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Coexpression cluster:C4292: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259647837921719!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00800163174548306
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259647837921719!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00800163174548306
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}}
}}

Revision as of 16:39, 26 November 2012


Full id: C4292_synovial_Pericytes_Astrocyte_Ciliary_Lens_Smooth_Fibroblast



Phase1 CAGE Peaks

Hg19::chr3:147123837..147123848,-p7@ZIC4
Hg19::chr3:147127358..147127369,+p16@ZIC1
Hg19::chr3:147127489..147127503,+p11@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>


Uber Anatomy
Ontology termp-valuen
central nervous system8.57e-3481
nervous system3.97e-3289
brain2.94e-3068
future brain2.94e-3068
neural plate2.13e-2982
presumptive neural plate2.13e-2982
posterior neural tube3.23e-2915
chordal neural plate3.23e-2915
neurectoderm1.01e-2786
neural tube1.14e-2656
neural rod1.14e-2656
future spinal cord1.14e-2656
neural keel1.14e-2656
segmental subdivision of hindbrain6.47e-2512
hindbrain6.47e-2512
presumptive hindbrain6.47e-2512
ecto-epithelium1.07e-23104
ectoderm-derived structure3.89e-23171
ectoderm3.89e-23171
presumptive ectoderm3.89e-23171
regional part of nervous system4.31e-2353
regional part of brain4.31e-2353
segmental subdivision of nervous system7.21e-2313
vasculature of organ2.05e-2211
regional part of metencephalon5.95e-219
metencephalon5.95e-219
future metencephalon5.95e-219
structure with developmental contribution from neural crest3.60e-20132
cerebellum4.43e-176
rhombic lip4.43e-176
atypical epithelium1.14e-164
pre-chordal neural plate1.04e-1361
ciliary epithelium3.59e-133
ciliary body3.59e-133
brain vasculature3.71e-135
pigment epithelium of eye7.99e-1311
blood-cerebrospinal fluid barrier1.01e-123
organ system subdivision3.73e-12223
vasculature of eye3.97e-116
uvea3.97e-116
vasculature of head3.97e-116
brainstem4.89e-106
anterior segment of eyeball6.37e-1014
vascular plexus3.04e-092
ventricle of nervous system3.04e-092
choroid plexus3.04e-092
brain ventricle3.04e-092
ventricular system of brain3.04e-092
ventricular system of central nervous system3.04e-092
corpus striatum8.25e-094
striatum8.25e-094
ventral part of telencephalon8.25e-094
future corpus striatum8.25e-094
anatomical cluster1.39e-08373
telencephalon1.48e-0834
regional part of forebrain1.98e-0841
forebrain1.98e-0841
anterior neural tube1.98e-0841
future forebrain1.98e-0841
articulation8.82e-088
skeletal joint8.82e-088
articular system8.82e-088
cerebral hemisphere2.01e-0732
cell layer3.81e-07309
intervertebral cartilage4.10e-075
symphysis4.10e-075
nonsynovial joint4.10e-075
fibrous joint4.10e-075
cartilaginous joint4.10e-075
developing mesenchymal condensation4.10e-075
pre-cartilage condensation4.10e-075
cartilaginous condensation4.10e-075
cartilage element4.10e-075
post-cranial axial skeletal system4.10e-075
vertebral column4.10e-075
intervertebral disk4.10e-075
intervertebral joint4.10e-075


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
ATF3#467214.97544968400580.005768294540793880.0259647837921719
SUZ12#23512233.41052060737530.00117826764536030.00800163174548306



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.