Personal tools

Coexpression cluster:C3078

From FANTOM5_SSTAR

Revision as of 14:28, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3078_pineal_extraskeletal_occipital_medial_cerebellum_amygdala_parietal



Phase1 CAGE Peaks

Hg19::chr11:105480996..105481007,+p13@GRIA4
Hg19::chr8:107282368..107282379,+p5@OXR1
Hg19::chr8:107282389..107282493,+p1@OXR1


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:0016998cell wall catabolic process0.0150194937569828
GO:0010382cell wall metabolic process0.0150194937569828
GO:0007047cell wall organization and biogenesis0.0150194937569828
GO:0007215glutamate signaling pathway0.0150194937569828
GO:0045229external encapsulating structure organization and biogenesis0.0150194937569828
GO:0004970ionotropic glutamate receptor activity0.019013430069202
GO:0005234extracellular-glutamate-gated ion channel activity0.019013430069202
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0306990760222157
GO:0008066glutamate receptor activity0.0356145402287207
GO:0006979response to oxidative stress0.0372431402806523
GO:0005230extracellular ligand-gated ion channel activity0.0372431402806523
GO:0045211postsynaptic membrane0.0372431402806523
GO:0044456synapse part0.0372431402806523
GO:0015276ligand-gated ion channel activity0.0372431402806523
GO:0022834ligand-gated channel activity0.0372431402806523



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
non-terminally differentiated cell1.06e-20180
fibroblast9.12e-1375
Uber Anatomy
Ontology termp-valuen
central nervous system4.16e-3182
regional part of nervous system6.73e-2994
nervous system6.73e-2994
neural tube9.56e-2857
neural rod9.56e-2857
future spinal cord9.56e-2857
neural keel9.56e-2857
brain1.54e-2769
future brain1.54e-2769
regional part of brain1.31e-2659
organism subdivision2.76e-26365
anterior neural tube3.19e-2242
ectoderm3.35e-22173
presumptive ectoderm3.35e-22173
regional part of forebrain3.71e-2241
forebrain3.71e-2241
future forebrain3.71e-2241
ectoderm-derived structure9.79e-22169
neurectoderm1.43e-2090
head2.82e-20123
neural plate2.83e-2086
presumptive neural plate2.83e-2086
anterior region of body9.46e-19129
craniocervical region9.46e-19129
gray matter1.29e-1834
brain grey matter1.29e-1834
telencephalon1.70e-1834
cerebral hemisphere6.81e-1832
regional part of telencephalon7.87e-1833
pre-chordal neural plate8.35e-1761
cell layer5.93e-16312
epithelium1.03e-15309
multi-cellular organism2.41e-15659
regional part of cerebral cortex5.01e-1522
multi-tissue structure1.17e-14347
anatomical cluster1.32e-14286
cerebral cortex3.52e-1425
pallium3.52e-1425
adult organism4.17e-14115
anatomical conduit5.55e-14241
neocortex8.10e-1420
tube3.27e-13194
anatomical system3.99e-13625
anatomical group4.35e-13626
embryo4.66e-12612
embryonic structure6.31e-12605
developing anatomical structure6.31e-12605
germ layer1.37e-11604
embryonic tissue1.37e-11604
presumptive structure1.37e-11604
epiblast (generic)1.37e-11604
organ1.40e-09511
organ part1.73e-09219
somite2.21e-0883
paraxial mesoderm2.21e-0883
presomitic mesoderm2.21e-0883
presumptive segmental plate2.21e-0883
trunk paraxial mesoderm2.21e-0883
presumptive paraxial mesoderm2.21e-0883
dermomyotome5.35e-0770
posterior neural tube8.74e-0715
chordal neural plate8.74e-0715


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
CTCF#1066435.360256373075030.0064925092527670.027822870372563
CTCFL#140690213.16431623931620.007433367036996010.0306669334377573
MEF2A#4205212.4954872730960.008235029478029740.0324721831781299
MEF2C#4208227.54090299508270.001729119938369690.010645968121405
SMC3#9126210.02995522995520.0126656379767470.0457094773369322
TFAP2A#7020211.01242291536330.01054990655215560.0389928757617788



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.