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Coexpression cluster:C2390: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!1.22e-27!312;UBERON:0000475!9.15e-27!365;UBERON:0000483!1.88e-26!309;UBERON:0004111!4.97e-23!241;UBERON:0002049!1.46e-22!79;UBERON:0007798!1.46e-22!79;UBERON:0000477!9.66e-22!286;UBERON:0000468!2.05e-19!659;UBERON:0000025!2.10e-19!194;UBERON:0003914!1.26e-18!118;UBERON:0000481!3.48e-18!347;UBERON:0000055!3.67e-18!69;UBERON:0000467!5.12e-17!625;UBERON:0000480!9.39e-17!626;UBERON:0001981!1.24e-14!60;UBERON:0007500!1.24e-14!60;UBERON:0004537!1.24e-14!60;UBERON:0006965!1.24e-14!60;UBERON:0004872!1.70e-14!84;UBERON:0002100!5.42e-14!216;UBERON:0000490!1.43e-13!138;UBERON:0001986!4.48e-13!18;UBERON:0004638!4.48e-13!18;UBERON:0004852!4.48e-13!18;UBERON:0005256!6.05e-13!143;UBERON:0004535!2.66e-12!110;UBERON:0001009!3.46e-12!113;UBERON:0000487!1.02e-11!22;UBERON:0002050!5.37e-11!605;UBERON:0005423!5.37e-11!605;UBERON:0000923!7.64e-11!604;UBERON:0005291!7.64e-11!604;UBERON:0006598!7.64e-11!604;UBERON:0002532!7.64e-11!604;UBERON:0000922!8.43e-11!612;UBERON:0000064!1.98e-10!219;UBERON:0004121!4.20e-10!169;UBERON:0003104!6.82e-10!238;UBERON:0009142!6.82e-10!238;UBERON:0006914!1.65e-09!25;UBERON:0000924!3.99e-09!173;UBERON:0006601!3.99e-09!173;UBERON:0000033!1.22e-08!123;UBERON:0001637!7.58e-08!42;UBERON:0003509!7.58e-08!42;UBERON:0004572!7.58e-08!42;UBERON:0000914!1.28e-07!83;UBERON:0002329!1.28e-07!83;UBERON:0003077!1.28e-07!83;UBERON:0003059!1.28e-07!83;UBERON:0007282!1.28e-07!83;UBERON:0009618!1.28e-07!83;UBERON:0007285!1.28e-07!83;UBERON:0000353!2.21e-07!17;UBERON:0000486!2.30e-07!82;UBERON:0003915!2.79e-07!9;UBERON:0004700!2.79e-07!9;UBERON:0001917!2.79e-07!9;UBERON:0000153!3.71e-07!129;UBERON:0007811!3.71e-07!129;UBERON:0001048!3.79e-07!168;UBERON:0004211!4.54e-07!16;UBERON:0001285!4.54e-07!16;UBERON:0007684!4.54e-07!16;UBERON:0003220!4.54e-07!16;UBERON:0004208!4.54e-07!16;UBERON:0004290!6.30e-07!70;UBERON:0005085!7.88e-07!29;UBERON:0003075!8.09e-07!86;UBERON:0007284!8.09e-07!86
|ontology_enrichment_uberon=UBERON:0000119!1.22e-27!312;UBERON:0000475!9.15e-27!365;UBERON:0000483!1.88e-26!309;UBERON:0004111!4.97e-23!241;UBERON:0002049!1.46e-22!79;UBERON:0007798!1.46e-22!79;UBERON:0000477!9.66e-22!286;UBERON:0000468!2.05e-19!659;UBERON:0000025!2.10e-19!194;UBERON:0003914!1.26e-18!118;UBERON:0000481!3.48e-18!347;UBERON:0000055!3.67e-18!69;UBERON:0000467!5.12e-17!625;UBERON:0000480!9.39e-17!626;UBERON:0001981!1.24e-14!60;UBERON:0007500!1.24e-14!60;UBERON:0004537!1.24e-14!60;UBERON:0006965!1.24e-14!60;UBERON:0004872!1.70e-14!84;UBERON:0002100!5.42e-14!216;UBERON:0000490!1.43e-13!138;UBERON:0001986!4.48e-13!18;UBERON:0004638!4.48e-13!18;UBERON:0004852!4.48e-13!18;UBERON:0005256!6.05e-13!143;UBERON:0004535!2.66e-12!110;UBERON:0001009!3.46e-12!113;UBERON:0000487!1.02e-11!22;UBERON:0002050!5.37e-11!605;UBERON:0005423!5.37e-11!605;UBERON:0000923!7.64e-11!604;UBERON:0005291!7.64e-11!604;UBERON:0006598!7.64e-11!604;UBERON:0002532!7.64e-11!604;UBERON:0000922!8.43e-11!612;UBERON:0000064!1.98e-10!219;UBERON:0004121!4.20e-10!169;UBERON:0003104!6.82e-10!238;UBERON:0009142!6.82e-10!238;UBERON:0006914!1.65e-09!25;UBERON:0000924!3.99e-09!173;UBERON:0006601!3.99e-09!173;UBERON:0000033!1.22e-08!123;UBERON:0001637!7.58e-08!42;UBERON:0003509!7.58e-08!42;UBERON:0004572!7.58e-08!42;UBERON:0000914!1.28e-07!83;UBERON:0002329!1.28e-07!83;UBERON:0003077!1.28e-07!83;UBERON:0003059!1.28e-07!83;UBERON:0007282!1.28e-07!83;UBERON:0009618!1.28e-07!83;UBERON:0007285!1.28e-07!83;UBERON:0000353!2.21e-07!17;UBERON:0000486!2.30e-07!82;UBERON:0003915!2.79e-07!9;UBERON:0004700!2.79e-07!9;UBERON:0001917!2.79e-07!9;UBERON:0000153!3.71e-07!129;UBERON:0007811!3.71e-07!129;UBERON:0001048!3.79e-07!168;UBERON:0004211!4.54e-07!16;UBERON:0001285!4.54e-07!16;UBERON:0007684!4.54e-07!16;UBERON:0003220!4.54e-07!16;UBERON:0004208!4.54e-07!16;UBERON:0004290!6.30e-07!70;UBERON:0005085!7.88e-07!29;UBERON:0003075!8.09e-07!86;UBERON:0007284!8.09e-07!86
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}}
}}

