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Coexpression cluster:C2627: Difference between revisions

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|tf_chipseq_enrich=PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444272336661611!REST#5978;4:9.65002871612802:0.000115282561421917:0.001572211469358!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797038973704977!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.82068742356338e-06
|tf_chipseq_enrich=PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444272336661611!REST#5978;4:9.65002871612802:0.000115282561421917:0.001572211469358!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797038973704977!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.82068742356338e-06
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}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2627_biphenotypic_acute_putamen_caudate_Dendritic_hippocampus_amygdala



Phase1 CAGE Peaks

Hg19::chr20:9495176..9495191,+p11@LAMP5
Hg19::chr20:9495194..9495205,+p7@LAMP5
Hg19::chr20:9495209..9495256,+p1@LAMP5
Hg19::chr20:9495263..9495313,+p3@LAMP5


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 tube2.79e-5456
neural rod2.79e-5456
future spinal cord2.79e-5456
neural keel2.79e-5456
regional part of nervous system1.41e-5053
regional part of brain1.41e-5053
adult organism1.12e-43114
central nervous system4.76e-4381
brain2.61e-4268
future brain2.61e-4268
nervous system1.67e-4089
neural plate3.21e-3682
presumptive neural plate3.21e-3682
regional part of forebrain5.61e-3641
forebrain5.61e-3641
anterior neural tube5.61e-3641
future forebrain5.61e-3641
neurectoderm1.02e-3386
cerebral hemisphere2.13e-3332
brain grey matter3.31e-3334
gray matter3.31e-3334
telencephalon3.56e-3334
regional part of telencephalon8.02e-3132
regional part of cerebral cortex8.37e-2622
ecto-epithelium6.59e-25104
cerebral cortex5.89e-2425
pallium5.89e-2425
pre-chordal neural plate3.30e-2361
neocortex4.00e-2320
organ system subdivision3.12e-22223
ectoderm-derived structure3.76e-20171
ectoderm3.76e-20171
presumptive ectoderm3.76e-20171
structure with developmental contribution from neural crest8.11e-20132
posterior neural tube3.24e-1915
chordal neural plate3.24e-1915
segmental subdivision of hindbrain1.02e-1512
hindbrain1.02e-1512
presumptive hindbrain1.02e-1512
segmental subdivision of nervous system3.07e-1413
regional part of metencephalon6.54e-129
metencephalon6.54e-129
future metencephalon6.54e-129
basal ganglion3.84e-119
nuclear complex of neuraxis3.84e-119
aggregate regional part of brain3.84e-119
collection of basal ganglia3.84e-119
cerebral subcortex3.84e-119
neural nucleus1.18e-109
nucleus of brain1.18e-109
anatomical cluster2.20e-10373
gyrus1.21e-096
brainstem2.67e-096
limbic system1.25e-085
anatomical conduit1.53e-08240
tube2.14e-08192
telencephalic nucleus2.53e-087
cerebellum4.34e-086
rhombic lip4.34e-086
parietal lobe7.25e-085
temporal lobe7.44e-086
corpus striatum1.72e-074
striatum1.72e-074
ventral part of telencephalon1.72e-074
future corpus striatum1.72e-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
PAX5#507946.669565531177830.0005052774169483260.00444272336661611
REST#597849.650028716128020.0001152825614219170.001572211469358
SIN3A#2594245.408884726815140.001168172384885160.00797038973704977
SUZ12#23512450.11578091106291.5827390373096e-078.82068742356338e-06



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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