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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4608_myeloma_CD4_anaplastic_liposarcoma_pons_Fibroblast_adult
|full_id=C4608_myeloma_CD4_anaplastic_liposarcoma_pons_Fibroblast_adult
|id=C4608
|id=C4608

Revision as of 17:43, 12 September 2012


Full id: C4608_myeloma_CD4_anaplastic_liposarcoma_pons_Fibroblast_adult



Phase1 CAGE Peaks

Hg19::chr6:46293524..46293563,-p10@RCAN2
Hg19::chr6:46293579..46293596,-p11@RCAN2
Hg19::chr6:46293606..46293620,-p18@RCAN2


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
neural tube3.24e-3457
neural rod3.24e-3457
future spinal cord3.24e-3457
neural keel3.24e-3457
regional part of brain6.40e-3259
central nervous system2.73e-3182
brain1.60e-2969
future brain1.60e-2969
neural plate4.93e-2786
presumptive neural plate4.93e-2786
regional part of forebrain2.47e-2541
forebrain2.47e-2541
future forebrain2.47e-2541
regional part of nervous system4.62e-2594
nervous system4.62e-2594
neurectoderm6.35e-2590
anterior neural tube2.00e-2442
adult organism1.01e-23115
gray matter1.95e-2234
brain grey matter1.95e-2234
telencephalon2.98e-2234
pre-chordal neural plate1.61e-2161
regional part of telencephalon3.53e-2133
cerebral hemisphere4.63e-2132
anterior region of body2.30e-18129
craniocervical region2.30e-18129
regional part of cerebral cortex2.92e-1722
head3.39e-17123
cerebral cortex4.88e-1725
pallium4.88e-1725
neocortex1.12e-1520
ectoderm-derived structure5.99e-12169
ectoderm3.22e-11173
presumptive ectoderm3.22e-11173
posterior neural tube7.77e-1115
chordal neural plate7.77e-1115
segmental subdivision of hindbrain2.95e-1012
hindbrain2.95e-1012
presumptive hindbrain2.95e-1012
organism subdivision2.45e-09365
segmental subdivision of nervous system3.37e-0913
gyrus7.17e-086
regional part of metencephalon8.18e-089
metencephalon8.18e-089
future metencephalon8.18e-089
nucleus of brain7.58e-079
neural nucleus7.58e-079


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
JUND#372736.994663941871030.002921845042734990.0157588604843111
STAT3#6774310.51946499715420.0008589184530415310.00645263877983056
TRIM28#10155318.59052504526250.0001555969297255280.00197982306817792



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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