Revision as of 12:45, 5 September 2012


Full id: C2390_Renal_Endothelial_Alveolar_Hepatic_Mesenchymal_Sebocyte_mesothelioma



Phase1 CAGE Peaks

Hg19::chr16:75285508..75285580,-p1@BCAR1
Hg19::chr16:75285587..75285599,-p6@BCAR1
Hg19::chr16:75285612..75285626,-p4@BCAR1
Hg19::chr16:75299845..75299883,-p2@BCAR1


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
cell layer1.22e-27312
organism subdivision9.15e-27365
epithelium1.88e-26309
anatomical conduit4.97e-23241
vasculature1.46e-2279
vascular system1.46e-2279
anatomical cluster9.66e-22286
multi-cellular organism2.05e-19659
tube2.10e-19194
epithelial tube1.26e-18118
multi-tissue structure3.48e-18347
vessel3.67e-1869
anatomical system5.12e-17625
anatomical group9.39e-17626
blood vessel1.24e-1460
epithelial tube open at both ends1.24e-1460
blood vasculature1.24e-1460
vascular cord1.24e-1460
splanchnic layer of lateral plate mesoderm1.70e-1484
trunk5.42e-14216
unilaminar epithelium1.43e-13138
endothelium4.48e-1318
blood vessel endothelium4.48e-1318
cardiovascular system endothelium4.48e-1318
trunk mesenchyme6.05e-13143
cardiovascular system2.66e-12110
circulatory system3.46e-12113
simple squamous epithelium1.02e-1122
embryonic structure5.37e-11605
developing anatomical structure5.37e-11605
germ layer7.64e-11604
embryonic tissue7.64e-11604
presumptive structure7.64e-11604
epiblast (generic)7.64e-11604
embryo8.43e-11612
organ part1.98e-10219
ectoderm-derived structure4.20e-10169
mesenchyme6.82e-10238
entire embryonic mesenchyme6.82e-10238
squamous epithelium1.65e-0925
ectoderm3.99e-09173
presumptive ectoderm3.99e-09173
head1.22e-08123
artery7.58e-0842
arterial blood vessel7.58e-0842
arterial system7.58e-0842
somite1.28e-0783
paraxial mesoderm1.28e-0783
presomitic mesoderm1.28e-0783
presumptive segmental plate1.28e-0783
trunk paraxial mesoderm1.28e-0783
presumptive paraxial mesoderm1.28e-0783
parenchyma2.21e-0717
multilaminar epithelium2.30e-0782
endothelial tube2.79e-079
arterial system endothelium2.79e-079
endothelium of artery2.79e-079
anterior region of body3.71e-07129
craniocervical region3.71e-07129
primordium3.79e-07168
nephron epithelium4.54e-0716
nephron4.54e-0716
uriniferous tubule4.54e-0716
metanephric mesenchyme4.54e-0716
nephrogenic mesenchyme4.54e-0716
dermomyotome6.30e-0770
ectodermal placode7.88e-0729
neural plate8.09e-0786
presumptive neural plate8.09e-0786


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
CCNT2#90534.752151182721970.01386206996689490.048717593474191
E2F4#187439.501045236463330.001850751034728270.0109265453542106
ETS1#211349.728760922202340.0001115955317418140.00154492652963723
FOXA1#316938.311064812039090.002740138182109850.0150350578754529
HEY1#2346244.040111043105710.00375304636917980.0185879646109342
MYC#460945.22228187160940.001344309395272740.00887081120445374
NFYB#4801312.56984494015230.000811456397697350.00618731800533793
POU2F2#545236.829593043306890.004860473775203740.0227562209444794
TAF1#687243.343046285745290.008005664898701650.0321912615545182
TBP#690843.706770687096390.005296377814784350.0243957132662196
YY1#752844.911170749853860.00171871838055440.0106750656524961
ZNF143#7702310.12565741417090.001534861610688180.00976542258657711



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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