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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1684_serous_gall_rectal_colon_chorionic_adult_non
|full_id=C1684_serous_gall_rectal_colon_chorionic_adult_non
|id=C1684
|id=C1684

Revision as of 14:16, 12 September 2012


Full id: C1684_serous_gall_rectal_colon_chorionic_adult_non



Phase1 CAGE Peaks

Hg19::chr12:71148228..71148248,-p6@PTPRR
Hg19::chr12:71148329..71148334,-p15@PTPRR
Hg19::chr12:71148357..71148369,-p7@PTPRR
Hg19::chr12:71148381..71148405,-p3@PTPRR
Hg19::chr12:71148413..71148422,-p11@PTPRR


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism5.79e-33115
neural tube9.61e-3157
neural rod9.61e-3157
future spinal cord9.61e-3157
neural keel9.61e-3157
regional part of forebrain1.63e-2641
forebrain1.63e-2641
future forebrain1.63e-2641
regional part of brain7.10e-2659
anterior neural tube1.23e-2542
gray matter1.50e-2234
brain grey matter1.50e-2234
brain1.78e-2269
future brain1.78e-2269
central nervous system1.37e-2182
cerebral hemisphere1.85e-2132
telencephalon2.88e-2134
regional part of telencephalon3.29e-2033
regional part of cerebral cortex9.74e-2022
regional part of nervous system1.32e-1894
nervous system1.32e-1894
neural plate6.97e-1886
presumptive neural plate6.97e-1886
neocortex1.64e-1720
neurectoderm2.10e-1790
cerebral cortex1.06e-1625
pallium1.06e-1625
pre-chordal neural plate1.69e-1561
head2.16e-10123
anterior region of body6.80e-10129
craniocervical region6.80e-10129
organ8.28e-09511
multi-tissue structure3.24e-08347
temporal lobe5.11e-087
tube6.37e-08194
basal ganglion7.69e-089
nuclear complex of neuraxis7.69e-089
aggregate regional part of brain7.69e-089
collection of basal ganglia7.69e-089
cerebral subcortex7.69e-089
anatomical conduit1.15e-07241
ectoderm-derived structure1.20e-07169
ectoderm1.29e-07173
presumptive ectoderm1.29e-07173
nucleus of brain2.62e-079
neural nucleus2.62e-079
organ part2.66e-07219
occipital lobe3.30e-075
limbic system6.92e-075
gastrointestinal system8.61e-0735
Disease
Ontology termp-valuen
carcinoma7.64e-08106
adenocarcinoma4.31e-0725


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
REST#597859.650028716128021.19441074361324e-050.000301384546151783
TAL1#6886423.89489334195226.10828383356726e-060.000181543271284556



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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