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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4439_ductus_seminal_pons_mesothelioma_medulla_rectal_brain
|full_id=C4439_ductus_seminal_pons_mesothelioma_medulla_rectal_brain
|id=C4439
|id=C4439

Revision as of 17:30, 12 September 2012


Full id: C4439_ductus_seminal_pons_mesothelioma_medulla_rectal_brain



Phase1 CAGE Peaks

Hg19::chr4:89079686..89079698,-p9@ABCG2
Hg19::chr4:89079714..89079746,-p4@ABCG2
Hg19::chr4:89079757..89079802,-p2@ABCG2


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 organism2.38e-39115
neural tube2.21e-2657
neural rod2.21e-2657
future spinal cord2.21e-2657
neural keel2.21e-2657
brain3.07e-2269
future brain3.07e-2269
regional part of brain3.59e-2259
central nervous system3.85e-2282
anterior neural tube1.85e-2142
regional part of forebrain2.09e-2141
forebrain2.09e-2141
future forebrain2.09e-2141
regional part of nervous system1.14e-2094
nervous system1.14e-2094
neural plate1.50e-1886
presumptive neural plate1.50e-1886
telencephalon3.87e-1734
gray matter5.90e-1734
brain grey matter5.90e-1734
anterior region of body1.01e-16129
craniocervical region1.01e-16129
regional part of telencephalon1.95e-1633
neurectoderm2.42e-1690
head2.82e-16123
cerebral hemisphere9.37e-1632
regional part of cerebral cortex5.67e-1522
anatomical cluster1.69e-14286
pre-chordal neural plate6.32e-1461
neocortex6.53e-1420
anatomical conduit3.31e-12241
ectoderm-derived structure8.76e-12169
cerebral cortex1.01e-1125
pallium1.01e-1125
ectoderm1.11e-10173
presumptive ectoderm1.11e-10173
tube2.48e-10194
organ8.54e-10511
organ part4.56e-08219
multi-cellular organism1.03e-07659
anatomical system1.13e-07625
multi-tissue structure1.29e-07347
anatomical group1.59e-07626
embryo6.82e-07612
nucleus of brain7.59e-079
neural nucleus7.59e-079
epithelium9.81e-07309


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#90536.336201576962630.003930750035764890.0190790353202235
E2F1#186934.907389214879320.008460985347239390.0326977557328523
EGR1#195834.988179094810140.008056488137383440.0321960497658295
FOS#235338.99795530889440.001372499272417130.00900731755133672
FOSL2#2355316.93020060456170.0002060162053171620.00243864065137924
GATA1#2623313.56030814380040.0004009615963782630.00389001655031579
JUN#3725312.51282919233630.0005103313992726250.0044578873376241
JUND#372736.994663941871030.002921845042734990.0157385411531384
TAL1#6886219.91241111829350.003287176608740550.017019107566937



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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