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Coexpression cluster:C4655: Difference between revisions

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|full_id=C4655_normal_sacrococcigeal_Prostate_Mesenchymal_Smooth_smooth_gall
|full_id=C4655_normal_sacrococcigeal_Prostate_Mesenchymal_Smooth_smooth_gall
|id=C4655
|id=C4655
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0002622!3.81e-07!3;CL:0002504!7.72e-07!3;CL:1000279!7.72e-07!3;CL:1000280!7.72e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.27e-22!115;UBERON:0001049!4.24e-18!57;UBERON:0005068!4.24e-18!57;UBERON:0006241!4.24e-18!57;UBERON:0007135!4.24e-18!57;UBERON:0003075!5.53e-16!86;UBERON:0007284!5.53e-16!86;UBERON:0002616!8.67e-16!59;UBERON:0002020!1.14e-15!34;UBERON:0003528!1.14e-15!34;UBERON:0002346!1.16e-15!90;UBERON:0001869!2.18e-15!32;UBERON:0000955!2.31e-15!69;UBERON:0006238!2.31e-15!69;UBERON:0001893!2.62e-15!34;UBERON:0002780!2.84e-15!41;UBERON:0001890!2.84e-15!41;UBERON:0006240!2.84e-15!41;UBERON:0003080!1.05e-14!42;UBERON:0000073!1.05e-14!94;UBERON:0001016!1.05e-14!94;UBERON:0005743!1.18e-14!86;UBERON:0002791!1.69e-14!33;UBERON:0002619!6.52e-14!22;UBERON:0000062!1.48e-13!511;UBERON:0001017!1.58e-13!82;UBERON:0001950!1.47e-12!20;UBERON:0000956!1.26e-11!25;UBERON:0000203!1.26e-11!25;UBERON:0003056!2.45e-11!61;UBERON:0000033!2.53e-11!123;UBERON:0000468!2.87e-11!659;UBERON:0000153!9.97e-11!129;UBERON:0007811!9.97e-11!129;UBERON:0000475!1.03e-10!365;UBERON:0000064!1.24e-10!219;UBERON:0000481!1.34e-10!347;UBERON:0004121!1.72e-10!169;UBERON:0000924!1.76e-10!173;UBERON:0006601!1.76e-10!173;UBERON:0000467!2.78e-08!625;UBERON:0000480!3.32e-08!626;UBERON:0004111!7.20e-08!241;UBERON:0000059!3.61e-07!11;UBERON:0001155!5.17e-07!9;UBERON:0000025!6.39e-07!194;UBERON:0000477!8.85e-07!286
|ontology_enrichment_uberon=UBERON:0007023!4.57e-20!114;UBERON:0000073!1.02e-15!53;UBERON:0002616!1.02e-15!53;UBERON:0001049!1.67e-14!56;UBERON:0005068!1.67e-14!56;UBERON:0006241!1.67e-14!56;UBERON:0007135!1.67e-14!56;UBERON:0002780!1.10e-13!41;UBERON:0001890!1.10e-13!41;UBERON:0003080!1.10e-13!41;UBERON:0006240!1.10e-13!41;UBERON:0011216!1.07e-12!223;UBERON:0003528!1.35e-12!34;UBERON:0002020!1.35e-12!34;UBERON:0001950!1.46e-12!20;UBERON:0001893!1.95e-12!34;UBERON:0000955!2.02e-12!68;UBERON:0006238!2.02e-12!68;UBERON:0001869!5.56e-12!32;UBERON:0002346!1.12e-11!86;UBERON:0003075!1.38e-11!82;UBERON:0007284!1.38e-11!82;UBERON:0002619!3.59e-11!22;UBERON:0002791!1.69e-10!32;UBERON:0000062!7.32e-10!503;UBERON:0000481!1.17e-09!342;UBERON:0000956!1.69e-09!25;UBERON:0000203!1.69e-09!25;UBERON:0001016!1.80e-09!89;UBERON:0001017!2.49e-09!81;UBERON:0003056!2.21e-08!61;UBERON:0010371!2.62e-08!104;UBERON:0000059!2.99e-08!11;UBERON:0001155!1.12e-07!9;UBERON:0000477!1.14e-07!373;UBERON:0000468!1.42e-07!656;UBERON:0010314!1.55e-07!132;UBERON:0002298!1.79e-07!6;UBERON:0000160!2.34e-07!17;UBERON:0001046!3.41e-07!19;UBERON:0004111!3.55e-07!240;UBERON:0000200!6.23e-07!6;UBERON:0000064!8.79e-07!218
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}}
}}

Revision as of 16:07, 19 October 2012


Full id: C4655_normal_sacrococcigeal_Prostate_Mesenchymal_Smooth_smooth_gall



Phase1 CAGE Peaks

Hg19::chr7:136553573..136553582,+p6@CHRM2
Hg19::chr7:136553987..136554036,+p3@CHRM2
Hg19::chr7:136554042..136554052,+p8@CHRM2


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
adult organism4.57e-20114
regional part of nervous system1.02e-1553
regional part of brain1.02e-1553
neural tube1.67e-1456
neural rod1.67e-1456
future spinal cord1.67e-1456
neural keel1.67e-1456
regional part of forebrain1.10e-1341
forebrain1.10e-1341
anterior neural tube1.10e-1341
future forebrain1.10e-1341
organ system subdivision1.07e-12223
brain grey matter1.35e-1234
gray matter1.35e-1234
neocortex1.46e-1220
telencephalon1.95e-1234
brain2.02e-1268
future brain2.02e-1268
cerebral hemisphere5.56e-1232
neurectoderm1.12e-1186
neural plate1.38e-1182
presumptive neural plate1.38e-1182
regional part of cerebral cortex3.59e-1122
regional part of telencephalon1.69e-1032
organ7.32e-10503
multi-tissue structure1.17e-09342
cerebral cortex1.69e-0925
pallium1.69e-0925
nervous system1.80e-0989
central nervous system2.49e-0981
pre-chordal neural plate2.21e-0861
ecto-epithelium2.62e-08104
large intestine2.99e-0811
colon1.12e-079
anatomical cluster1.14e-07373
multi-cellular organism1.42e-07656
structure with developmental contribution from neural crest1.55e-07132
brainstem1.79e-076
intestine2.34e-0717
hindgut3.41e-0719
anatomical conduit3.55e-07240
gyrus6.23e-076
organ part8.79e-07218


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

No analysis results for this cluster

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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