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Coexpression cluster:C3950: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.08e-27!365;UBERON:0000119!2.64e-19!312;UBERON:0000483!8.50e-19!309;UBERON:0000481!1.39e-16!347;UBERON:0000477!2.36e-15!286;UBERON:0004111!9.04e-14!241;UBERON:0000025!2.42e-13!194;UBERON:0000468!2.77e-13!659;UBERON:0007023!2.93e-13!115;UBERON:0000064!9.53e-13!219;UBERON:0005743!1.51e-12!86;UBERON:0001017!5.79e-12!82;UBERON:0003075!7.45e-12!86;UBERON:0007284!7.45e-12!86;UBERON:0000073!1.07e-11!94;UBERON:0001016!1.07e-11!94;UBERON:0004121!1.19e-11!169;UBERON:0000924!2.31e-11!173;UBERON:0006601!2.31e-11!173;UBERON:0002346!2.65e-11!90;UBERON:0002616!4.97e-11!59;UBERON:0000955!5.74e-11!69;UBERON:0006238!5.74e-11!69;UBERON:0001049!5.78e-11!57;UBERON:0005068!5.78e-11!57;UBERON:0006241!5.78e-11!57;UBERON:0007135!5.78e-11!57;UBERON:0002100!5.95e-11!216;UBERON:0000033!7.48e-10!123;UBERON:0005256!7.91e-10!143;UBERON:0000153!6.31e-09!129;UBERON:0007811!6.31e-09!129;UBERON:0000467!6.33e-09!625;UBERON:0000480!9.01e-09!626;UBERON:0000914!3.14e-08!83;UBERON:0002329!3.14e-08!83;UBERON:0003077!3.14e-08!83;UBERON:0003059!3.14e-08!83;UBERON:0007282!3.14e-08!83;UBERON:0009618!3.14e-08!83;UBERON:0007285!3.14e-08!83;UBERON:0004290!6.49e-08!70;UBERON:0001893!7.50e-08!34;UBERON:0002020!8.49e-08!34;UBERON:0003528!8.49e-08!34;UBERON:0002791!1.59e-07!33;UBERON:0003080!4.23e-07!42;UBERON:0002780!4.48e-07!41;UBERON:0001890!4.48e-07!41;UBERON:0006240!4.48e-07!41;UBERON:0002385!5.07e-07!63;UBERON:0001015!5.07e-07!63;UBERON:0000383!5.07e-07!63;UBERON:0001869!5.14e-07!32;UBERON:0003056!5.78e-07!61;UBERON:0001134!6.33e-07!61;UBERON:0002036!6.33e-07!61;UBERON:0003082!6.33e-07!61;UBERON:0002199!9.41e-07!45;UBERON:0002416!9.41e-07!45
|ontology_enrichment_uberon=UBERON:0000475!1.08e-27!365;UBERON:0000119!2.64e-19!312;UBERON:0000483!8.50e-19!309;UBERON:0000481!1.39e-16!347;UBERON:0000477!2.36e-15!286;UBERON:0004111!9.04e-14!241;UBERON:0000025!2.42e-13!194;UBERON:0000468!2.77e-13!659;UBERON:0007023!2.93e-13!115;UBERON:0000064!9.53e-13!219;UBERON:0005743!1.51e-12!86;UBERON:0001017!5.79e-12!82;UBERON:0003075!7.45e-12!86;UBERON:0007284!7.45e-12!86;UBERON:0000073!1.07e-11!94;UBERON:0001016!1.07e-11!94;UBERON:0004121!1.19e-11!169;UBERON:0000924!2.31e-11!173;UBERON:0006601!2.31e-11!173;UBERON:0002346!2.65e-11!90;UBERON:0002616!4.97e-11!59;UBERON:0000955!5.74e-11!69;UBERON:0006238!5.74e-11!69;UBERON:0001049!5.78e-11!57;UBERON:0005068!5.78e-11!57;UBERON:0006241!5.78e-11!57;UBERON:0007135!5.78e-11!57;UBERON:0002100!5.95e-11!216;UBERON:0000033!7.48e-10!123;UBERON:0005256!7.91e-10!143;UBERON:0000153!6.31e-09!129;UBERON:0007811!6.31e-09!129;UBERON:0000467!6.33e-09!625;UBERON:0000480!9.01e-09!626;UBERON:0000914!3.14e-08!83;UBERON:0002329!3.14e-08!83;UBERON:0003077!3.14e-08!83;UBERON:0003059!3.14e-08!83;UBERON:0007282!3.14e-08!83;UBERON:0009618!3.14e-08!83;UBERON:0007285!3.14e-08!83;UBERON:0004290!6.49e-08!70;UBERON:0001893!7.50e-08!34;UBERON:0002020!8.49e-08!34;UBERON:0003528!8.49e-08!34;UBERON:0002791!1.59e-07!33;UBERON:0003080!4.23e-07!42;UBERON:0002780!4.48e-07!41;UBERON:0001890!4.48e-07!41;UBERON:0006240!4.48e-07!41;UBERON:0002385!5.07e-07!63;UBERON:0001015!5.07e-07!63;UBERON:0000383!5.07e-07!63;UBERON:0001869!5.14e-07!32;UBERON:0003056!5.78e-07!61;UBERON:0001134!6.33e-07!61;UBERON:0002036!6.33e-07!61;UBERON:0003082!6.33e-07!61;UBERON:0002199!9.41e-07!45;UBERON:0002416!9.41e-07!45
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0.252796,0.205954,0.361435
}}
}}

