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Coexpression cluster:C2617: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!4.92e-27!90;UBERON:0003075!1.52e-25!86;UBERON:0007284!1.52e-25!86;UBERON:0000475!2.01e-25!365;UBERON:0001049!2.87e-25!57;UBERON:0005068!2.87e-25!57;UBERON:0006241!2.87e-25!57;UBERON:0007135!2.87e-25!57;UBERON:0000924!3.40e-25!173;UBERON:0006601!3.40e-25!173;UBERON:0002616!4.41e-24!59;UBERON:0005743!8.03e-24!86;UBERON:0004121!8.55e-24!169;UBERON:0000119!1.51e-23!312;UBERON:0000483!1.97e-23!309;UBERON:0001017!2.35e-23!82;UBERON:0000073!1.18e-21!94;UBERON:0001016!1.18e-21!94;UBERON:0000481!3.51e-21!347;UBERON:0007023!6.49e-21!115;UBERON:0000955!8.39e-21!69;UBERON:0006238!8.39e-21!69;UBERON:0002780!1.43e-19!41;UBERON:0001890!1.43e-19!41;UBERON:0006240!1.43e-19!41;UBERON:0000064!1.87e-19!219;UBERON:0000033!5.82e-19!123;UBERON:0003056!1.90e-18!61;UBERON:0003080!2.10e-18!42;UBERON:0000468!2.51e-18!659;UBERON:0000153!3.03e-18!129;UBERON:0007811!3.03e-18!129;UBERON:0001869!5.05e-18!32;UBERON:0001893!5.86e-18!34;UBERON:0002020!6.10e-18!34;UBERON:0003528!6.10e-18!34;UBERON:0002791!2.65e-17!33;UBERON:0000922!2.48e-16!612;UBERON:0000480!4.63e-16!626;UBERON:0004111!8.19e-16!241;UBERON:0000467!1.15e-15!625;UBERON:0002619!2.55e-15!22;UBERON:0002050!3.11e-15!605;UBERON:0005423!3.11e-15!605;UBERON:0000025!4.01e-15!194;UBERON:0000923!5.24e-15!604;UBERON:0005291!5.24e-15!604;UBERON:0006598!5.24e-15!604;UBERON:0002532!5.24e-15!604;UBERON:0000956!8.45e-15!25;UBERON:0000203!8.45e-15!25;UBERON:0000477!9.55e-15!286;UBERON:0001950!4.02e-14!20;UBERON:0000062!2.66e-11!511;UBERON:0003076!4.68e-08!15;UBERON:0003057!4.68e-08!15;UBERON:0002100!7.14e-07!216;UBERON:0004733!7.57e-07!12;UBERON:0002028!7.57e-07!12;UBERON:0007277!7.57e-07!12
|ontology_enrichment_uberon=UBERON:0002346!4.92e-27!90;UBERON:0003075!1.52e-25!86;UBERON:0007284!1.52e-25!86;UBERON:0000475!2.01e-25!365;UBERON:0001049!2.87e-25!57;UBERON:0005068!2.87e-25!57;UBERON:0006241!2.87e-25!57;UBERON:0007135!2.87e-25!57;UBERON:0000924!3.40e-25!173;UBERON:0006601!3.40e-25!173;UBERON:0002616!4.41e-24!59;UBERON:0005743!8.03e-24!86;UBERON:0004121!8.55e-24!169;UBERON:0000119!1.51e-23!312;UBERON:0000483!1.97e-23!309;UBERON:0001017!2.35e-23!82;UBERON:0000073!1.18e-21!94;UBERON:0001016!1.18e-21!94;UBERON:0000481!3.51e-21!347;UBERON:0007023!6.49e-21!115;UBERON:0000955!8.39e-21!69;UBERON:0006238!8.39e-21!69;UBERON:0002780!1.43e-19!41;UBERON:0001890!1.43e-19!41;UBERON:0006240!1.43e-19!41;UBERON:0000064!1.87e-19!219;UBERON:0000033!5.82e-19!123;UBERON:0003056!1.90e-18!61;UBERON:0003080!2.10e-18!42;UBERON:0000468!2.51e-18!659;UBERON:0000153!3.03e-18!129;UBERON:0007811!3.03e-18!129;UBERON:0001869!5.05e-18!32;UBERON:0001893!5.86e-18!34;UBERON:0002020!6.10e-18!34;UBERON:0003528!6.10e-18!34;UBERON:0002791!2.65e-17!33;UBERON:0000922!2.48e-16!612;UBERON:0000480!4.63e-16!626;UBERON:0004111!8.19e-16!241;UBERON:0000467!1.15e-15!625;UBERON:0002619!2.55e-15!22;UBERON:0002050!3.11e-15!605;UBERON:0005423!3.11e-15!605;UBERON:0000025!4.01e-15!194;UBERON:0000923!5.24e-15!604;UBERON:0005291!5.24e-15!604;UBERON:0006598!5.24e-15!604;UBERON:0002532!5.24e-15!604;UBERON:0000956!8.45e-15!25;UBERON:0000203!8.45e-15!25;UBERON:0000477!9.55e-15!286;UBERON:0001950!4.02e-14!20;UBERON:0000062!2.66e-11!511;UBERON:0003076!4.68e-08!15;UBERON:0003057!4.68e-08!15;UBERON:0002100!7.14e-07!216;UBERON:0004733!7.57e-07!12;UBERON:0002028!7.57e-07!12;UBERON:0007277!7.57e-07!12
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}}
}}

