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Coexpression cluster:C4292: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.07e-52!94;UBERON:0001016!3.07e-52!94;UBERON:0001017!1.02e-51!82;UBERON:0005743!1.45e-50!86;UBERON:0000955!6.24e-49!69;UBERON:0006238!6.24e-49!69;UBERON:0002616!1.72e-45!59;UBERON:0003075!7.21e-42!86;UBERON:0007284!7.21e-42!86;UBERON:0001049!7.65e-42!57;UBERON:0005068!7.65e-42!57;UBERON:0006241!7.65e-42!57;UBERON:0007135!7.65e-42!57;UBERON:0002346!3.22e-41!90;UBERON:0000033!3.42e-34!123;UBERON:0000924!3.17e-32!173;UBERON:0006601!3.17e-32!173;UBERON:0004121!3.89e-32!169;UBERON:0000153!7.67e-32!129;UBERON:0007811!7.67e-32!129;UBERON:0003056!1.15e-25!61;UBERON:0002780!1.15e-24!41;UBERON:0001890!1.15e-24!41;UBERON:0006240!1.15e-24!41;UBERON:0001893!4.05e-24!34;UBERON:0003080!6.69e-24!42;UBERON:0002791!6.93e-23!33;UBERON:0002020!3.61e-22!34;UBERON:0003528!3.61e-22!34;UBERON:0001869!1.28e-21!32;UBERON:0003076!1.67e-20!15;UBERON:0003057!1.67e-20!15;UBERON:0004733!6.84e-19!12;UBERON:0002028!6.84e-19!12;UBERON:0007277!6.84e-19!12;UBERON:0004732!3.33e-17!13;UBERON:0000956!7.71e-15!25;UBERON:0000203!7.71e-15!25;UBERON:0002680!4.47e-14!9;UBERON:0001895!4.47e-14!9;UBERON:0010092!4.47e-14!9;UBERON:0002037!7.76e-13!6;UBERON:0006215!7.76e-13!6;UBERON:0000475!3.39e-12!365;UBERON:0002200!1.49e-11!11;UBERON:0006876!1.49e-11!11;UBERON:0007023!1.82e-11!115;UBERON:0002619!4.94e-11!22;UBERON:0000488!4.30e-09!4;UBERON:0002308!4.87e-09!9;UBERON:0000125!4.87e-09!9;UBERON:0002420!5.20e-09!9;UBERON:0007245!5.20e-09!9;UBERON:0010009!5.20e-09!9;UBERON:0010011!5.20e-09!9;UBERON:0000454!5.20e-09!9;UBERON:0001950!7.87e-09!20;UBERON:0009663!1.10e-08!7;UBERON:0000119!1.45e-08!312;UBERON:0002298!5.19e-08!8;UBERON:0000064!1.64e-07!219;UBERON:0001778!1.92e-07!3;UBERON:0001775!1.92e-07!3;UBERON:0005284!2.63e-07!5;UBERON:0003210!3.12e-07!3;UBERON:0000483!3.66e-07!309;UBERON:0004905!8.56e-07!5;UBERON:0000982!8.56e-07!5;UBERON:0004770!8.56e-07!5
|ontology_enrichment_uberon=UBERON:0000073!3.07e-52!94;UBERON:0001016!3.07e-52!94;UBERON:0001017!1.02e-51!82;UBERON:0005743!1.45e-50!86;UBERON:0000955!6.24e-49!69;UBERON:0006238!6.24e-49!69;UBERON:0002616!1.72e-45!59;UBERON:0003075!7.21e-42!86;UBERON:0007284!7.21e-42!86;UBERON:0001049!7.65e-42!57;UBERON:0005068!7.65e-42!57;UBERON:0006241!7.65e-42!57;UBERON:0007135!7.65e-42!57;UBERON:0002346!3.22e-41!90;UBERON:0000033!3.42e-34!123;UBERON:0000924!3.17e-32!173;UBERON:0006601!3.17e-32!173;UBERON:0004121!3.89e-32!169;UBERON:0000153!7.67e-32!129;UBERON:0007811!7.67e-32!129;UBERON:0003056!1.15e-25!61;UBERON:0002780!1.15e-24!41;UBERON:0001890!1.15e-24!41;UBERON:0006240!1.15e-24!41;UBERON:0001893!4.05e-24!34;UBERON:0003080!6.69e-24!42;UBERON:0002791!6.93e-23!33;UBERON:0002020!3.61e-22!34;UBERON:0003528!3.61e-22!34;UBERON:0001869!1.28e-21!32;UBERON:0003076!1.67e-20!15;UBERON:0003057!1.67e-20!15;UBERON:0004733!6.84e-19!12;UBERON:0002028!6.84e-19!12;UBERON:0007277!6.84e-19!12;UBERON:0004732!3.33e-17!13;UBERON:0000956!7.71