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Coexpression cluster:C1999: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.04e-11!216;UBERON:0002204!5.97e-11!167;UBERON:0005256!6.67e-09!143;UBERON:0002049!1.04e-08!79;UBERON:0007798!1.04e-08!79;UBERON:0000914!2.27e-08!83;UBERON:0002329!2.27e-08!83;UBERON:0003077!2.27e-08!83;UBERON:0003059!2.27e-08!83;UBERON:0007282!2.27e-08!83;UBERON:0009618!2.27e-08!83;UBERON:0007285!2.27e-08!83;UBERON:0000486!2.32e-08!82;UBERON:0004290!4.58e-08!70;UBERON:0002385!1.30e-07!63;UBERON:0001015!1.30e-07!63;UBERON:0000383!1.30e-07!63;UBERON:0001134!2.12e-07!61;UBERON:0002036!2.12e-07!61;UBERON:0003082!2.12e-07!61;UBERON:0004535!2.91e-07!110;UBERON:0000055!2.94e-07!69;UBERON:0001637!3.04e-07!42;UBERON:0003509!3.04e-07!42;UBERON:0004572!3.04e-07!42;UBERON:0001981!8.98e-07!60;UBERON:0007500!8.98e-07!60;UBERON:0004537!8.98e-07!60;UBERON:0006965!8.98e-07!60
|ontology_enrichment_uberon=UBERON:0003081!1.04e-11!216;UBERON:0002204!5.97e-11!167;UBERON:0005256!6.67e-09!143;UBERON:0002049!1.04e-08!79;UBERON:0007798!1.04e-08!79;UBERON:0000914!2.27e-08!83;UBERON:0002329!2.27e-08!83;UBERON:0003077!2.27e-08!83;UBERON:0003059!2.27e-08!83;UBERON:0007282!2.27e-08!83;UBERON:0009618!2.27e-08!83;UBERON:0007285!2.27e-08!83;UBERON:0000486!2.32e-08!82;UBERON:0004290!4.58e-08!70;UBERON:0002385!1.30e-07!63;UBERON:0001015!1.30e-07!63;UBERON:0000383!1.30e-07!63;UBERON:0001134!2.12e-07!61;UBERON:0002036!2.12e-07!61;UBERON:0003082!2.12e-07!61;UBERON:0004535!2.91e-07!110;UBERON:0000055!2.94e-07!69;UBERON:0001637!3.04e-07!42;UBERON:0003509!3.04e-07!42;UBERON:0004572!3.04e-07!42;UBERON:0001981!8.98e-07!60;UBERON:0007500!8.98e-07!60;UBERON:0004537!8.98e-07!60;UBERON:0006965!8.98e-07!60
|tf_chipseq_enrich=BCLAF1#9774;5:21.6526476101218:2.09874458450681e-07:1.12118048931615e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239462107708295!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406798166851804!ETS1#2113;5:9.72876092220234:1.14685159850452e-05:0.000292421958242709!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675052839368579!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000985575125720515!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276791830796034!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542757311170157!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232509582753184!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204565011954032!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157570727916959!ZBTB33#10009;5:31.6647250299812:3.13617771034015e-08:2.11588671763705e-06
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}}
}}

Revision as of 13:00, 5 September 2012


Full id: C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic



Phase1 CAGE Peaks

Hg19::chr7:5567947..5567983,-p10@ACTB
Hg19::chr7:5567987..5568010,-p7@ACTB
Hg19::chr7:5568016..5568065,-p3@ACTB
Hg19::chr7:5568084..5568101,-p14@ACTB
Hg19::chr7:5568284..5568346,-p4@ACTB


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>


Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.04e-11216
musculoskeletal system5.97e-11167
trunk mesenchyme6.67e-09143
vasculature1.04e-0879
vascular system1.04e-0879
somite2.27e-0883
paraxial mesoderm2.27e-0883
presomitic mesoderm2.27e-0883
presumptive segmental plate2.27e-0883
trunk paraxial mesoderm2.27e-0883
presumptive paraxial mesoderm2.27e-0883
multilaminar epithelium2.32e-0882
dermomyotome4.58e-0870
muscle tissue1.30e-0763
musculature1.30e-0763
musculature of body1.30e-0763
skeletal muscle tissue2.12e-0761
striated muscle tissue2.12e-0761
myotome2.12e-0761
cardiovascular system2.91e-07110
vessel2.94e-0769
artery3.04e-0742
arterial blood vessel3.04e-0742
arterial system3.04e-0742
blood vessel8.98e-0760
epithelial tube open at both ends8.98e-0760
blood vasculature8.98e-0760
vascular cord8.98e-0760


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#9774521.65264761012182.09874458450681e-071.12118048931615e-05
CTCF#1066444.288205098460020.005152015588243280.0239462107708295
EBF1#187958.9064668465691.78355672307702e-050.000406798166851804
ETS1#211359.728760922202341.14685159850452e-050.000292421958242709
HEY1#2346254.040111043105710.0009288852205177990.00675052839368579
JUND#372756.994663941871035.97069468343598e-050.000985575125720515
MYC#460955.22228187160940.0002573944848850610.00276791830796034
POU2F2#545247.284899246194020.0006631223288743860.00542757311170157
SIN3A#2594244.327107781452110.004977052855762880.0232509582753184
SP1#666755.69838137814090.000166391843712550.00204565011954032
TAF7#6879511.43306940492395.11611886715123e-060.000157570727916959
ZBTB33#10009531.66472502998123.13617771034015e-082.11588671763705e-06



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.