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Coexpression cluster:C1550: Difference between revisions

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|full_id=C1550_Osteoblast_Mesothelial_acute_leukemia_Prostate_Fibroblast_Lens
|full_id=C1550_Osteoblast_Mesothelial_acute_leukemia_Prostate_Fibroblast_Lens
|id=C1550
|id=C1550
|ontology_enrichment_celltype=CL:0000359!1.19e-15!32;CL:0000192!8.96e-13!42;CL:0000514!8.96e-13!42;CL:0000548!9.10e-13!679;CL:0000004!9.10e-13!679;CL:0000255!9.10e-13!679;CL:0000012!4.85e-12!682;CL:0000066!7.85e-11!254;CL:0000055!5.12e-10!180;CL:0000220!5.65e-10!246;CL:0000680!6.45e-10!57;CL:0000056!6.45e-10!57;CL:0000355!6.45e-10!57;CL:0002321!1.30e-09!248;CL:0000183!2.04e-09!59;CL:0000187!5.27e-09!54;CL:0000003!8.13e-09!722;CL:0002371!1.74e-07!591;CL:0000393!6.01e-07!60;CL:0000211!6.01e-07!60;CL:0000222!9.11e-07!119
|ontology_enrichment_celltype=CL:0000359!3.90e-18!32;CL:0000548!4.75e-15!679;CL:0000255!4.75e-15!679;CL:0000192!4.27e-14!43;CL:0000514!4.27e-14!43;CL:0000066!4.14e-10!253;CL:0000680!4.38e-10!58;CL:0000056!4.38e-10!58;CL:0000355!4.38e-10!58;CL:0002321!5.59e-10!250;CL:0000003!1.64e-09!722;CL:0000187!3.87e-09!55;CL:0000183!7.02e-09!59;CL:0002371!1.03e-07!588;CL:0000222!4.11e-07!121;CL:0000393!6.84e-07!61;CL:0000211!6.84e-07!61
|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!2.27e-20!42;UBERON:0003509!2.27e-20!42;UBERON:0004572!2.27e-20!42;UBERON:0002049!1.56e-17!78;UBERON:0007798!1.56e-17!78;UBERON:0004573!1.56e-16!33;UBERON:0004571!1.56e-16!33;UBERON:0007500!5.17e-16!59;UBERON:0001981!5.17e-16!59;UBERON:0004537!5.17e-16!59;UBERON:0006965!5.17e-16!59;UBERON:0000055!1.03e-15!68;UBERON:0004872!6.53e-13!83;UBERON:0000486!1.01e-11!83;UBERON:0004535!4.13e-11!109;UBERON:0001009!1.15e-10!112;UBERON:0007503!3.09e-10!78;UBERON:0002329!8.59e-10!71;UBERON:0003059!8.59e-10!71;UBERON:0007282!8.59e-10!71;UBERON:0004290!8.59e-10!71;UBERON:0009618!8.59e-10!71;UBERON:0007524!1.08e-09!73;UBERON:0000947!1.74e-09!21;UBERON:0010191!1.74e-09!21;UBERON:0003077!2.05e-09!72;UBERON:0007285!2.05e-09!72;UBERON:0003914!2.55e-09!117;UBERON:0000475!7.26e-09!264;UBERON:0001134!1.91e-08!62;UBERON:0002036!1.91e-08!62;UBERON:0003082!1.91e-08!62;UBERON:0000483!2.93e-08!306;UBERON:0000119!8.36e-08!309;UBERON:0002385!9.99e-08!64;UBERON:0001015!9.99e-08!64;UBERON:0000383!9.99e-08!64;UBERON:0001737!1.11e-07!9;UBERON:0000490!1.41e-07!148;UBERON:0003102!3.36e-07!99;UBERON:0002100!4.03e-07!199
|tf_chipseq_enrich=CTBP2#1488;6:62.7170003393281:1.6349770986689e-11:1.99247810044202e-09!EBF1#1879;6:8.906466846569:2.00211291586927e-06:7.32651264262336e-05!ELK4#2005;6:16.235681658468:5.45305335722442e-08:3.44740580856635e-06!GABPB1#2553;6:7.06768383618217:8.01905956107035e-06:0.000222917902980736!MXI1#4601;6:9.9615716287593:1.02262624227062e-06:4.31001057774419e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380813038825108!SMARCB1#6598;6:18.2527157811574:2.70039220880305e-08:1.85665741866479e-06!SP1#6667;6:5.6983813781409:2.91961319085282e-05:0.000610331229062206!SUZ12#23512;4:33.4105206073753:2.29902183370319e-06:8.19479663106236e-05!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573959680666815!TFAP2A#7020;6:16.518634373045:4.91595718330683e-08:3.16338664366841e-06!TFAP2C#7022;6:10.8092286098602:6.2644941908553e-07:2.86955047718744e-05!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108895947971769
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}}
}}

Revision as of 11:25, 19 October 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
artery2.27e-2042
arterial blood vessel2.27e-2042
arterial system2.27e-2042
vasculature1.56e-1778
vascular system1.56e-1778
systemic artery1.56e-1633
systemic arterial system1.56e-1633
epithelial tube open at both ends5.17e-1659
blood vessel5.17e-1659
blood vasculature5.17e-1659
vascular cord5.17e-1659
vessel1.03e-1568
splanchnic layer of lateral plate mesoderm6.53e-1383
multilaminar epithelium1.01e-1183
cardiovascular system4.13e-11109
circulatory system1.15e-10112
epithelial vesicle3.09e-1078
somite8.59e-1071
presomitic mesoderm8.59e-1071
presumptive segmental plate8.59e-1071
dermomyotome8.59e-1071
trunk paraxial mesoderm8.59e-1071
dense mesenchyme tissue1.08e-0973
aorta1.74e-0921
aortic system1.74e-0921
paraxial mesoderm2.05e-0972
presumptive paraxial mesoderm2.05e-0972
epithelial tube2.55e-09117
organism subdivision7.26e-09264
skeletal muscle tissue1.91e-0862
striated muscle tissue1.91e-0862
myotome1.91e-0862
epithelium2.93e-08306
cell layer8.36e-08309
muscle tissue9.99e-0864
musculature9.99e-0864
musculature of body9.99e-0864
larynx1.11e-079
unilaminar epithelium1.41e-07148
surface structure3.36e-0799
trunk4.03e-07199


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.