Revision as of 13:59, 5 September 2012


Full id: C2617_brain_occipital_Alveolar_parietal_hippocampus_temporal_left



Phase1 CAGE Peaks

Hg19::chr20:36531379..36531393,+p4@VSTM2L
Hg19::chr20:36531506..36531540,+p1@VSTM2L
Hg19::chr20:36531547..36531550,+p3@VSTM2L
Hg19::chr20:36531551..36531561,+p2@VSTM2L


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neurectoderm4.92e-2790
neural plate1.52e-2586
presumptive neural plate1.52e-2586
organism subdivision2.01e-25365
neural tube2.87e-2557
neural rod2.87e-2557
future spinal cord2.87e-2557
neural keel2.87e-2557
ectoderm3.40e-25173
presumptive ectoderm3.40e-25173
regional part of brain4.41e-2459
ectoderm-derived structure8.55e-24169
cell layer1.51e-23312
epithelium1.97e-23309
central nervous system2.35e-2382
regional part of nervous system1.18e-2194
nervous system1.18e-2194
multi-tissue structure3.51e-21347
adult organism6.49e-21115
brain8.39e-2169
future brain8.39e-2169
regional part of forebrain1.43e-1941
forebrain1.43e-1941
future forebrain1.43e-1941
organ part1.87e-19219
head5.82e-19123
pre-chordal neural plate1.90e-1861
anterior neural tube2.10e-1842
multi-cellular organism2.51e-18659
anterior region of body3.03e-18129
craniocervical region3.03e-18129
cerebral hemisphere5.05e-1832
telencephalon5.86e-1834
gray matter6.10e-1834
brain grey matter6.10e-1834
regional part of telencephalon2.65e-1733
embryo2.48e-16612
anatomical group4.63e-16626
anatomical conduit8.19e-16241
anatomical system1.15e-15625
regional part of cerebral cortex2.55e-1522
embryonic structure3.11e-15605
developing anatomical structure3.11e-15605
tube4.01e-15194
germ layer5.24e-15604
embryonic tissue5.24e-15604
presumptive structure5.24e-15604
epiblast (generic)5.24e-15604
cerebral cortex8.45e-1525
pallium8.45e-1525
anatomical cluster9.55e-15286
neocortex4.02e-1420
organ2.66e-11511
posterior neural tube4.68e-0815
chordal neural plate4.68e-0815
trunk7.14e-07216
segmental subdivision of hindbrain7.57e-0712
hindbrain7.57e-0712
presumptive hindbrain7.57e-0712


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
EGR1#195844.988179094810140.001615011500076050.0101510704174556
TAF1#687243.343046285745290.008005664898701650.0322595739005904
ZNF263#1012748.221841637010680.0002187871180958320.00249208286910356



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2617&oldid=2132859"