Personal tools

Coexpression cluster:C3045

From FANTOM5_SSTAR

Revision as of 15:54, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr10:75255724..75255792,-p1@PPP3CB
Hg19::chr2:86790580..86790591,-p4@CHMP3
p4@RNF103-CHMP3
Hg19::chr5:171433662..171433686,-p2@FBXW11


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


p.valueFDRnGenesnPathwayName
1.58091305570944e-050.008797648614571242114Oocyte meiosis (KEGG):04114
2.77966780871129e-050.008797648614571242151Wnt signaling pathway (KEGG):04310



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:0005955calcineurin complex0.0134222261032357
GO:0008287protein serine/threonine phosphatase complex0.03969244056313
GO:0004722protein serine/threonine phosphatase activity0.03969244056313
GO:0016567protein ubiquitination0.03969244056313
GO:0043687post-translational protein modification0.03969244056313
GO:0032446protein modification by small protein conjugation0.03969244056313
GO:0000151ubiquitin ligase complex0.03969244056313
GO:0006464protein modification process0.03969244056313
GO:0043412biopolymer modification0.03969244056313
GO:0043234protein complex0.03969244056313
GO:0005516calmodulin binding0.03969244056313
GO:0016055Wnt receptor signaling pathway0.03969244056313
GO:0004842ubiquitin-protein ligase activity0.03969244056313
GO:0008639small protein conjugating enzyme activity0.03969244056313
GO:0032991macromolecular complex0.0485798812421496
GO:0019787small conjugating protein ligase activity0.0485798812421496
GO:0006470protein amino acid dephosphorylation0.0485798812421496



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
adult organism2.02e-29115
neural tube4.17e-2957
neural rod4.17e-2957
future spinal cord4.17e-2957
neural keel4.17e-2957
central nervous system3.25e-2582
regional part of brain4.66e-2559
regional part of nervous system4.98e-2594
nervous system4.98e-2594
brain1.44e-2369
future brain1.44e-2369
neural plate3.48e-2386
presumptive neural plate3.48e-2386
neurectoderm3.51e-2390
anterior neural tube1.92e-2242
regional part of forebrain4.72e-2241
forebrain4.72e-2241
future forebrain4.72e-2241
gray matter1.50e-1834
brain grey matter1.50e-1834
ectoderm1.93e-18173
presumptive ectoderm1.93e-18173
telencephalon2.48e-1834
ectoderm-derived structure3.65e-18169
regional part of telencephalon9.61e-1833
cerebral hemisphere1.36e-1732
head7.94e-17123
anterior region of body1.66e-16129
craniocervical region1.66e-16129
pre-chordal neural plate4.49e-1661
organism subdivision1.20e-15365
regional part of cerebral cortex2.61e-1522
neocortex5.10e-1420
tube6.50e-14194
cerebral cortex2.05e-1325
pallium2.05e-1325
anatomical conduit3.51e-13241
anatomical cluster2.78e-11286
multi-tissue structure1.01e-10347
cell layer1.23e-10312
epithelium1.42e-10309
posterior neural tube8.23e-0815
chordal neural plate8.23e-0815
multi-cellular organism3.85e-07659
basal ganglion8.05e-079
nuclear complex of neuraxis8.05e-079
aggregate regional part of brain8.05e-079
collection of basal ganglia8.05e-079
cerebral subcortex8.05e-079
organ part9.09e-07219


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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013882993095627
EGR1#195834.988179094810140.008056488137383440.031899441353459
ELK4#2005210.8237877723120.01091284719516480.0401722480073249
FAM48A#555781385.056250.002594789661407470.014348347405503
IRF1#365937.63716375356390.002244692747297240.0127589782211264
JUND#372736.994663941871030.002921845042734990.0156129227126221
MAX#414936.452555509007120.003721913834265510.0185667252071482
MEF2A#4205212.4954872730960.008235029478029740.0324709572113092
MYC#460935.22228187160940.007020843755740150.0293159243965195
NFKB1#479035.488063424193840.006049381815655430.0268527451311305
NRF1#4899312.21027944771090.0005492172401020010.00469276767888513
PAX5#507936.669565531177830.003370290999677260.0172223222289507
POU2F2#545239.106124057742520.001324165192682130.00879344366748451
SIX5#147912211.3911435703060.009873820081429030.0370566298506672
STAT1#6772213.80439166479950.006770931708444080.0287424028247852



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.