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Coexpression cluster:C3827: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.05e-86!56;UBERON:0005068!2.05e-86!56;UBERON:0006241!2.05e-86!56;UBERON:0007135!2.05e-86!56;UBERON:0000073!5.31e-78!53;UBERON:0002616!5.31e-78!53;UBERON:0002780!8.18e-67!41;UBERON:0001890!8.18e-67!41;UBERON:0003080!8.18e-67!41;UBERON:0006240!8.18e-67!41;UBERON:0001017!1.05e-65!81;UBERON:0000955!9.14e-65!68;UBERON:0006238!9.14e-65!68;UBERON:0001016!3.30e-64!89;UBERON:0003528!6.89e-62!34;UBERON:0002020!6.89e-62!34;UBERON:0001893!6.81e-61!34;UBERON:0003075!3.79e-59!82;UBERON:0007284!3.79e-59!82;UBERON:0002346!7.41e-59!86;UBERON:0001869!7.54e-56!32;UBERON:0002791!8.11e-56!32;UBERON:0007023!4.31e-49!114;UBERON:0010371!6.19e-47!104;UBERON:0003056!1.20e-45!61;UBERON:0002619!8.97e-42!22;UBERON:0010314!1.14e-36!132;UBERON:0000956!2.19e-36!25;UBERON:0000203!2.19e-36!25;UBERON:0001950!6.42e-36!20;UBERON:0004121!1.09e-31!171;UBERON:0000924!1.09e-31!171;UBERON:0006601!1.09e-31!171;UBERON:0000125!1.02e-28!9;UBERON:0002308!1.02e-28!9;UBERON:0011216!7.28e-28!223;UBERON:0000025!7.24e-23!192;UBERON:0002420!1.48e-22!9;UBERON:0007245!1.48e-22!9;UBERON:0010009!1.48e-22!9;UBERON:0010011!1.48e-22!9;UBERON:0000454!1.48e-22!9;UBERON:0009663!2.21e-22!7;UBERON:0003076!8.90e-20!15;UBERON:0003057!8.90e-20!15;UBERON:0002298!1.31e-19!6;UBERON:0000200!3.22e-19!6;UBERON:0004111!4.34e-17!240;UBERON:0001872!4.51e-16!5;UBERON:0004732!6.53e-15!13;UBERON:0000369!1.57e-13!4;UBERON:0002435!1.57e-13!4;UBERON:0000204!1.57e-13!4;UBERON:0010082!1.57e-13!4;UBERON:0000483!1.07e-12!306;UBERON:0000064!1.52e-12!218;UBERON:0000119!1.84e-12!309;UBERON:0004733!1.87e-12!12;UBERON:0002028!1.87e-12!12;UBERON:0007277!1.87e-12!12;UBERON:0000477!7.71e-12!373;UBERON:0005383!3.64e-11!3;UBERON:0005382!3.64e-11!3;UBERON:0000988!7.52e-11!3;UBERON:0000349!9.00e-11!5;UBERON:0002021!1.42e-10!5;UBERON:0001896!1.75e-10!3;UBERON:0005290!1.75e-10!3;UBERON:0010096!1.75e-10!3;UBERON:0002240!2.48e-10!3;UBERON:0005174!2.48e-10!3;UBERON:0001137!2.48e-10!3;UBERON:0000481!2.21e-09!342;UBERON:0002784!4.12e-08!4;UBERON:0001873!4.30e-08!2;UBERON:0010122!4.30e-08!2;UBERON:0002148!4.76e-08!2;UBERON:0006331!4.76e-08!2;UBERON:0009662!4.76e-08!2;UBERON:0001875!5.82e-08!2;UBERON:0006514!5.82e-08!2;UBERON:0001954!6.88e-08!2;UBERON:0003022!6.88e-08!2;UBERON:0002421!6.88e-08!2;UBERON:0002600!6.88e-08!2;UBERON:0001871!7.66e-08!6;UBERON:0002050!7.83e-08!564;UBERON:0002771!7.86e-08!2;UBERON:0001897!7.86e-08!2;UBERON:0002702!7.86e-08!2;UBERON:0010225!7.86e-08!2;UBERON:0000062!8.41e-08!503;UBERON:0001894!8.83e-08!7;UBERON:0006222!8.83e-08!7;UBERON:0000923!2.31e-07!560;UBERON:0010316!2.31e-07!560;UBERON:0005291!2.31e-07!560;UBERON:0006598!2.31e-07!560;UBERON:0010317!2.31e-07!560;UBERON:0002532!2.31e-07!560;UBERON:0005423!3.29e-07!581;UBERON:0005162!4.19e-07!2;UBERON:0000122!4.19e-07!2;UBERON:0000922!7.96e-07!592
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}}
}}

