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Coexpression cluster:C982: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!5.71e-86!114;UBERON:0001049!6.09e-66!56;UBERON:0005068!6.09e-66!56;UBERON:0006241!6.09e-66!56;UBERON:0007135!6.09e-66!56;UBERON:0000073!2.10e-61!53;UBERON:0002616!2.10e-61!53;UBERON:0001017!2.15e-58!81;UBERON:0001016!2.61e-54!89;UBERON:0000955!7.78e-54!68;UBERON:0006238!7.78e-54!68;UBERON:0002780!1.56e-53!41;UBERON:0001890!1.56e-53!41;UBERON:0003080!1.56e-53!41;UBERON:0006240!1.56e-53!41;UBERON:0003075!1.84e-52!82;UBERON:0007284!1.84e-52!82;UBERON:0002346!9.51e-51!86;UBERON:0001893!4.90e-43!34;UBERON:0003528!6.15e-43!34;UBERON:0002020!6.15e-43!34;UBERON:0003056!8.65e-41!61;UBERON:0002791!5.10e-40!32;UBERON:0010371!5.44e-40!104;UBERON:0001869!7.34e-40!32;UBERON:0010314!8.32e-34!132;UBERON:0011216!4.57e-30!223;UBERON:0000956!2.15e-29!25;UBERON:0000203!2.15e-29!25;UBERON:0002619!2.35e-29!22;UBERON:0004121!4.54e-29!171;UBERON:0000924!4.54e-29!171;UBERON:0006601!4.54e-29!171;UBERON:0001950!1.62e-26!20;UBERON:0000477!4.74e-18!373;UBERON:0000025!5.04e-17!192;UBERON:0004111!4.02e-15!240;UBERON:0000125!4.85e-15!9;UBERON:0002308!4.85e-15!9;UBERON:0002420!6.04e-15!9;UBERON:0007245!6.04e-15!9;UBERON:0010009!6.04e-15!9;UBERON:0010011!6.04e-15!9;UBERON:0000454!6.04e-15!9;UBERON:0000481!2.30e-14!342;UBERON:0003076!2.16e-13!15;UBERON:0003057!2.16e-13!15;UBERON:0000483!1.82e-12!306;UBERON:0009663!3.27e-12!7;UBERON:0000119!3.96e-12!309;UBERON:0001894!9.38e-12!7;UBERON:0006222!9.38e-12!7;UBERON:0004732!1.17e-10!13;UBERON:0000062!2.67e-10!503;UBERON:0002298!3.96e-10!6;UBERON:0000200!6.18e-10!6;UBERON:0000922!1.31e-09!592;UBERON:0004733!1.84e-09!12;UBERON:0002028!1.84e-09!12;UBERON:0007277!1.84e-09!12;UBERON:0000064!2.49e-09!218;UBERON:0000349!9.50e-09!5;UBERON:0005423!1.42e-08!581;UBERON:0002050!1.95e-08!564;UBERON:0000923!2.70e-08!560;UBERON:0010316!2.70e-08!560;UBERON:0005291!2.70e-08!560;UBERON:0006598!2.70e-08!560;UBERON:0010317!2.70e-08!560;UBERON:0002532!2.70e-08!560;UBERON:0002021!3.84e-08!5;UBERON:0001872!3.89e-08!5;UBERON:0000468!4.23e-08!656;UBERON:0001871!5.00e-08!6;UBERON:0002784!7.78e-08!4;UBERON:0000369!1.04e-07!4;UBERON:0002435!1.04e-07!4;UBERON:0000204!1.04e-07!4;UBERON:0010082!1.04e-07!4;UBERON:0003296!3.44e-07!4;UBERON:0010133!3.44e-07!4
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}}
}}

Revision as of 14:36, 26 November 2012


Full id: C982_pineal_substantia_thalamus_globus_spinal_corpus_medulla



Phase1 CAGE Peaks

Hg19::chr10:75118611..75118626,-p2@TTC18
Hg19::chr15:48010462..48010480,+p8@SEMA6D
Hg19::chr17:20979154..20979174,+p2@ENST00000456235
Hg19::chr17:73472575..73472603,+p3@KIAA0195
Hg19::chr19:35417728..35417761,-p1@BC047554
Hg19::chr3:118753758..118753785,-p4@IGSF11
Hg19::chr4:87855851..87855903,-p1@C4orf36
Hg19::chr7:29519662..29519677,+p4@CHN2


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 organism5.71e-86114
neural tube6.09e-6656
neural rod6.09e-6656
future spinal cord6.09e-6656
neural keel6.09e-6656
regional part of nervous system2.10e-6153
regional part of brain2.10e-6153
central nervous system2.15e-5881
nervous system2.61e-5489
brain7.78e-5468
future brain7.78e-5468
regional part of forebrain1.56e-5341
forebrain1.56e-5341
anterior neural tube1.56e-5341
future forebrain1.56e-5341
neural plate1.84e-5282
presumptive neural plate1.84e-5282
neurectoderm9.51e-5186
telencephalon4.90e-4334
brain grey matter6.15e-4334
gray matter6.15e-4334
pre-chordal neural plate8.65e-4161
regional part of telencephalon5.10e-4032
ecto-epithelium5.44e-40104
cerebral hemisphere7.34e-4032
structure with developmental contribution from neural crest8.32e-34132
organ system subdivision4.57e-30223
cerebral cortex2.15e-2925
pallium2.15e-2925
regional part of cerebral cortex2.35e-2922
ectoderm-derived structure4.54e-29171
ectoderm4.54e-29171
presumptive ectoderm4.54e-29171
neocortex1.62e-2620
anatomical cluster4.74e-18373
tube5.04e-17192
anatomical conduit4.02e-15240
neural nucleus4.85e-159
nucleus of brain4.85e-159
basal ganglion6.04e-159
nuclear complex of neuraxis6.04e-159
aggregate regional part of brain6.04e-159
collection of basal ganglia6.04e-159
cerebral subcortex6.04e-159
multi-tissue structure2.30e-14342
posterior neural tube2.16e-1315
chordal neural plate2.16e-1315
epithelium1.82e-12306
telencephalic nucleus3.27e-127
cell layer3.96e-12309
diencephalon9.38e-127
future diencephalon9.38e-127
segmental subdivision of nervous system1.17e-1013
organ2.67e-10503
brainstem3.96e-106
gyrus6.18e-106
embryo1.31e-09592
segmental subdivision of hindbrain1.84e-0912
hindbrain1.84e-0912
presumptive hindbrain1.84e-0912
organ part2.49e-09218
limbic system9.50e-095
developing anatomical structure1.42e-08581
embryonic structure1.95e-08564
germ layer2.70e-08560
germ layer / neural crest2.70e-08560
embryonic tissue2.70e-08560
presumptive structure2.70e-08560
germ layer / neural crest derived structure2.70e-08560
epiblast (generic)2.70e-08560
occipital lobe3.84e-085
parietal lobe3.89e-085
multi-cellular organism4.23e-08656
temporal lobe5.00e-086
regional part of diencephalon7.78e-084
corpus striatum1.04e-074
striatum1.04e-074
ventral part of telencephalon1.04e-074
future corpus striatum1.04e-074
gland of diencephalon3.44e-074
neuroendocrine gland3.44e-074


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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