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Coexpression cluster:C3742: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.38e-17!86;UBERON:0007023!3.59e-17!115;UBERON:0001017!5.64e-17!82;UBERON:0002616!8.53e-17!59;UBERON:0000073!4.15e-16!94;UBERON:0001016!4.15e-16!94;UBERON:0001049!7.23e-16!57;UBERON:0005068!7.23e-16!57;UBERON:0006241!7.23e-16!57;UBERON:0007135!7.23e-16!57;UBERON:0000955!1.19e-14!69;UBERON:0006238!1.19e-14!69;UBERON:0003075!1.58e-14!86;UBERON:0007284!1.58e-14!86;UBERON:0002346!7.85e-14!90;UBERON:0002780!3.16e-12!41;UBERON:0001890!3.16e-12!41;UBERON:0006240!3.16e-12!41;UBERON:0001869!7.26e-12!32;UBERON:0001893!8.39e-12!34;UBERON:0003080!1.00e-11!42;UBERON:0002619!1.05e-11!22;UBERON:0002791!3.88e-11!33;UBERON:0002020!1.13e-10!34;UBERON:0003528!1.13e-10!34;UBERON:0003056!1.51e-10!61;UBERON:0001950!4.77e-10!20;UBERON:0000153!6.20e-10!129;UBERON:0007811!6.20e-10!129;UBERON:0000956!1.21e-09!25;UBERON:0000203!1.21e-09!25;UBERON:0000033!1.27e-09!123;UBERON:0004121!4.41e-09!169;UBERON:0000924!7.73e-09!173;UBERON:0006601!7.73e-09!173;UBERON:0000119!1.54e-07!312;UBERON:0000922!3.09e-07!612;UBERON:0002050!9.24e-07!605;UBERON:0005423!9.24e-07!605
|ontology_enrichment_uberon=UBERON:0005743!2.38e-17!86;UBERON:0007023!3.59e-17!115;UBERON:0001017!5.64e-17!82;UBERON:0002616!8.53e-17!59;UBERON:0000073!4.15e-16!94;UBERON:0001016!4.15e-16!94;UBERON:0001049!7.23e-16!57;UBERON:0005068!7.23e-16!57;UBERON:0006241!7.23e-16!57;UBERON:0007135!7.23e-16!57;UBERON:0000955!1.19e-14!69;UBERON:0006238!1.19e-14!69;UBERON:0003075!1.58e-14!86;UBERON:0007284!1.58e-14!86;UBERON:0002346!7.85e-14!90;UBERON:0002780!3.16e-12!41;UBERON:0001890!3.16e-12!41;UBERON:0006240!3.16e-12!41;UBERON:0001869!7.26e-12!32;UBERON:0001893!8.39e-12!34;UBERON:0003080!1.00e-11!42;UBERON:0002619!1.05e-11!22;UBERON:0002791!3.88e-11!33;UBERON:0002020!1.13e-10!34;UBERON:0003528!1.13e-10!34;UBERON:0003056!1.51e-10!61;UBERON:0001950!4.77e-10!20;UBERON:0000153!6.20e-10!129;UBERON:0007811!6.20e-10!129;UBERON:0000956!1.21e-09!25;UBERON:0000203!1.21e-09!25;UBERON:0000033!1.27e-09!123;UBERON:0004121!4.41e-09!169;UBERON:0000924!7.73e-09!173;UBERON:0006601!7.73e-09!173;UBERON:0000119!1.54e-07!312;UBERON:0000922!3.09e-07!612;UBERON:0002050!9.24e-07!605;UBERON:0005423!9.24e-07!605
|tf_chipseq_enrich=BCL3#602;2:23.0314018691589:0.00246467476084291:0.013851809037705!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279340518188075!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663888191480374!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109372110450069
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}}
}}

Revision as of 12:10, 5 September 2012


Full id: C3742_Dendritic_granulocyte_Smooth_Mesenchymal_Fibroblast_merkel_Prostate



Phase1 CAGE Peaks

Hg19::chr18:77557932..77557943,+p@chr18:77557932..77557943
+
Hg19::chr18:77557948..77557968,+p@chr18:77557948..77557968
+
Hg19::chr18:77557973..77557984,+p@chr18:77557973..77557984
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.59e-17115
central nervous system5.64e-1782
regional part of brain8.53e-1759
regional part of nervous system4.15e-1694
nervous system4.15e-1694
neural tube7.23e-1657
neural rod7.23e-1657
future spinal cord7.23e-1657
neural keel7.23e-1657
brain1.19e-1469
future brain1.19e-1469
neural plate1.58e-1486
presumptive neural plate1.58e-1486
neurectoderm7.85e-1490
regional part of forebrain3.16e-1241
forebrain3.16e-1241
future forebrain3.16e-1241
cerebral hemisphere7.26e-1232
telencephalon8.39e-1234
anterior neural tube1.00e-1142
regional part of cerebral cortex1.05e-1122
regional part of telencephalon3.88e-1133
gray matter1.13e-1034
brain grey matter1.13e-1034
pre-chordal neural plate1.51e-1061
neocortex4.77e-1020
anterior region of body6.20e-10129
craniocervical region6.20e-10129
cerebral cortex1.21e-0925
pallium1.21e-0925
head1.27e-09123
ectoderm-derived structure4.41e-09169
ectoderm7.73e-09173
presumptive ectoderm7.73e-09173
cell layer1.54e-07312
embryo3.09e-07612
embryonic structure9.24e-07605
developing anatomical structure9.24e-07605


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
BCL3#602223.03140186915890.002464674760842910.013851809037705
CTCF#1066435.360256373075030.0064925092527670.0279340518188075
RAD21#5885310.35503389545630.0009004912073565420.00663888191480374
ZNF263#1012738.221841637010680.001799043925565870.0109372110450069



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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