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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2693_anaplastic_nonsmall_bronchogenic_ovary_small_medulloblastoma_glassy
|full_id=C2693_anaplastic_nonsmall_bronchogenic_ovary_small_medulloblastoma_glassy
|id=C2693
|id=C2693

Revision as of 15:27, 12 September 2012


Full id: C2693_anaplastic_nonsmall_bronchogenic_ovary_small_medulloblastoma_glassy



Phase1 CAGE Peaks

Hg19::chr2:233352519..233352525,-p3@ECEL1
Hg19::chr2:233352531..233352550,-p1@ECEL1
Hg19::chr2:233352555..233352566,-p2@ECEL1
Hg19::chr2:233352573..233352580,-p4@ECEL1


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>

Cell Type
Ontology termp-valuen
embryonic stem cell2.53e-085
Uber Anatomy
Ontology termp-valuen
adult organism3.75e-30115
central nervous system2.73e-2282
neural tube1.85e-2157
neural rod1.85e-2157
future spinal cord1.85e-2157
neural keel1.85e-2157
regional part of nervous system8.72e-2194
nervous system8.72e-2194
neural plate2.75e-1986
presumptive neural plate2.75e-1986
neurectoderm6.24e-1990
regional part of brain3.86e-1659
brain2.74e-1569
future brain2.74e-1569
regional part of forebrain4.95e-1441
forebrain4.95e-1441
future forebrain4.95e-1441
anterior neural tube1.60e-1342
pre-chordal neural plate1.28e-1061
diencephalon1.63e-107
future diencephalon1.63e-107
posterior neural tube1.23e-0915
chordal neural plate1.23e-0915
nucleus of brain1.33e-099
neural nucleus1.33e-099
ectoderm1.46e-09173
presumptive ectoderm1.46e-09173
ectoderm-derived structure1.58e-09169
organ segment8.62e-0997
organ2.00e-08511
gray matter2.62e-0834
brain grey matter2.62e-0834
embryo5.22e-08612
telencephalon7.14e-0834
organ part1.07e-07219
segmental subdivision of nervous system1.26e-0713
cerebral hemisphere1.36e-0732
regional part of telencephalon2.38e-0733
telencephalic nucleus4.03e-077
basal ganglion5.38e-079
nuclear complex of neuraxis5.38e-079
aggregate regional part of brain5.38e-079
collection of basal ganglia5.38e-079
cerebral subcortex5.38e-079
anterior region of body6.79e-07129
craniocervical region6.79e-07129
gland of diencephalon7.09e-074
neuroendocrine gland7.09e-074
head8.21e-07123


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
SUZ12#23512450.11578091106291.5827390373096e-078.83011123491334e-06



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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