Revision as of 14:22, 5 September 2012


Full id: C3950_Hepatic_Hair_Ewing_Preadipocyte_Adipocyte_corpus_neurofibroma



Phase1 CAGE Peaks

Hg19::chr1:231004162..231004173,-p4@C1orf198
Hg19::chr1:231004220..231004294,-p1@C1orf198
Hg19::chr1:231004738..231004754,-p11@C1orf198


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.12e-21180
fibroblast4.44e-1475
fat cell1.37e-0715
Uber Anatomy
Ontology termp-valuen
organism subdivision1.08e-27365
cell layer2.64e-19312
epithelium8.50e-19309
multi-tissue structure1.39e-16347
anatomical cluster2.36e-15286
anatomical conduit9.04e-14241
tube2.42e-13194
multi-cellular organism2.77e-13659
adult organism2.93e-13115
organ part9.53e-13219
central nervous system5.79e-1282
neural plate7.45e-1286
presumptive neural plate7.45e-1286
regional part of nervous system1.07e-1194
nervous system1.07e-1194
ectoderm-derived structure1.19e-11169
ectoderm2.31e-11173
presumptive ectoderm2.31e-11173
neurectoderm2.65e-1190
regional part of brain4.97e-1159
brain5.74e-1169
future brain5.74e-1169
neural tube5.78e-1157
neural rod5.78e-1157
future spinal cord5.78e-1157
neural keel5.78e-1157
trunk5.95e-11216
head7.48e-10123
trunk mesenchyme7.91e-10143
anterior region of body6.31e-09129
craniocervical region6.31e-09129
anatomical system6.33e-09625
anatomical group9.01e-09626
somite3.14e-0883
paraxial mesoderm3.14e-0883
presomitic mesoderm3.14e-0883
presumptive segmental plate3.14e-0883
trunk paraxial mesoderm3.14e-0883
presumptive paraxial mesoderm3.14e-0883
dermomyotome6.49e-0870
telencephalon7.50e-0834
gray matter8.49e-0834
brain grey matter8.49e-0834
regional part of telencephalon1.59e-0733
anterior neural tube4.23e-0742
regional part of forebrain4.48e-0741
forebrain4.48e-0741
future forebrain4.48e-0741
muscle tissue5.07e-0763
musculature5.07e-0763
musculature of body5.07e-0763
cerebral hemisphere5.14e-0732
pre-chordal neural plate5.78e-0761
skeletal muscle tissue6.33e-0761
striated muscle tissue6.33e-0761
myotome6.33e-0761
integument9.41e-0745
integumental system9.41e-0745


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
E2F1#186934.907389214879320.008460985347239390.0325604056406034
E2F6#187635.017155731697390.00791769806886330.0322485168323069
SIN3A#2594235.408884726815140.006318961977991520.027700892797996
SMARCB1#6598212.16847718743830.008675002221921740.0329925551529546
THAP1#55145220.91276306856750.002983447413736940.0158698311318769
YY1#752834.911170749853860.008441455341808260.0329662773227803



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.