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Coexpression cluster:C2380

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Full id: C2380_Melanocyte_mesothelioma_Renal_Neural_renal_Endothelial_Hepatic



Phase1 CAGE Peaks

Hg19::chr16:57662515..57662526,+p8@GPR56
Hg19::chr16:57662527..57662556,+p1@GPR56
Hg19::chr16:57662566..57662582,+p6@GPR56
Hg19::chr16:57662596..57662613,+p2@GPR56


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.26e-29114
neural plate3.98e-2282
presumptive neural plate3.98e-2282
neural tube3.61e-2156
neural rod3.61e-2156
future spinal cord3.61e-2156
neural keel3.61e-2156
central nervous system1.04e-1981
regional part of nervous system1.12e-1953
regional part of brain1.12e-1953
anatomical cluster3.46e-19373
tube5.82e-19192
anatomical conduit6.35e-19240
neurectoderm8.98e-1986
brain2.98e-1868
future brain2.98e-1868
structure with developmental contribution from neural crest4.02e-17132
ecto-epithelium2.15e-16104
nervous system7.18e-1689
pre-chordal neural plate7.25e-1661
regional part of forebrain1.38e-1541
forebrain1.38e-1541
anterior neural tube1.38e-1541
future forebrain1.38e-1541
cell layer2.77e-14309
epithelium6.97e-14306
brain grey matter1.85e-1334
gray matter1.85e-1334
telencephalon3.21e-1334
regional part of telencephalon2.24e-1232
cerebral hemisphere2.78e-1232
blood vessel endothelium4.16e-1118
endothelium4.16e-1118
cardiovascular system endothelium4.16e-1118
ectoderm-derived structure2.22e-10171
ectoderm2.22e-10171
presumptive ectoderm2.22e-10171
multi-tissue structure2.49e-09342
cerebral cortex7.32e-0925
pallium7.32e-0925
simple squamous epithelium2.70e-0822
anatomical system3.12e-08624
regional part of cerebral cortex3.33e-0822
anatomical group5.49e-08625
vasculature6.68e-0878
vascular system6.68e-0878
neocortex3.51e-0720
vessel5.46e-0768
posterior neural tube7.69e-0715
chordal neural plate7.69e-0715
circulatory system8.74e-07112
compound organ9.15e-0768


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#105147.971147625824820.0002476385788090830.00267928369752841
CTCF#1066445.360256373075030.001211145381643620.00816807519782244
EGR1#195844.988179094810140.001615011500076050.0101388666780742
ESR1#2099430.76860329615451.11467714392546e-064.60323314489643e-05
FOS#235348.99795530889440.0001525147711168630.00194748626735225
FOSL1#8061439.7135797163734.01511434669553e-071.93867095355772e-05
FOSL2#2355416.93020060456171.2165416097647e-050.000303377242555434
HDAC8#558691194.1460084033610.005140863901003430.0239028886544786
IRF1#365947.63716375356390.0002938853996185490.00307238210718335
JUN#3725412.51282919233634.07770316866756e-050.000742712314671209
JUNB#3726430.61063265982111.13787152942193e-064.65666789425146e-05
JUND#372746.994663941871030.000417684217818580.00391444023912013
NR3C1#2908414.9730233311731.98868032687801e-050.000442659387593377
RAD21#5885410.35503389545638.6948481184721e-050.00129282637050841
SMARCB1#6598418.25271578115749.00423392720929e-060.000241188301391077
SMARCC1#6599443.66335931963152.74744977017458e-071.40588391252946e-05
SMC3#9126415.04493284493281.95092670935632e-050.000437519507404906
ZNF263#1012748.221841637010680.0002187871180958320.00248611770501693



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.