Revision as of 16:22, 26 November 2012


Full id: C3827_globus_locus_caudate_cerebral_parietal_thalamus_occipital



Phase1 CAGE Peaks

Hg19::chr19:57322667..57322678,-p@chr19:57322667..57322678
-
Hg19::chr19:57324701..57324716,-p2@PEG3
Hg19::chr20:34818589..34818600,+p@chr20:34818589..34818600
+


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 tube2.05e-8656
neural rod2.05e-8656
future spinal cord2.05e-8656
neural keel2.05e-8656
regional part of nervous system5.31e-7853
regional part of brain5.31e-7853
regional part of forebrain8.18e-6741
forebrain8.18e-6741
anterior neural tube8.18e-6741
future forebrain8.18e-6741
central nervous system1.05e-6581
brain9.14e-6568
future brain9.14e-6568
nervous system3.30e-6489
brain grey matter6.89e-6234
gray matter6.89e-6234
telencephalon6.81e-6134
neural plate3.79e-5982
presumptive neural plate3.79e-5982
neurectoderm7.41e-5986
cerebral hemisphere7.54e-5632
regional part of telencephalon8.11e-5632
adult organism4.31e-49114
ecto-epithelium6.19e-47104
pre-chordal neural plate1.20e-4561
regional part of cerebral cortex8.97e-4222
structure with developmental contribution from neural crest1.14e-36132
cerebral cortex2.19e-3625
pallium2.19e-3625
neocortex6.42e-3620
ectoderm-derived structure1.09e-31171
ectoderm1.09e-31171
presumptive ectoderm1.09e-31171
neural nucleus1.02e-289
nucleus of brain1.02e-289
organ system subdivision7.28e-28223
tube7.24e-23192
basal ganglion1.48e-229
nuclear complex of neuraxis1.48e-229
aggregate regional part of brain1.48e-229
collection of basal ganglia1.48e-229
cerebral subcortex1.48e-229
telencephalic nucleus2.21e-227
posterior neural tube8.90e-2015
chordal neural plate8.90e-2015
brainstem1.31e-196
gyrus3.22e-196
anatomical conduit4.34e-17240
parietal lobe4.51e-165
segmental subdivision of nervous system6.53e-1513
corpus striatum1.57e-134
striatum1.57e-134
ventral part of telencephalon1.57e-134
future corpus striatum1.57e-134
epithelium1.07e-12306
organ part1.52e-12218
cell layer1.84e-12309
segmental subdivision of hindbrain1.87e-1212
hindbrain1.87e-1212
presumptive hindbrain1.87e-1212
anatomical cluster7.71e-12373
caudate-putamen3.64e-113
dorsal striatum3.64e-113
pons7.52e-113
limbic system9.00e-115
occipital lobe1.42e-105
medulla oblongata1.75e-103
myelencephalon1.75e-103
future myelencephalon1.75e-103
spinal cord2.48e-103
dorsal region element2.48e-103
dorsum2.48e-103
multi-tissue structure2.21e-09342
regional part of diencephalon4.12e-084
caudate nucleus4.30e-082
future caudate nucleus4.30e-082
locus ceruleus4.76e-082
brainstem nucleus4.76e-082
hindbrain nucleus4.76e-082
globus pallidus5.82e-082
pallidum5.82e-082
Ammon's horn6.88e-082
lobe parts of cerebral cortex6.88e-082
hippocampal formation6.88e-082
limbic lobe6.88e-082
temporal lobe7.66e-086
embryonic structure7.83e-08564
middle temporal gyrus7.86e-082
dorsal plus ventral thalamus7.86e-082
middle frontal gyrus7.86e-082
thalamic complex7.86e-082
organ8.41e-08503
diencephalon8.83e-087
future diencephalon8.83e-087
germ layer2.31e-07560
germ layer / neural crest2.31e-07560
embryonic tissue2.31e-07560
presumptive structure2.31e-07560
germ layer / neural crest derived structure2.31e-07560
epiblast (generic)2.31e-07560


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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