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Coexpression cluster:C1186: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:4.55494150047132:0.00632108033306846:0.0275287648098635!CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.00022243573344448!EBF1#1879;7:8.906466846569:2.2473547136215e-07:1.19263962873941e-05!EGR1#1958;7:4.98817909481014:1.30079520165561e-05:0.000318158665259274!ELF1#1997;7:4.25809795880754:3.93848941900192e-05:0.000735177652245115!IRF4#3662;7:21.9145126867441:4.11002992557057e-10:4.03049216334897e-08!NFKB1#4790;7:5.48806342419384:6.66568321176054e-06:0.000194838312049555!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223360693252836!RAD21#5885;7:10.3550338954563:7.82487927673307e-08:4.69398372649469e-06!SPI1#6688;4:4.68818486201299:0.00568568052914417:0.0256659227516981!STAT2#6773;7:65.2637711864407:1.96843608096737e-13:2.98376626792673e-11!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246549270396749!TCF12#6938;5:7.59604635870459:0.000131112637393808:0.00172415924663459
|tf_chipseq_enrich=CEBPB#1051;4:4.55494150047132:0.00632108033306846:0.0275287648098635!CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.00022243573344448!EBF1#1879;7:8.906466846569:2.2473547136215e-07:1.19263962873941e-05!EGR1#1958;7:4.98817909481014:1.30079520165561e-05:0.000318158665259274!ELF1#1997;7:4.25809795880754:3.93848941900192e-05:0.000735177652245115!IRF4#3662;7:21.9145126867441:4.11002992557057e-10:4.03049216334897e-08!NFKB1#4790;7:5.48806342419384:6.66568321176054e-06:0.000194838312049555!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223360693252836!RAD21#5885;7:10.3550338954563:7.82487927673307e-08:4.69398372649469e-06!SPI1#6688;4:4.68818486201299:0.00568568052914417:0.0256659227516981!STAT2#6773;7:65.2637711864407:1.96843608096737e-13:2.98376626792673e-11!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246549270396749!TCF12#6938;5:7.59604635870459:0.000131112637393808:0.00172415924663459
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}}
}}

Revision as of 14:44, 26 November 2012


Full id: C1186_acute_Neutrophils_CD14_Eosinophils_Whole_Smooth_granulocyte



Phase1 CAGE Peaks

Hg19::chr13:108922228..108922246,+p3@TNFSF13B
Hg19::chr13:108922311..108922328,+p4@TNFSF13B
Hg19::chr13:108922418..108922428,+p7@TNFSF13B
Hg19::chr13:108922429..108922446,+p6@TNFSF13B
Hg19::chr13:108922469..108922474,+p10@TNFSF13B
Hg19::chr13:108922478..108922493,+p5@TNFSF13B
Hg19::chr13:108922574..108922585,+p8@TNFSF13B


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
myeloid cell4.33e-67108
common myeloid progenitor4.33e-67108
myeloid leukocyte1.12e-5872
hematopoietic stem cell1.48e-56168
angioblastic mesenchymal cell1.48e-56168
monopoietic cell1.45e-5559
monocyte1.45e-5559
monoblast1.45e-5559
promonocyte1.45e-5559
defensive cell2.52e-5448
phagocyte2.52e-5448
hematopoietic oligopotent progenitor cell3.32e-53161
hematopoietic multipotent progenitor cell3.32e-53161
macrophage dendritic cell progenitor4.90e-5361
hematopoietic cell8.39e-52177
granulocyte monocyte progenitor cell1.43e-4867
classical monocyte2.47e-4842
CD14-positive, CD16-negative classical monocyte2.47e-4842
myeloid lineage restricted progenitor cell2.18e-4766
leukocyte1.05e-44136
nongranular leukocyte6.77e-39115
hematopoietic lineage restricted progenitor cell2.99e-32120
stuff accumulating cell1.72e-2187
intermediate monocyte3.45e-109
CD14-positive, CD16-positive monocyte3.45e-109
granulocyte3.50e-108
mesenchymal cell6.03e-10354
connective tissue cell3.16e-09361
macrophage3.09e-076
motile cell4.15e-07386
blood cell8.46e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.82e-5398
blood island2.82e-5398
hemolymphoid system8.29e-49108
bone marrow5.73e-4276
immune system2.39e-3993
bone element2.66e-3782
skeletal element4.45e-3290
skeletal system7.57e-29100
lateral plate mesoderm5.82e-17203
adult organism2.57e-13114
musculoskeletal system1.10e-11167
blood6.72e-1015
haemolymphatic fluid6.72e-1015
organism substance6.72e-1015
connective tissue1.22e-08371
Disease
Ontology termp-valuen
myeloid leukemia2.95e-0931
leukemia6.39e-0739


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
CEBPB#105144.554941500471320.006321080333068460.0275287648098635
CTCF#1066475.360256373075037.86114662284756e-060.00022243573344448
EBF1#187978.9064668465692.2473547136215e-071.19263962873941e-05
EGR1#195874.988179094810141.30079520165561e-050.000318158665259274
ELF1#199774.258097958807543.93848941900192e-050.000735177652245115
IRF4#3662721.91451268674414.11002992557057e-104.03049216334897e-08
NFKB1#479075.488063424193846.66568321176054e-060.000194838312049555
POLR2A#543072.147453176558070.004747636447610280.0223360693252836
RAD21#5885710.35503389545637.82487927673307e-084.69398372649469e-06
SPI1#668844.688184862012990.005685680529144170.0256659227516981
STAT2#6773765.26377118644071.96843608096737e-132.98376626792673e-11
TAF1#687273.343046285745290.0002142336319622450.00246549270396749
TCF12#693857.596046358704590.0001311126373938080.00172415924663459



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.