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Coexpression cluster:C2222: Difference between revisions

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}}
}}

Revision as of 15:22, 26 November 2012


Full id: C2222_caudate_globus_thalamus_medial_amygdala_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr12:57674546..57674557,-p25@R3HDM2
Hg19::chr1:33360074..33360107,+p1@BC127891
Hg19::chr6:12757225..12757236,+p@chr6:12757225..12757236
+
Hg19::chr6:12955443..12955446,+p@chr6:12955443..12955446
+


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
regional part of forebrain7.79e-6641
forebrain7.79e-6641
anterior neural tube7.79e-6641
future forebrain7.79e-6641
cerebral hemisphere1.81e-6432
brain grey matter9.76e-6134
gray matter9.76e-6134
telencephalon1.65e-6034
regional part of nervous system5.97e-5953
regional part of brain5.97e-5953
regional part of telencephalon1.42e-5832
neural tube1.52e-5556
neural rod1.52e-5556
future spinal cord1.52e-5556
neural keel1.52e-5556
brain7.29e-4868
future brain7.29e-4868
nervous system8.15e-4489
pre-chordal neural plate7.68e-4361
central nervous system1.26e-4281
neural plate2.51e-3682
presumptive neural plate2.51e-3682
cerebral cortex8.45e-3625
pallium8.45e-3625
regional part of cerebral cortex2.56e-3522
neurectoderm2.18e-3486
neocortex4.99e-3320
basal ganglion2.38e-289
nuclear complex of neuraxis2.38e-289
aggregate regional part of brain2.38e-289
collection of basal ganglia2.38e-289
cerebral subcortex2.38e-289
neural nucleus4.35e-289
nucleus of brain4.35e-289
ecto-epithelium1.70e-27104
telencephalic nucleus4.27e-277
adult organism8.99e-23114
structure with developmental contribution from neural crest2.21e-22132
corpus striatum1.16e-214
striatum1.16e-214
ventral part of telencephalon1.16e-214
future corpus striatum1.16e-214
gyrus2.83e-216
ectoderm-derived structure3.90e-20171
ectoderm3.90e-20171
presumptive ectoderm3.90e-20171
organ system subdivision8.92e-18223
caudate-putamen8.40e-173
dorsal striatum8.40e-173
tube8.88e-15192
temporal lobe4.56e-126
globus pallidus8.17e-122
pallidum8.17e-122
caudate nucleus9.57e-122
future caudate nucleus9.57e-122
middle temporal gyrus1.53e-112
anatomical conduit1.27e-10240
limbic system4.02e-105
parietal lobe6.74e-105
organ part4.56e-09218
frontal cortex5.54e-083
anatomical cluster5.84e-08373
epithelium8.29e-08306
cell layer1.13e-07309
diencephalon2.51e-077
future diencephalon2.51e-077
multi-tissue structure4.96e-07342
putamen9.30e-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)

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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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