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Coexpression cluster:C3951: Difference between revisions

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}}
}}

Revision as of 16:27, 26 November 2012


Full id: C3951_caudate_putamen_mucinous_large_clear_nucleus_bile



Phase1 CAGE Peaks

Hg19::chr1:234040407..234040525,+p2@SLC35F3
Hg19::chr1:234070964..234070965,+p@chr1:234070964..234070965
+
Hg19::chr1:234149057..234149066,+p@chr1:234149057..234149066
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.72e-09253
Uber Anatomy
Ontology termp-valuen
neural tube4.09e-3856
neural rod4.09e-3856
future spinal cord4.09e-3856
neural keel4.09e-3856
regional part of nervous system2.56e-3753
regional part of brain2.56e-3753
regional part of forebrain5.32e-3141
forebrain5.32e-3141
anterior neural tube5.32e-3141
future forebrain5.32e-3141
central nervous system9.22e-3181
brain2.49e-3068
future brain2.49e-3068
telencephalon5.31e-3034
brain grey matter7.62e-3034
gray matter7.62e-3034
cerebral hemisphere1.19e-2832
nervous system1.49e-2889
regional part of telencephalon3.21e-2832
neural plate5.32e-2682
presumptive neural plate5.32e-2682
neurectoderm4.68e-2486
organ system subdivision1.59e-23223
ecto-epithelium1.64e-23104
pre-chordal neural plate4.96e-2261
cerebral cortex1.61e-1925
pallium1.61e-1925
structure with developmental contribution from neural crest4.08e-19132
ectoderm-derived structure3.88e-16171
ectoderm3.88e-16171
presumptive ectoderm3.88e-16171
regional part of cerebral cortex5.04e-1622
neocortex5.34e-1620
adult organism1.73e-15114
anatomical cluster1.76e-14373
organ part2.06e-13218
multi-tissue structure2.64e-13342
neural nucleus3.88e-129
nucleus of brain3.88e-129
telencephalic nucleus1.11e-107
basal ganglion2.09e-109
nuclear complex of neuraxis2.09e-109
aggregate regional part of brain2.09e-109
collection of basal ganglia2.09e-109
cerebral subcortex2.09e-109
tube6.01e-10192
anatomical conduit7.20e-10240
organ1.56e-09503
gyrus1.06e-086
embryo1.69e-08592
posterior neural tube2.22e-0815
chordal neural plate2.22e-0815
larynx3.11e-089
developing anatomical structure1.03e-07581
segmental subdivision of hindbrain1.43e-0712
hindbrain1.43e-0712
presumptive hindbrain1.43e-0712
epithelium1.69e-07306
parietal lobe1.94e-075
corpus striatum2.69e-074
striatum2.69e-074
ventral part of telencephalon2.69e-074
future corpus striatum2.69e-074
cell layer3.03e-07309
brainstem5.30e-076
segmental subdivision of nervous system7.87e-0713
embryonic structure8.95e-07564
Disease
Ontology termp-valuen
carcinoma2.11e-15106
cell type cancer1.74e-12143


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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