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Coexpression cluster:C4507: Difference between revisions

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|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770523287662626
|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770523287662626
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}}
}}

Revision as of 16:47, 26 November 2012


Full id: C4507_large_thalamus_small_pituitary_medial_Mast_locus



Phase1 CAGE Peaks

Hg19::chr5:57877892..57877903,+p6@RAB3C
Hg19::chr5:57877953..57877971,+p5@RAB3C
Hg19::chr5:57877973..57878025,+p2@RAB3C


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>

Uber Anatomy
Ontology termp-valuen
neural tube2.18e-6056
neural rod2.18e-6056
future spinal cord2.18e-6056
neural keel2.18e-6056
regional part of nervous system5.21e-5653
regional part of brain5.21e-5653
adult organism5.27e-55114
central nervous system1.22e-5081
nervous system1.15e-4889
regional part of forebrain2.01e-4841
forebrain2.01e-4841
anterior neural tube2.01e-4841
future forebrain2.01e-4841
brain3.49e-4568
future brain3.49e-4568
neural plate2.61e-4082
presumptive neural plate2.61e-4082
brain grey matter2.26e-3934
gray matter2.26e-3934
neurectoderm5.05e-3986
telencephalon8.47e-3934
cerebral hemisphere9.26e-3732
regional part of telencephalon1.85e-3632
regional part of cerebral cortex4.48e-3222
pre-chordal neural plate2.60e-3161
neocortex2.43e-2920
ecto-epithelium3.62e-29104
cerebral cortex2.14e-2725
pallium2.14e-2725
organ system subdivision1.06e-23223
structure with developmental contribution from neural crest3.43e-23132
ectoderm-derived structure6.88e-20171
ectoderm6.88e-20171
presumptive ectoderm6.88e-20171
tube2.36e-18192
anatomical conduit2.79e-14240
neural nucleus1.99e-139
nucleus of brain1.99e-139
basal ganglion2.33e-139
nuclear complex of neuraxis2.33e-139
aggregate regional part of brain2.33e-139
collection of basal ganglia2.33e-139
cerebral subcortex2.33e-139
posterior neural tube6.92e-1315
chordal neural plate6.92e-1315
anatomical cluster2.09e-12373
diencephalon6.08e-117
future diencephalon6.08e-117
temporal lobe9.73e-116
telencephalic nucleus1.44e-107
brainstem1.01e-096
gyrus1.51e-096
segmental subdivision of hindbrain4.53e-0912
hindbrain4.53e-0912
presumptive hindbrain4.53e-0912
parietal lobe1.69e-085
limbic system2.08e-085
segmental subdivision of nervous system3.37e-0813
occipital lobe8.74e-085
organ part2.57e-07218
corpus striatum3.89e-074
striatum3.89e-074
ventral part of telencephalon3.89e-074
future corpus striatum3.89e-074
gland of diencephalon5.42e-074
neuroendocrine gland5.42e-074


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#597839.650028716128020.001112636247114590.00770523287662626



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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