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Coexpression cluster:C4768: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281532561282846
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281532561282846
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}}
}}

Revision as of 16:57, 26 November 2012


Full id: C4768_lung_parietal_cerebellum_occipital_temporal_duodenum_medulla



Phase1 CAGE Peaks

Hg19::chr8:69242969..69242990,+p3@C8orf34
Hg19::chr8:69243002..69243020,+p2@C8orf34
Hg19::chr8:69243028..69243043,+p4@C8orf34


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
neural tube3.42e-6056
neural rod3.42e-6056
future spinal cord3.42e-6056
neural keel3.42e-6056
adult organism7.21e-58114
regional part of nervous system1.26e-5553
regional part of brain1.26e-5553
central nervous system3.81e-5281
brain3.49e-4668
future brain3.49e-4668
nervous system2.84e-4589
regional part of forebrain2.31e-4441
forebrain2.31e-4441
anterior neural tube2.31e-4441
future forebrain2.31e-4441
neural plate6.24e-4282
presumptive neural plate6.24e-4282
neurectoderm3.04e-3986
brain grey matter1.04e-3634
gray matter1.04e-3634
telencephalon1.38e-3634
cerebral hemisphere1.53e-3332
regional part of telencephalon1.71e-3332
ecto-epithelium1.54e-32104
regional part of cerebral cortex5.07e-3022
pre-chordal neural plate5.47e-2861
structure with developmental contribution from neural crest7.44e-27132
neocortex7.56e-2720
cerebral cortex9.30e-2625
pallium9.30e-2625
ectoderm-derived structure2.69e-22171
ectoderm2.69e-22171
presumptive ectoderm2.69e-22171
tube5.22e-17192
organ system subdivision2.02e-16223
posterior neural tube2.54e-1615
chordal neural plate2.54e-1615
neural nucleus2.14e-129
nucleus of brain2.14e-129
basal ganglion2.77e-129
nuclear complex of neuraxis2.77e-129
aggregate regional part of brain2.77e-129
collection of basal ganglia2.77e-129
cerebral subcortex2.77e-129
anatomical conduit3.35e-12240
segmental subdivision of hindbrain4.19e-1212
hindbrain4.19e-1212
presumptive hindbrain4.19e-1212
brainstem7.92e-126
segmental subdivision of nervous system5.41e-1113
gyrus2.17e-106
anatomical cluster5.97e-10373
limbic system1.33e-095
telencephalic nucleus3.42e-097
parietal lobe3.71e-095
diencephalon4.70e-097
future diencephalon4.70e-097
temporal lobe5.06e-096
corpus striatum2.31e-084
striatum2.31e-084
ventral part of telencephalon2.31e-084
future corpus striatum2.31e-084
epithelium2.37e-08306
cell layer4.09e-08309
regional part of metencephalon1.73e-079
metencephalon1.73e-079
future metencephalon1.73e-079
organ part1.86e-07218
multi-tissue structure1.99e-07342
medulla oblongata8.17e-073
myelencephalon8.17e-073
future myelencephalon8.17e-073
caudate-putamen9.48e-073
dorsal striatum9.48e-073


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
CTCF#1066435.360256373075030.0064925092527670.0281532561282846



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.