e-15!25;UBERON:0000203!7.71e-15!25;UBERON:0002680!4.47e-14!9;UBERON:0001895!4.47e-14!9;UBERON:0010092!4.47e-14!9;UBERON:0002037!7.76e-13!6;UBERON:0006215!7.76e-13!6;UBERON:0000475!3.39e-12!365;UBERON:0002200!1.49e-11!11;UBERON:0006876!1.49e-11!11;UBERON:0007023!1.82e-11!115;UBERON:0002619!4.94e-11!22;UBERON:0000488!4.30e-09!4;UBERON:0002308!4.87e-09!9;UBERON:0000125!4.87e-09!9;UBERON:0002420!5.20e-09!9;UBERON:0007245!5.20e-09!9;UBERON:0010009!5.20e-09!9;UBERON:0010011!5.20e-09!9;UBERON:0000454!5.20e-09!9;UBERON:0001950!7.87e-09!20;UBERON:0009663!1.10e-08!7;UBERON:0000119!1.45e-08!312;UBERON:0002298!5.19e-08!8;UBERON:0000064!1.64e-07!219;UBERON:0001778!1.92e-07!3;UBERON:0001775!1.92e-07!3;UBERON:0005284!2.63e-07!5;UBERON:0003210!3.12e-07!3;UBERON:0000483!3.66e-07!309;UBERON:0004905!8.56e-07!5;UBERON:0000982!8.56e-07!5;UBERON:0004770!8.56e-07!5
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}}
}}

Revision as of 12:29, 5 September 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
regional part of nervous system3.07e-5294
nervous system3.07e-5294
central nervous system1.02e-5182
brain6.24e-4969
future brain6.24e-4969
regional part of brain1.72e-4559
neural plate7.21e-4286
presumptive neural plate7.21e-4286
neural tube7.65e-4257
neural rod7.65e-4257
future spinal cord7.65e-4257
neural keel7.65e-4257
neurectoderm3.22e-4190
head3.42e-34123
ectoderm3.17e-32173
presumptive ectoderm3.17e-32173
ectoderm-derived structure3.89e-32169
anterior region of body7.67e-32129
craniocervical region7.67e-32129
pre-chordal neural plate1.15e-2561
regional part of forebrain1.15e-2441
forebrain1.15e-2441
future forebrain1.15e-2441
telencephalon4.05e-2434
anterior neural tube6.69e-2442
regional part of telencephalon6.93e-2333
gray matter3.61e-2234
brain grey matter3.61e-2234
cerebral hemisphere1.28e-2132
posterior neural tube1.67e-2015
chordal neural plate1.67e-2015
segmental subdivision of hindbrain6.84e-1912
hindbrain6.84e-1912
presumptive hindbrain6.84e-1912
segmental subdivision of nervous system3.33e-1713
cerebral cortex7.71e-1525
pallium7.71e-1525
regional part of metencephalon4.47e-149
metencephalon4.47e-149
future metencephalon4.47e-149
cerebellum7.76e-136
rhombic lip7.76e-136
organism subdivision3.39e-12365
vasculature of head1.49e-1111
vasculature of organ1.49e-1111
adult organism1.82e-11115
regional part of cerebral cortex4.94e-1122
atypical epithelium4.30e-094
nucleus of brain4.87e-099
neural nucleus4.87e-099
basal ganglion5.20e-099
nuclear complex of neuraxis5.20e-099
aggregate regional part of brain5.20e-099
collection of basal ganglia5.20e-099
cerebral subcortex5.20e-099
neocortex7.87e-0920
telencephalic nucleus1.10e-087
cell layer1.45e-08312
brainstem5.19e-088
organ part1.64e-07219
ciliary epithelium1.92e-073
ciliary body1.92e-073
brain vasculature2.63e-075
blood-cerebrospinal fluid barrier3.12e-073
epithelium3.66e-07309
articulation8.56e-075
skeletal joint8.56e-075
articular system8.56e-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.