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Coexpression cluster:C2536

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Full id: C2536_cervix_occipital_breast_parietal_uterus_smooth_temporal



Phase1 CAGE Peaks

Hg19::chr1:164528340..164528379,+p4@PBX1
Hg19::chr1:164528384..164528409,+p3@PBX1
Hg19::chr1:164528410..164528428,+p1@PBX1
Hg19::chr1:164528445..164528459,+p2@PBX1


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


No GOStat results

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 organism3.18e-37114
organ system subdivision4.85e-26223
central nervous system3.48e-2581
nervous system2.13e-2389
anatomical cluster3.30e-23373
multi-tissue structure2.49e-22342
brain3.75e-2168
future brain3.75e-2168
ectoderm-derived structure4.04e-21171
ectoderm4.04e-21171
presumptive ectoderm4.04e-21171
neurectoderm6.03e-2186
neural plate9.00e-2182
presumptive neural plate9.00e-2182
neural tube1.11e-2056
neural rod1.11e-2056
future spinal cord1.11e-2056
neural keel1.11e-2056
regional part of nervous system1.47e-1953
regional part of brain1.47e-1953
regional part of forebrain3.08e-1841
forebrain3.08e-1841
anterior neural tube3.08e-1841
future forebrain3.08e-1841
structure with developmental contribution from neural crest6.57e-18132
multi-cellular organism3.04e-17656
pre-chordal neural plate9.92e-1761
telencephalon2.38e-1634
cerebral hemisphere4.63e-1632
brain grey matter1.11e-1534
gray matter1.11e-1534
regional part of telencephalon1.56e-1532
ecto-epithelium9.76e-15104
organ part1.22e-14218
cerebral cortex4.75e-1425
pallium4.75e-1425
regional part of cerebral cortex1.57e-1322
neocortex1.01e-1220
germ layer6.22e-12560
germ layer / neural crest6.22e-12560
embryonic tissue6.22e-12560
presumptive structure6.22e-12560
germ layer / neural crest derived structure6.22e-12560
epiblast (generic)6.22e-12560
anatomical group6.72e-12625
anatomical conduit7.03e-12240
anatomical system8.90e-12624
embryonic structure1.36e-11564
cell layer1.89e-11309
organ2.04e-11503
epithelium2.78e-11306
embryo1.36e-10592
developing anatomical structure2.98e-10581
tube3.17e-10192
subdivision of digestive tract8.25e-07118


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
CEBPB#105147.971147625824820.0002476385788090830.00268178406597281
GATA2#2624412.7449317335543.78864877853583e-050.000722048703980846
GTF2F1#2962412.73966087675773.79492332235515e-050.000718524287279641
IRF1#365947.63716375356390.0002938853996185490.00307638541152266
MXI1#460149.96157162875930.0001015224754950450.00142435596698374
NFYA#4800418.42558069983058.67100748407158e-060.000234487661996104
NFYB#4801416.75979325353651.26678572070404e-050.000311444995020267
PBX3#5090421.91451268674414.33289161192893e-060.000136466485843862
RAD21#5885410.35503389545638.6948481184721e-050.00129430051688299
SP2#6668426.15353049384462.13562021071447e-067.74720525136537e-05
TAF1#687243.343046285745290.008005664898701650.0322384282381146
TAF7#687938.574802053692940.00250055433515240.0140353304782599
TBP#690843.706770687096390.005296377814784350.0244355878693406
ZNF263#1012748.221841637010680.0002187871180958320.00248963911819684



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.