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Coexpression cluster:C4318: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.11e-83!115;UBERON:0001049!1.46e-44!57;UBERON:0005068!1.46e-44!57;UBERON:0006241!1.46e-44!57;UBERON:0007135!1.46e-44!57;UBERON:0002616!6.05e-40!59;UBERON:0001017!1.01e-34!82;UBERON:0003080!1.76e-34!42;UBERON:0000955!3.68e-34!69;UBERON:0006238!3.68e-34!69;UBERON:0002346!4.76e-34!90;UBERON:0005743!1.01e-33!86;UBERON:0002780!3.26e-33!41;UBERON:0001890!3.26e-33!41;UBERON:0006240!3.26e-33!41;UBERON:0003075!1.59e-32!86;UBERON:0007284!1.59e-32!86;UBERON:0000073!3.92e-30!94;UBERON:0001016!3.92e-30!94;UBERON:0002020!1.19e-25!34;UBERON:0003528!1.19e-25!34;UBERON:0001893!1.52e-25!34;UBERON:0002791!9.92e-25!33;UBERON:0001869!2.75e-23!32;UBERON:0000153!2.17e-22!129;UBERON:0007811!2.17e-22!129;UBERON:0003056!3.88e-22!61;UBERON:0000033!1.25e-21!123;UBERON:0000924!1.31e-20!173;UBERON:0006601!1.31e-20!173;UBERON:0002619!1.20e-19!22;UBERON:0004121!2.52e-19!169;UBERON:0001950!1.76e-17!20;UBERON:0000956!1.61e-16!25;UBERON:0000203!1.61e-16!25;UBERON:0004111!2.28e-14!241;UBERON:0000477!2.82e-13!286;UBERON:0000025!4.34e-12!194;UBERON:0002420!2.62e-11!9;UBERON:0007245!2.62e-11!9;UBERON:0010009!2.62e-11!9;UBERON:0010011!2.62e-11!9;UBERON:0000454!2.62e-11!9;UBERON:0000475!4.65e-11!365;UBERON:0002308!4.98e-11!9;UBERON:0000125!4.98e-11!9;UBERON:0003076!5.53e-11!15;UBERON:0003057!5.53e-11!15;UBERON:0002298!2.79e-10!8;UBERON:0000064!5.94e-10!219;UBERON:0000062!7.68e-10!511;UBERON:0000468!1.45e-09!659;UBERON:0000483!2.03e-09!309;UBERON:0001894!2.56e-09!7;UBERON:0006222!2.56e-09!7;UBERON:0000119!4.21e-09!312;UBERON:0009663!4.91e-09!7;UBERON:0000481!5.41e-09!347;UBERON:0004732!8.83e-09!13;UBERON:0000467!6.26e-08!625;UBERON:0000480!7.46e-08!626;UBERON:0004733!1.08e-07!12;UBERON:0002028!1.08e-07!12;UBERON:0007277!1.08e-07!12;UBERON:0000200!1.38e-07!6;UBERON:0000922!1.51e-07!612;UBERON:0002050!3.16e-07!605;UBERON:0005423!3.16e-07!605;UBERON:0000923!5.92e-07!604;UBERON:0005291!5.92e-07!604;UBERON:0006598!5.92e-07!604;UBERON:0002532!5.92e-07!604;UBERON:0000349!7.71e-07!5
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}}
}}

Revision as of 19:55, 8 August 2012


Full id: C4318_spinal_medulla_thalamus_melanoma_occipital_breast_amygdala



Phase1 CAGE Peaks

Hg19::chr3:195295690..195295718,-p@chr3:195295690..195295718
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Hg19::chr3:195295735..195295762,-p@chr3:195295735..195295762
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Hg19::chr3:195295785..195295796,-p@chr3:195295785..195295796
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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
adult organism1.11e-83115
neural tube1.46e-4457
neural rod1.46e-4457
future spinal cord1.46e-4457
neural keel1.46e-4457
regional part of brain6.05e-4059
central nervous system1.01e-3482
anterior neural tube1.76e-3442
brain3.68e-3469
future brain3.68e-3469
neurectoderm4.76e-3490
regional part of forebrain3.26e-3341
forebrain3.26e-3341
future forebrain3.26e-3341
neural plate1.59e-3286
presumptive neural plate1.59e-3286
regional part of nervous system3.92e-3094
nervous system3.92e-3094
gray matter1.19e-2534
brain grey matter1.19e-2534
telencephalon1.52e-2534
regional part of telencephalon9.92e-2533
cerebral hemisphere2.75e-2332
anterior region of body2.17e-22129
craniocervical region2.17e-22129
pre-chordal neural plate3.88e-2261
head1.25e-21123
ectoderm1.31e-20173
presumptive ectoderm1.31e-20173
regional part of cerebral cortex1.20e-1922
ectoderm-derived structure2.52e-19169
neocortex1.76e-1720
cerebral cortex1.61e-1625
pallium1.61e-1625
anatomical conduit2.28e-14241
anatomical cluster2.82e-13286
tube4.34e-12194
basal ganglion2.62e-119
nuclear complex of neuraxis2.62e-119
aggregate regional part of brain2.62e-119
collection of basal ganglia2.62e-119
cerebral subcortex2.62e-119
organism subdivision4.65e-11365
nucleus of brain4.98e-119
neural nucleus4.98e-119
posterior neural tube5.53e-1115
chordal neural plate5.53e-1115
brainstem2.79e-108
organ part5.94e-10219
organ7.68e-10511
multi-cellular organism1.45e-09659
epithelium2.03e-09309
diencephalon2.56e-097
future diencephalon2.56e-097
cell layer4.21e-09312
telencephalic nucleus4.91e-097
multi-tissue structure5.41e-09347
segmental subdivision of nervous system8.83e-0913
anatomical system6.26e-08625
anatomical group7.46e-08626
segmental subdivision of hindbrain1.08e-0712
hindbrain1.08e-0712
presumptive hindbrain1.08e-0712
gyrus1.38e-076
embryo1.51e-07612
embryonic structure3.16e-07605
developing anatomical structure3.16e-07605
germ layer5.92e-07604
embryonic tissue5.92e-07604
presumptive structure5.92e-07604
epiblast (generic)5.92e-07604
limbic system7.71e-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


No analysis results for this cluster

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.