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Coexpression cluster:C3108: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.56e-68!56;UBERON:0005068!3.56e-68!56;UBERON:0006241!3.56e-68!56;UBERON:0007135!3.56e-68!56;UBERON:0000073!7.81e-63!53;UBERON:0002616!7.81e-63!53;UBERON:0002346!4.44e-56!86;UBERON:0001017!3.28e-55!81;UBERON:0002780!5.46e-55!41;UBERON:0001890!5.46e-55!41;UBERON:0003080!5.46e-55!41;UBERON:0006240!5.46e-55!41;UBERON:0000955!5.75e-55!68;UBERON:0006238!5.75e-55!68;UBERON:0003075!7.07e-55!82;UBERON:0007284!7.07e-55!82;UBERON:0001016!1.46e-54!89;UBERON:0007023!2.86e-49!114;UBERON:0003056!2.72e-44!61;UBERON:0001893!4.23e-43!34;UBERON:0003528!5.38e-43!34;UBERON:0002020!5.38e-43!34;UBERON:0010371!7.47e-40!104;UBERON:0001869!9.09e-40!32;UBERON:0002791!1.56e-39!32;UBERON:0001950!1.34e-32!20;UBERON:0002619!1.42e-32!22;UBERON:0010314!1.08e-30!132;UBERON:0004121!1.23e-29!171;UBERON:0000924!1.23e-29!171;UBERON:0006601!1.23e-29!171;UBERON:0000956!4.80e-28!25;UBERON:0000203!4.80e-28!25;UBERON:0011216!9.84e-21!223;UBERON:0000025!1.32e-17!192;UBERON:0002420!7.71e-17!9;UBERON:0007245!7.71e-17!9;UBERON:0010009!7.71e-17!9;UBERON:0010011!7.71e-17!9;UBERON:0000454!7.71e-17!9;UBERON:0000125!9.32e-17!9;UBERON:0002308!9.32e-17!9;UBERON:0003076!4.51e-14!15;UBERON:0003057!4.51e-14!15;UBERON:0009663!2.65e-13!7;UBERON:0001894!2.80e-13!7;UBERON:0006222!2.80e-13!7;UBERON:0000200!4.64e-13!6;UBERON:0004111!6.27e-13!240;UBERON:0002298!4.92e-12!6;UBERON:0000477!3.96e-11!373;UBERON:0002021!8.91e-11!5;UBERON:0001871!2.97e-10!6;UBERON:0004733!1.70e-09!12;UBERON:0002028!1.70e-09!12;UBERON:0007277!1.70e-09!12;UBERON:0000062!1.91e-09!503;UBERON:0000483!5.39e-09!306;UBERON:0000119!9.27e-09!309;UBERON:0002784!1.09e-08!4;UBERON:0004732!1.23e-08!13;UBERON:0003296!2.26e-08!4;UBERON:0010133!2.26e-08!4;UBERON:0000922!2.40e-08!592;UBERON:0000369!2.49e-08!4;UBERON:0002435!2.49e-08!4;UBERON:0000204!2.49e-08!4;UBERON:0010082!2.49e-08!4;UBERON:0000064!4.36e-08!218;UBERON:0000473!6.56e-08!8;UBERON:0000923!1.39e-07!560;UBERON:0010316!1.39e-07!560;UBERON:0005291!1.39e-07!560;UBERON:0006598!1.39e-07!560;UBERON:0010317!1.39e-07!560;UBERON:0002532!1.39e-07!560;UBERON:0001872!1.56e-07!5;UBERON:0003135!1.61e-07!11;UBERON:0005423!1.97e-07!581;UBERON:0001870!2.12e-07!3;UBERON:0002050!2.25e-07!564;UBERON:0000481!3.33e-07!342;UBERON:0000349!5.41e-07!5;UBERON:0000988!5.47e-07!3;UBERON:0002240!8.27e-07!3;UBERON:0005174!8.27e-07!3;UBERON:0001137!8.27e-07!3
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}}
}}

Revision as of 15:55, 26 November 2012


Full id: C3108_occipital_retina_eye_pineal_parietal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr11:123396370..123396395,+p3@GRAMD1B
Hg19::chr15:33486388..33486392,-p@chr15:33486388..33486392
-
Hg19::chr15:33486907..33486928,-p1@FMN1


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
neural tube3.56e-6856
neural rod3.56e-6856
future spinal cord3.56e-6856
neural keel3.56e-6856
regional part of nervous system7.81e-6353
regional part of brain7.81e-6353
neurectoderm4.44e-5686
central nervous system3.28e-5581
regional part of forebrain5.46e-5541
forebrain5.46e-5541
anterior neural tube5.46e-5541
future forebrain5.46e-5541
brain5.75e-5568
future brain5.75e-5568
neural plate7.07e-5582
presumptive neural plate7.07e-5582
nervous system1.46e-5489
adult organism2.86e-49114
pre-chordal neural plate2.72e-4461
telencephalon4.23e-4334
brain grey matter5.38e-4334
gray matter5.38e-4334
ecto-epithelium7.47e-40104
cerebral hemisphere9.09e-4032
regional part of telencephalon1.56e-3932
neocortex1.34e-3220
regional part of cerebral cortex1.42e-3222
structure with developmental contribution from neural crest1.08e-30132
ectoderm-derived structure1.23e-29171
ectoderm1.23e-29171
presumptive ectoderm1.23e-29171
cerebral cortex4.80e-2825
pallium4.80e-2825
organ system subdivision9.84e-21223
tube1.32e-17192
basal ganglion7.71e-179
nuclear complex of neuraxis7.71e-179
aggregate regional part of brain7.71e-179
collection of basal ganglia7.71e-179
cerebral subcortex7.71e-179
neural nucleus9.32e-179
nucleus of brain9.32e-179
posterior neural tube4.51e-1415
chordal neural plate4.51e-1415
telencephalic nucleus2.65e-137
diencephalon2.80e-137
future diencephalon2.80e-137
gyrus4.64e-136
anatomical conduit6.27e-13240
brainstem4.92e-126
anatomical cluster3.96e-11373
occipital lobe8.91e-115
temporal lobe2.97e-106
segmental subdivision of hindbrain1.70e-0912
hindbrain1.70e-0912
presumptive hindbrain1.70e-0912
organ1.91e-09503
epithelium5.39e-09306
cell layer9.27e-09309
regional part of diencephalon1.09e-084
segmental subdivision of nervous system1.23e-0813
gland of diencephalon2.26e-084
neuroendocrine gland2.26e-084
embryo2.40e-08592
corpus striatum2.49e-084
striatum2.49e-084
ventral part of telencephalon2.49e-084
future corpus striatum2.49e-084
organ part4.36e-08218
testis6.56e-088
germ layer1.39e-07560
germ layer / neural crest1.39e-07560
embryonic tissue1.39e-07560
presumptive structure1.39e-07560
germ layer / neural crest derived structure1.39e-07560
epiblast (generic)1.39e-07560
parietal lobe1.56e-075
male reproductive organ1.61e-0711
developing anatomical structure1.97e-07581
frontal cortex2.12e-073
embryonic structure2.25e-07564
multi-tissue structure3.33e-07342
limbic system5.41e-075
pons5.47e-073
spinal cord8.27e-073
dorsal region element8.27e-073
dorsum8.27e-073


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.

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