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Coexpression cluster:C1550: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001637!3.04e-17!42;UBERON:0003509!3.04e-17!42;UBERON:0004572!3.04e-17!42;UBERON:0002049!5.11e-17!79;UBERON:0007798!5.11e-17!79;UBERON:0001981!3.59e-15!60;UBERON:0007500!3.59e-15!60;UBERON:0004537!3.59e-15!60;UBERON:0006965!3.59e-15!60;UBERON:0000055!4.10e-15!69;UBERON:0004573!7.14e-14!33;UBERON:0004571!7.14e-14!33;UBERON:0004872!3.83e-13!84;UBERON:0000486!1.91e-11!82;UBERON:0000914!1.77e-10!83;UBERON:0002329!1.77e-10!83;UBERON:0003077!1.77e-10!83;UBERON:0003059!1.77e-10!83;UBERON:0007282!1.77e-10!83;UBERON:0009618!1.77e-10!83;UBERON:0007285!1.77e-10!83;UBERON:0000483!2.91e-10!309;UBERON:0000477!2.94e-10!286;UBERON:0000119!4.13e-10!312;UBERON:0000475!8.63e-10!365;UBERON:0003914!1.15e-09!118;UBERON:0004290!2.39e-09!70;UBERON:0004535!4.27e-09!110;UBERON:0002100!4.56e-09!216;UBERON:0001009!9.77e-09!113;UBERON:0005256!1.75e-08!143;UBERON:0001134!3.16e-08!61;UBERON:0002036!3.16e-08!61;UBERON:0003082!3.16e-08!61;UBERON:0000947!6.64e-08!21;UBERON:0010191!6.64e-08!21;UBERON:0004111!7.75e-08!241;UBERON:0003104!1.27e-07!238;UBERON:0009142!1.27e-07!238;UBERON:0002385!2.44e-07!63;UBERON:0001015!2.44e-07!63;UBERON:0000383!2.44e-07!63;UBERON:0000481!3.70e-07!347;UBERON:0001737!4.63e-07!9;UBERON:0000064!5.52e-07!219
|ontology_enrichment_uberon=UBERON:0001637!3.04e-17!42;UBERON:0003509!3.04e-17!42;UBERON:0004572!3.04e-17!42;UBERON:0002049!5.11e-17!79;UBERON:0007798!5.11e-17!79;UBERON:0001981!3.59e-15!60;UBERON:0007500!3.59e-15!60;UBERON:0004537!3.59e-15!60;UBERON:0006965!3.59e-15!60;UBERON:0000055!4.10e-15!69;UBERON:0004573!7.14e-14!33;UBERON:0004571!7.14e-14!33;UBERON:0004872!3.83e-13!84;UBERON:0000486!1.91e-11!82;UBERON:0000914!1.77e-10!83;UBERON:0002329!1.77e-10!83;UBERON:0003077!1.77e-10!83;UBERON:0003059!1.77e-10!83;UBERON:0007282!1.77e-10!83;UBERON:0009618!1.77e-10!83;UBERON:0007285!1.77e-10!83;UBERON:0000483!2.91e-10!309;UBERON:0000477!2.94e-10!286;UBERON:0000119!4.13e-10!312;UBERON:0000475!8.63e-10!365;UBERON:0003914!1.15e-09!118;UBERON:0004290!2.39e-09!70;UBERON:0004535!4.27e-09!110;UBERON:0002100!4.56e-09!216;UBERON:0001009!9.77e-09!113;UBERON:0005256!1.75e-08!143;UBERON:0001134!3.16e-08!61;UBERON:0002036!3.16e-08!61;UBERON:0003082!3.16e-08!61;UBERON:0000947!6.64e-08!21;UBERON:0010191!6.64e-08!21;UBERON:0004111!7.75e-08!241;UBERON:0003104!1.27e-07!238;UBERON:0009142!1.27e-07!238;UBERON:0002385!2.44e-07!63;UBERON:0001015!2.44e-07!63;UBERON:0000383!2.44e-07!63;UBERON:0000481!3.70e-07!347;UBERON:0001737!4.63e-07!9;UBERON:0000064!5.52e-07!219
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}}
}}

Revision as of 13:54, 5 September 2012


Full id: C1550_Osteoblast_Mesothelial_acute_leukemia_Prostate_Fibroblast_Lens



Phase1 CAGE Peaks

Hg19::chr9:21974796..21974810,-p16@CDKN2A
Hg19::chr9:21974820..21974906,-p2@CDKN2A
Hg19::chr9:21975060..21975078,-p4@CDKN2A
Hg19::chr9:21975088..21975104,-p11@CDKN2A
Hg19::chr9:21975118..21975140,-p8@CDKN2A
Hg19::chr9:21975146..21975164,-p5@CDKN2A


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
artery3.04e-1742
arterial blood vessel3.04e-1742
arterial system3.04e-1742
vasculature5.11e-1779
vascular system5.11e-1779
blood vessel3.59e-1560
epithelial tube open at both ends3.59e-1560
blood vasculature3.59e-1560
vascular cord3.59e-1560
vessel4.10e-1569
systemic artery7.14e-1433
systemic arterial system7.14e-1433
splanchnic layer of lateral plate mesoderm3.83e-1384
multilaminar epithelium1.91e-1182
somite1.77e-1083
paraxial mesoderm1.77e-1083
presomitic mesoderm1.77e-1083
presumptive segmental plate1.77e-1083
trunk paraxial mesoderm1.77e-1083
presumptive paraxial mesoderm1.77e-1083
epithelium2.91e-10309
anatomical cluster2.94e-10286
cell layer4.13e-10312
organism subdivision8.63e-10365
epithelial tube1.15e-09118
dermomyotome2.39e-0970
cardiovascular system4.27e-09110
trunk4.56e-09216
circulatory system9.77e-09113
trunk mesenchyme1.75e-08143
skeletal muscle tissue3.16e-0861
striated muscle tissue3.16e-0861
myotome3.16e-0861
aorta6.64e-0821
aortic system6.64e-0821
anatomical conduit7.75e-08241
mesenchyme1.27e-07238
entire embryonic mesenchyme1.27e-07238
muscle tissue2.44e-0763
musculature2.44e-0763
musculature of body2.44e-0763
multi-tissue structure3.70e-07347
larynx4.63e-079
organ part5.52e-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
CTBP2#1488662.71700033932811.6349770986689e-111.99247810044202e-09
EBF1#187968.9064668465692.00211291586927e-067.32651264262336e-05
ELK4#2005616.2356816584685.45305335722442e-083.44740580856635e-06
GABPB1#255367.067683836182178.01905956107035e-060.000222917902980736
MXI1#460169.96157162875931.02262624227062e-064.31001057774419e-05
POLR2A#543062.147453176558070.01019570676818780.0380813038825108
SMARCB1#6598618.25271578115742.70039220880305e-081.85665741866479e-06
SP1#666765.69838137814092.91961319085282e-050.000610331229062206
SUZ12#23512433.41052060737532.29902183370319e-068.19479663106236e-05
TAF1#687263.343046285745290.0007162474284635620.00573959680666815
TFAP2A#7020616.5186343730454.91595718330683e-083.16338664366841e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.86955047718744e-05
ZNF263#1012768.221841637010683.23542093046082e-060.000108895947971769



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.

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