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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1606_occipital_parietal_uterus_medulloblastoma_cervix_glioma_lung
|full_id=C1606_occipital_parietal_uterus_medulloblastoma_cervix_glioma_lung
|id=C1606
|id=C1606

Revision as of 14:11, 12 September 2012


Full id: C1606_occipital_parietal_uterus_medulloblastoma_cervix_glioma_lung



Phase1 CAGE Peaks

Hg19::chr11:106889099..106889110,-p5@GUCY1A2
Hg19::chr11:106889125..106889143,-p2@GUCY1A2
Hg19::chr11:106889187..106889209,-p1@GUCY1A2
Hg19::chr11:106889216..106889227,-p6@GUCY1A2
Hg19::chr11:106889252..106889264,-p4@GUCY1A2


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 organism4.50e-42115
regional part of nervous system3.18e-3694
nervous system3.18e-3694
central nervous system1.26e-3582
neural tube9.50e-3257
neural rod9.50e-3257
future spinal cord9.50e-3257
neural keel9.50e-3257
brain1.74e-3069
future brain1.74e-3069
neural plate7.91e-2986
presumptive neural plate7.91e-2986
regional part of brain1.22e-2859
neurectoderm2.18e-2790
anterior neural tube2.04e-2442
regional part of forebrain8.39e-2441
forebrain8.39e-2441
future forebrain8.39e-2441
ectoderm-derived structure5.75e-22169
pre-chordal neural plate7.74e-2261
gray matter1.65e-2134
brain grey matter1.65e-2134
ectoderm2.31e-21173
presumptive ectoderm2.31e-21173
telencephalon2.48e-2134
cerebral hemisphere1.15e-2032
anterior region of body1.22e-20129
craniocervical region1.22e-20129
regional part of telencephalon1.27e-2033
head2.13e-20123
tube2.30e-19194
anatomical cluster8.55e-19286
regional part of cerebral cortex3.56e-1622
epithelium8.80e-16309
cerebral cortex9.09e-1625
pallium9.09e-1625
anatomical conduit1.85e-15241
cell layer4.62e-15312
neocortex5.19e-1520
multi-tissue structure1.26e-14347
multi-cellular organism6.31e-14659
organ part2.87e-13219
organism subdivision6.24e-13365
anatomical system8.95e-13625
anatomical group1.36e-12626
embryo2.92e-12612
embryonic structure4.08e-11605
developing anatomical structure4.08e-11605
organ9.22e-11511
germ layer1.02e-10604
embryonic tissue1.02e-10604
presumptive structure1.02e-10604
epiblast (generic)1.02e-10604
posterior neural tube1.96e-0815
chordal neural plate1.96e-0815
primary circulatory organ6.35e-0827
segmental subdivision of nervous system3.20e-0713
nucleus of brain3.24e-079
neural nucleus3.24e-079
basal ganglion4.52e-079
nuclear complex of neuraxis4.52e-079
aggregate regional part of brain4.52e-079
collection of basal ganglia4.52e-079
cerebral subcortex4.52e-079
primordium5.23e-07168
segmental subdivision of hindbrain5.48e-0712
hindbrain5.48e-0712
presumptive hindbrain5.48e-0712


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
E2F6#187655.017155731697390.0003144978599297790.00322428997675529
TAF1#687253.343046285745290.002394600090870310.0135117855578586
USF1#739156.361499277207969.59569864925045e-050.00136702383198618



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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