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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4082_caudate_testicular_putamen_nonsmall_globus_nucleus_diencephalon
|full_id=C4082_caudate_testicular_putamen_nonsmall_globus_nucleus_diencephalon
|id=C4082
|id=C4082

Revision as of 17:07, 12 September 2012


Full id: C4082_caudate_testicular_putamen_nonsmall_globus_nucleus_diencephalon



Phase1 CAGE Peaks

Hg19::chr21:45788894..45788919,+p7@TRPM2
Hg19::chr21:45788947..45788956,+p19@TRPM2
Hg19::chr21:45788974..45788984,+p14@TRPM2


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
germ line cell5.59e-137
germ cell5.59e-137
embryonic stem cell4.39e-105
lung fibroblast3.52e-071
Uber Anatomy
Ontology termp-valuen
regional part of forebrain1.86e-3441
forebrain1.86e-3441
future forebrain1.86e-3441
anterior neural tube1.44e-3342
basal ganglion1.53e-309
nuclear complex of neuraxis1.53e-309
aggregate regional part of brain1.53e-309
collection of basal ganglia1.53e-309
cerebral subcortex1.53e-309
neural tube3.31e-3057
neural rod3.31e-3057
future spinal cord3.31e-3057
neural keel3.31e-3057
telencephalic nucleus2.53e-297
regional part of brain4.65e-2959
brain1.10e-2669
future brain1.10e-2669
pre-chordal neural plate5.57e-2561
regional part of telencephalon7.85e-2533
telencephalon4.80e-2434
corpus striatum1.39e-234
striatum1.39e-234
ventral part of telencephalon1.39e-234
future corpus striatum1.39e-234
nucleus of brain1.10e-229
neural nucleus1.10e-229
central nervous system7.16e-2282
cerebral hemisphere7.16e-2232
neural plate5.77e-2186
presumptive neural plate5.77e-2186
gray matter1.75e-2034
brain grey matter1.75e-2034
neurectoderm7.53e-2090
regional part of nervous system2.38e-1894
nervous system2.38e-1894
caudate-putamen3.51e-183
dorsal striatum3.51e-183
head8.16e-15123
adult organism9.08e-15115
anterior region of body6.30e-14129
craniocervical region6.30e-14129
diencephalon4.50e-137
future diencephalon4.50e-137
caudate nucleus1.08e-122
future caudate nucleus1.08e-122
globus pallidus1.71e-122
pallidum1.71e-122
testis2.27e-118
limbic system1.21e-105
ectoderm-derived structure1.53e-09169
ectoderm3.18e-09173
presumptive ectoderm3.18e-09173
male reproductive organ2.72e-0811
tube5.75e-08194
regional part of cerebral cortex6.95e-0822
putamen3.32e-071
nucleus accumbens3.95e-071
ventral striatum3.95e-071
cerebral cortex6.56e-0725
pallium6.56e-0725
insula6.60e-071


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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