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Coexpression cluster:C1798: Difference between revisions

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}}
}}

Revision as of 15:06, 26 November 2012


Full id: C1798_brain_temporal_medial_postcentral_insula_parietal_occipital



Phase1 CAGE Peaks

Hg19::chr18:3874426..3874429,-p21@DLGAP1
Hg19::chr2:56410925..56410946,+p5@CCDC85A
Hg19::chr4:6565771..6565783,-p22@PPP2R2C
Hg19::chr5:149630260..149630271,+p@chr5:149630260..149630271
+
Hg19::chr6:40555176..40555188,-p6@LRFN2


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

GO IDGO nameFDR corrected p-value
GO:0000159protein phosphatase type 2A complex0.0404544285717854
GO:0008601protein phosphatase type 2A regulator activity0.0404544285717854
GO:0008287protein serine/threonine phosphatase complex0.0404544285717854
GO:0019888protein phosphatase regulator activity0.0404544285717854
GO:0019208phosphatase regulator activity0.0404544285717854



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
telencephalon5.23e-7834
cerebral hemisphere1.30e-7532
regional part of nervous system2.17e-7453
regional part of brain2.17e-7453
regional part of cerebral cortex2.69e-7222
brain8.17e-7168
future brain8.17e-7168
brain grey matter9.18e-7134
gray matter9.18e-7134
neocortex1.64e-7020
neural tube3.34e-7056
neural rod3.34e-7056
future spinal cord3.34e-7056
neural keel3.34e-7056
regional part of telencephalon2.65e-6832
regional part of forebrain2.95e-6441
forebrain2.95e-6441
anterior neural tube2.95e-6441
future forebrain2.95e-6441
cerebral cortex1.52e-6325
pallium1.52e-6325
central nervous system3.36e-6381
nervous system1.76e-5689
neural plate1.39e-4682
presumptive neural plate1.39e-4682
neurectoderm3.35e-4486
pre-chordal neural plate4.62e-4261
adult organism3.03e-38114
gyrus4.48e-366
ecto-epithelium1.01e-35104
structure with developmental contribution from neural crest2.09e-29132
ectoderm-derived structure3.21e-27171
ectoderm3.21e-27171
presumptive ectoderm3.21e-27171
organ system subdivision8.74e-23223
parietal lobe7.57e-205
occipital lobe1.28e-195
frontal cortex7.15e-193
tube5.34e-17192
brainstem3.11e-156
temporal lobe4.30e-146
corpus striatum1.98e-134
striatum1.98e-134
ventral part of telencephalon1.98e-134
future corpus striatum1.98e-134
middle frontal gyrus3.25e-132
organ part4.69e-13218
middle temporal gyrus5.28e-132
anatomical conduit1.55e-12240
segmental subdivision of hindbrain1.49e-1112
hindbrain1.49e-1112
presumptive hindbrain1.49e-1112
anatomical cluster2.36e-11373
limbic system4.32e-115
segmental subdivision of nervous system1.19e-1013
basal ganglion1.86e-109
nuclear complex of neuraxis1.86e-109
aggregate regional part of brain1.86e-109
collection of basal ganglia1.86e-109
cerebral subcortex1.86e-109
neural nucleus2.52e-109
nucleus of brain2.52e-109
posterior neural tube3.30e-0915
chordal neural plate3.30e-0915
multi-tissue structure7.51e-09342
epithelium1.12e-08306
cell layer1.54e-08309
medulla oblongata1.69e-083
caudate-putamen1.69e-083
myelencephalon1.69e-083
dorsal striatum1.69e-083
future myelencephalon1.69e-083
pons2.04e-083
telencephalic nucleus6.89e-087
postcentral gyrus1.20e-071
occipital pole1.27e-071
pole of cerebral hemisphere1.27e-071
insula1.54e-071
paracentral gyrus1.85e-071
olfactory region3.85e-071
primary subdivision of skull3.85e-071
cranium3.85e-071
neurocranium3.85e-071
chondrocranium3.85e-071
cartilaginous neurocranium3.85e-071
head paraxial mesoderm3.85e-071
nucleus accumbens4.08e-071
ventral striatum4.08e-071
putamen4.89e-071
corpus callosum5.19e-071
central nervous system cell part cluster5.19e-071
axon tract5.19e-071
intercerebral commissure5.19e-071
dorsal telencephalic commissure5.19e-071
brain white matter5.19e-071
brain commissure5.19e-071
white matter5.19e-071
nervous system commissure5.19e-071
cerebral hemisphere white matter5.19e-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)

{{{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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