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Coexpression cluster:C711

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Full id: C711_cerebellum_Pericytes_Fibroblast_Meningeal_spinal_Astrocyte_Hair



Phase1 CAGE Peaks

Hg19::chr3:147114993..147115013,-p5@ZIC4
Hg19::chr3:147115338..147115349,+p@chr3:147115338..147115349
+
Hg19::chr3:147115400..147115411,+p@chr3:147115400..147115411
+
Hg19::chr3:147126815..147126825,-p@chr3:147126815..147126825
-
Hg19::chr3:147127177..147127194,+p2@ZIC1
Hg19::chr3:147129975..147129992,+p@chr3:147129975..147129992
+
Hg19::chr3:147130332..147130352,+p@chr3:147130332..147130352
+
Hg19::chr3:147131290..147131301,+p@chr3:147131290..147131301
+
Hg19::chr3:147137194..147137222,+p1@FLJ30375
Hg19::chr3:147139053..147139112,+p5@ZIC1
Hg19::chr3:147139152..147139163,+p15@ZIC1
Hg19::chr3:147139238..147139247,+p26@ZIC1


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:0008589regulation of smoothened signaling pathway0.0197690591558547
GO:0007224smoothened signaling pathway0.0197690591558547
GO:0042472inner ear morphogenesis0.0197690591558547
GO:0042471ear morphogenesis0.0197690591558547
GO:0048839inner ear development0.0197690591558547
GO:0043583ear development0.0197690591558547
GO:0007423sensory organ development0.0328060999854834
GO:0048598embryonic morphogenesis0.0328060999854834
GO:0007389pattern specification process0.0388635391999214
GO:0007420brain development0.0391996244308409
GO:0003677DNA binding0.0464642615688377



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
skin fibroblast1.84e-0823
neural cell2.68e-0825
glial cell (sensu Vertebrata)1.97e-0715
glial cell1.97e-0715
glioblast1.97e-0715
glioblast (sensu Vertebrata)1.97e-0715
neurectodermal cell2.28e-0759
neuron associated cell3.77e-0717
neuron associated cell (sensu Vertebrata)3.77e-0717
Uber Anatomy
Ontology termp-valuen
central nervous system1.21e-4782
regional part of nervous system1.98e-4594
nervous system1.98e-4594
brain2.63e-4269
future brain2.63e-4269
regional part of brain1.05e-4059
neural tube7.13e-3957
neural rod7.13e-3957
future spinal cord7.13e-3957
neural keel7.13e-3957
neural plate3.30e-3386
presumptive neural plate3.30e-3386
neurectoderm1.33e-3290
ectoderm-derived structure2.02e-29169
ectoderm2.16e-29173
presumptive ectoderm2.16e-29173
regional part of forebrain2.31e-2641
forebrain2.31e-2641
future forebrain2.31e-2641
anterior neural tube2.42e-2542
head1.24e-24123
anterior region of body2.63e-24129
craniocervical region2.63e-24129
telencephalon6.76e-2334
gray matter6.93e-2334
brain grey matter6.93e-2334
pre-chordal neural plate9.16e-2361
regional part of telencephalon3.16e-2233
cerebral hemisphere2.62e-2132
cerebral cortex3.64e-1625
pallium3.64e-1625
adult organism6.11e-16115
organism subdivision6.45e-15365
posterior neural tube7.64e-1515
chordal neural plate7.64e-1515
regional part of cerebral cortex3.10e-1422
segmental subdivision of nervous system4.81e-1313
neocortex9.68e-1320
segmental subdivision of hindbrain3.18e-1212
hindbrain3.18e-1212
presumptive hindbrain3.18e-1212
cell layer6.02e-10312
regional part of metencephalon1.29e-099
metencephalon1.29e-099
future metencephalon1.29e-099
skin of body1.43e-0940
epithelium7.27e-09309
nucleus of brain2.97e-089
neural nucleus2.97e-089
integument4.36e-0845
integumental system4.36e-0845
basal ganglion5.75e-089
nuclear complex of neuraxis5.75e-089
aggregate regional part of brain5.75e-089
collection of basal ganglia5.75e-089
cerebral subcortex5.75e-089
cerebellum2.21e-076
rhombic lip2.21e-076
vasculature of head3.43e-0711
vasculature of organ3.43e-0711
telencephalic nucleus8.19e-077


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
CTBP2#1488420.9056667797762.88227050924922e-050.000603733352818851
SUZ12#23512937.58683568329721.0350112335066e-131.620622761862e-11



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.