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Coexpression cluster:C2297

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Full id: C2297_cerebellum_pituitary_insula_putamen_nucleus_parietal_caudate



Phase1 CAGE Peaks

Hg19::chr14:50159813..50159853,+p1@KLHDC1
Hg19::chr14:50159858..50159893,+p2@KLHDC1
Hg19::chr1:8585945..8586056,-p3@RERE
Hg19::chr6:163148780..163148813,-p1@PARK2


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:0008267poly-glutamine tract binding0.00529848110208407
GO:0006607NLS-bearing substrate import into nucleus0.0344340443057272



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>


Cell Type
Ontology termp-valuen
mature alpha-beta T cell4.73e-0718
alpha-beta T cell4.73e-0718
immature T cell4.73e-0718
mature T cell4.73e-0718
immature alpha-beta T cell4.73e-0718
Uber Anatomy
Ontology termp-valuen
adult organism1.20e-48114
neural tube2.12e-2856
neural rod2.12e-2856
future spinal cord2.12e-2856
neural keel2.12e-2856
regional part of nervous system7.23e-2753
regional part of brain7.23e-2753
brain1.53e-2368
future brain1.53e-2368
nervous system2.22e-2289
central nervous system2.68e-2281
regional part of forebrain6.21e-2241
forebrain6.21e-2241
anterior neural tube6.21e-2241
future forebrain6.21e-2241
neural plate6.18e-2182
presumptive neural plate6.18e-2182
neurectoderm1.57e-2086
telencephalon5.89e-1834
brain grey matter1.08e-1734
gray matter1.08e-1734
cerebral hemisphere9.90e-1732
regional part of telencephalon1.18e-1632
regional part of cerebral cortex1.31e-1422
pre-chordal neural plate2.43e-1461
structure with developmental contribution from neural crest1.58e-13132
neocortex1.84e-1320
ecto-epithelium6.04e-13104
ectoderm-derived structure1.41e-12171
ectoderm1.41e-12171
presumptive ectoderm1.41e-12171
cerebral cortex2.44e-1225
pallium2.44e-1225
posterior neural tube1.21e-0715
chordal neural plate1.21e-0715
organ system subdivision2.88e-07223
basal ganglion4.39e-079
nuclear complex of neuraxis4.39e-079
aggregate regional part of brain4.39e-079
collection of basal ganglia4.39e-079
cerebral subcortex4.39e-079
neural nucleus6.08e-079
nucleus of brain6.08e-079
segmental subdivision of nervous system7.75e-0713


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
E2F6#187645.017155731697390.00157802193473060.00995812887258785
ELF1#199744.258097958807540.003041525565781240.0160690959411487
FOXA2#3170212.31523187633260.009361916285467240.035337351365713
HDAC2#3066310.06171517746970.00156372754474740.0099224825958973
HMGN3#932436.133910792512940.006640696683324720.0282872877440962
PAX5#507935.002174148383370.01196533174786410.0434826292638984
REST#597837.237521537096020.004104697304192610.0195758017148076
SIN3A#2594245.408884726815140.001168172384885160.00795168843805128
TAF1#687243.343046285745290.008005664898701650.0321615431148018
YY1#752844.911170749853860.00171871838055440.0106680868267396
ZNF263#1012736.166381227758010.006539814347975980.0279659202672998



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.