Personal tools

Coexpression cluster:C1251

From FANTOM5_SSTAR

Revision as of 13:45, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1251_adipose_heart_left_trachea_dura_cervix_bladder



Phase1 CAGE Peaks

Hg19::chr1:159174510..159174521,+p5@DARC
Hg19::chr1:159174575..159174586,+p4@DARC
Hg19::chr1:159174623..159174628,+p6@DARC
Hg19::chr1:159174649..159174700,+p1@DARC
Hg19::chr1:159174701..159174727,+p2@DARC
Hg19::chr1:159175250..159175264,+p9@DARC
Hg19::chr3:64673656..64673667,-p3@ADAMTS9


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:0006516glycoprotein catabolic process0.0273899974692192
GO:0001637G-protein chemoattractant receptor activity0.0273899974692192
GO:0004950chemokine receptor activity0.0273899974692192
GO:0019956chemokine binding0.0273899974692192



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 organism4.13e-82115
neural tube6.00e-2957
neural rod6.00e-2957
future spinal cord6.00e-2957
neural keel6.00e-2957
regional part of brain6.19e-2559
neural plate2.18e-2386
presumptive neural plate2.18e-2386
brain1.13e-2269
future brain1.13e-2269
central nervous system2.78e-2282
anterior neural tube2.79e-2142
neurectoderm2.90e-2190
regional part of forebrain1.93e-2041
forebrain1.93e-2041
future forebrain1.93e-2041
anatomical conduit2.06e-19241
regional part of nervous system6.06e-1994
nervous system6.06e-1994
anatomical cluster3.30e-18286
gray matter9.67e-1734
brain grey matter9.67e-1734
telencephalon1.79e-1634
regional part of telencephalon5.39e-1633
tube1.02e-15194
anterior region of body1.91e-15129
craniocervical region1.91e-15129
cerebral hemisphere4.31e-1532
pre-chordal neural plate5.39e-1561
head3.21e-14123
regional part of cerebral cortex5.44e-1222
cerebral cortex1.98e-1125
pallium1.98e-1125
ectoderm-derived structure2.32e-11169
neocortex1.03e-1020
ectoderm1.57e-10173
presumptive ectoderm1.57e-10173
multi-cellular organism7.70e-10659
posterior neural tube8.71e-0915
chordal neural plate8.71e-0915
epithelium1.60e-08309
anatomical system2.07e-08625
multi-tissue structure2.53e-08347
anatomical group2.67e-08626
cell layer3.90e-08312
organ6.93e-08511
brainstem1.26e-078
segmental subdivision of nervous system2.18e-0713
embryo4.56e-07612
organ part5.30e-07219
nucleus of brain5.82e-079
neural nucleus5.82e-079
basal ganglion7.02e-079
nuclear complex of neuraxis7.02e-079
aggregate regional part of brain7.02e-079
collection of basal ganglia7.02e-079
cerebral subcortex7.02e-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
GATA1#262359.685934388428894.03236593682386e-050.000738835554519206
NFKB1#479053.92004530299560.003036581424484610.0161212651175146
POLR2A#543072.147453176558070.004747636447610280.0223501646586419
REST#597868.271453185252597.89289295030691e-060.000222850999415275
TAL1#6886417.06778095853734.05034184451705e-050.000741218944979002



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.