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Coexpression cluster:C1377

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Full id: C1377_skeletal_cerebellum_corpus_thalamus_heart_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr13:114144998..114145038,-p1@DCUN1D2
Hg19::chr14:77564569..77564685,+p1@KIAA1737
Hg19::chr17:42925242..42925265,+p1@HIGD1B
Hg19::chr19:17579587..17579618,+p3@SLC27A1
Hg19::chr1:202317815..202317854,+p1@PPP1R12B
Hg19::chr7:56160666..56160678,-p2@PHKG1


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:0005964phosphorylase kinase complex0.0348414601404088
GO:0004689phosphorylase kinase activity0.0348414601404088
GO:0009250glucan biosynthetic process0.0365625377286801
GO:0005978glycogen biosynthetic process0.0365625377286801
GO:0004683calmodulin-dependent protein kinase activity0.0365625377286801
GO:0006937regulation of muscle contraction0.0417359612450667
GO:0033692cellular polysaccharide biosynthetic process0.0417359612450667
GO:0000271polysaccharide biosynthetic process0.0417359612450667
GO:0005977glycogen metabolic process0.0417359612450667
GO:0006073glucan metabolic process0.0417359612450667
GO:0006112energy reserve metabolic process0.0434615205705794



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 organism5.25e-49115
neural tube8.69e-2957
neural rod8.69e-2957
future spinal cord8.69e-2957
neural keel8.69e-2957
central nervous system3.92e-2882
regional part of nervous system8.37e-2794
nervous system8.37e-2794
brain1.08e-2569
future brain1.08e-2569
regional part of brain2.58e-2459
anterior neural tube1.56e-2342
regional part of forebrain2.83e-2341
forebrain2.83e-2341
future forebrain2.83e-2341
telencephalon1.47e-1934
gray matter1.59e-1934
brain grey matter1.59e-1934
regional part of telencephalon5.87e-1933
cerebral hemisphere2.85e-1832
neural plate1.07e-1786
presumptive neural plate1.07e-1786
neurectoderm2.44e-1790
anterior region of body1.10e-14129
craniocervical region1.10e-14129
regional part of cerebral cortex3.30e-1422
cerebral cortex4.35e-1425
pallium4.35e-1425
ectoderm-derived structure1.58e-13169
ectoderm1.69e-13173
presumptive ectoderm1.69e-13173
head2.38e-13123
neocortex5.07e-1320
pre-chordal neural plate8.87e-1361
nucleus of brain6.00e-079
neural nucleus6.00e-079
basal ganglion7.07e-079
nuclear complex of neuraxis7.07e-079
aggregate regional part of brain7.07e-079
collection of basal ganglia7.07e-079
cerebral subcortex7.07e-079


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#9774310.82632380506090.001772351046991060.0108883865292176
NRF1#489936.105139723855450.009090162079396740.0344036034575146
SIX5#14791238.54335767772950.003504759488012430.0177971301681592
SMARCB1#659839.126357890578710.002900247150367020.0156763747095115
ZNF143#770236.750438276113950.006850259204468580.0290378367178949



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.