAX#414936.452555509007120.003721913834265510.0185960368816369
MYC#460935.22228187160940.007020843755740150.0293464300410528
NFKB1#479035.488063424193840.006049381815655430.0268813082349163
PBX3#5090321.91451268674419.49854535978121e-050.00136247572974892
SPI1#668838.204323508522730.001810593189410520.010887013766414



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.