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Coexpression cluster:C2485

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Full id: C2485_pineal_cerebellum_pituitary_parietal_occipital_CD4_duodenum



Phase1 CAGE Peaks

Hg19::chr19:36980429..36980448,-p1@ZNF566
Hg19::chr19:38270215..38270251,-p1@ZNF573
Hg19::chr19:40562072..40562143,-p1@ZNF780B
Hg19::chr5:179285785..179285846,-p1@C5orf45


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
1.00202116011964e-050.006342793943557343390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent0.00519923459098235
GO:0006351transcription, DNA-dependent0.00519923459098235
GO:0032774RNA biosynthetic process0.00519923459098235
GO:0003677DNA binding0.00519923459098235
GO:0045449regulation of transcription0.00519923459098235
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00519923459098235
GO:0006350transcription0.00519923459098235
GO:0010468regulation of gene expression0.00519923459098235
GO:0031323regulation of cellular metabolic process0.00519923459098235
GO:0019222regulation of metabolic process0.00519923459098235
GO:0016070RNA metabolic process0.00519923459098235
GO:0008270zinc ion binding0.00519923459098235
GO:0046914transition metal ion binding0.00784871922371737
GO:0010467gene expression0.0100445935106716
GO:0050794regulation of cellular process0.0107243941177873
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0108351071276006
GO:0005634nucleus0.011147418527857
GO:0050789regulation of biological process0.011147418527857
GO:0003676nucleic acid binding0.0118316479005403
GO:0043169cation binding0.0118867181787075
GO:0065007biological regulation0.0125886689188592
GO:0046872metal ion binding0.0126208906693392
GO:0043167ion binding0.0126967359708667
GO:0043283biopolymer metabolic process0.0180817341916611
GO:0043231intracellular membrane-bound organelle0.0229336055866812
GO:0043227membrane-bound organelle0.0229336055866812
GO:0043229intracellular organelle0.0386616181848527
GO:0043226organelle0.0386616181848527
GO:0043170macromolecule metabolic process0.0413773157609536



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
lymphocyte8.83e-0753
common lymphoid progenitor8.83e-0753
Uber Anatomy
Ontology termp-valuen
adult organism3.64e-38115
central nervous system1.85e-2682
neural tube1.93e-2657
neural rod1.93e-2657
future spinal cord1.93e-2657
neural keel1.93e-2657
regional part of nervous system1.21e-2594
nervous system1.21e-2594
regional part of forebrain8.40e-2341
forebrain8.40e-2341
future forebrain8.40e-2341
brain1.74e-2269
future brain1.74e-2269
anterior neural tube9.01e-2242
regional part of brain9.45e-2259
neurectoderm8.34e-2090
neural plate4.04e-1986
presumptive neural plate4.04e-1986
telencephalon8.58e-1934
gray matter1.32e-1834
brain grey matter1.32e-1834
regional part of telencephalon2.88e-1833
cerebral hemisphere1.20e-1732
pre-chordal neural plate3.55e-1461
regional part of cerebral cortex3.60e-1422
cerebral cortex6.92e-1425
pallium6.92e-1425
neocortex4.98e-1320
ectoderm9.93e-13173
presumptive ectoderm9.93e-13173
anterior region of body1.27e-12129
craniocervical region1.27e-12129
ectoderm-derived structure4.28e-12169
head2.59e-11123


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#187645.017155731697390.00157802193473060.00996957430532508
GABPB1#255335.300762877136630.01012678824234270.0378604488005023
HEY1#2346244.040111043105710.00375304636917980.0186082610022204
NR2C2#7182216.30730545262040.005411825344648220.0245538740679315
SETDB1#9869220.16001308900520.00356908685407640.018086848559022
SIX5#147912312.81503651659420.0007664471136930380.006016307411273
TAF1#687243.343046285745290.008005664898701650.0322272446945537
TAF7#687938.574802053692940.00250055433515240.0140330679317024
TBP#690843.706770687096390.005296377814784350.0244258766492212
ZNF143#7702413.50087655222793.00867915035614e-050.000621117694769806
ZNF263#1012736.166381227758010.006539814347975980.0279750837881738



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.