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Coexpression cluster:C2027: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.43e-26!56;UBERON:0005068!1.43e-26!56;UBERON:0006241!1.43e-26!56;UBERON:0007135!1.43e-26!56;UBERON:0000073!2.70e-24!53;UBERON:0002616!2.70e-24!53;UBERON:0001017!9.78e-22!81;UBERON:0000955!5.25e-21!68;UBERON:0006238!5.25e-21!68;UBERON:0002780!1.36e-19!41;UBERON:0001890!1.36e-19!41;UBERON:0003080!1.36e-19!41;UBERON:0006240!1.36e-19!41;UBERON:0001016!1.47e-18!89;UBERON:0003528!1.01e-17!34;UBERON:0002020!1.01e-17!34;UBERON:0003075!1.30e-16!82;UBERON:0007284!1.30e-16!82;UBERON:0002346!1.49e-16!86;UBERON:0002791!5.34e-15!32;UBERON:0002420!1.85e-14!9;UBERON:0007245!1.85e-14!9;UBERON:0010009!1.85e-14!9;UBERON:0010011!1.85e-14!9;UBERON:0000454!1.85e-14!9;UBERON:0000125!2.46e-14!9;UBERON:0002308!2.46e-14!9;UBERON:0001893!7.47e-14!34;UBERON:0007023!1.78e-13!114;UBERON:0001869!4.30e-13!32;UBERON:0010371!4.67e-13!104;UBERON:0003056!2.10e-12!61;UBERON:0009663!8.59e-11!7;UBERON:0000002!1.70e-10!6;UBERON:0001560!1.70e-10!6;UBERON:0010314!7.57e-10!132;UBERON:0002784!1.93e-09!4;UBERON:0002619!1.98e-09!22;UBERON:0003076!3.83e-08!15;UBERON:0003057!3.83e-08!15;UBERON:0004121!3.90e-08!171;UBERON:0000924!3.90e-08!171;UBERON:0006601!3.90e-08!171;UBERON:0000956!5.06e-08!25;UBERON:0000203!5.06e-08!25;UBERON:0001894!5.83e-08!7;UBERON:0006222!5.83e-08!7;UBERON:0005383!2.39e-07!3;UBERON:0005382!2.39e-07!3;UBERON:0000349!2.64e-07!5;UBERON:0001950!5.43e-07!20;UBERON:0011216!7.43e-07!223
|ontology_enrichment_uberon=UBERON:0001049!1.43e-26!56;UBERON:0005068!1.43e-26!56;UBERON:0006241!1.43e-26!56;UBERON:0007135!1.43e-26!56;UBERON:0000073!2.70e-24!53;UBERON:0002616!2.70e-24!53;UBERON:0001017!9.78e-22!81;UBERON:0000955!5.25e-21!68;UBERON:0006238!5.25e-21!68;UBERON:0002780!1.36e-19!41;UBERON:0001890!1.36e-19!41;UBERON:0003080!1.36e-19!41;UBERON:0006240!1.36e-19!41;UBERON:0001016!1.47e-18!89;UBERON:0003528!1.01e-17!34;UBERON:0002020!1.01e-17!34;UBERON:0003075!1.30e-16!82;UBERON:0007284!1.30e-16!82;UBERON:0002346!1.49e-16!86;UBERON:0002791!5.34e-15!32;UBERON:0002420!1.85e-14!9;UBERON:0007245!1.85e-14!9;UBERON:0010009!1.85e-14!9;UBERON:0010011!1.85e-14!9;UBERON:0000454!1.85e-14!9;UBERON:0000125!2.46e-14!9;UBERON:0002308!2.46e-14!9;UBERON:0001893!7.47e-14!34;UBERON:0007023!1.78e-13!114;UBERON:0001869!4.30e-13!32;UBERON:0010371!4.67e-13!104;UBERON:0003056!2.10e-12!61;UBERON:0009663!8.59e-11!7;UBERON:0000002!1.70e-10!6;UBERON:0001560!1.70e-10!6;UBERON:0010314!7.57e-10!132;UBERON:0002784!1.93e-09!4;UBERON:0002619!1.98e-09!22;UBERON:0003076!3.83e-08!15;UBERON:0003057!3.83e-08!15;UBERON:0004121!3.90e-08!171;UBERON:0000924!3.90e-08!171;UBERON:0006601!3.90e-08!171;UBERON:0000956!5.06e-08!25;UBERON:0000203!5.06e-08!25;UBERON:0001894!5.83e-08!7;UBERON:0006222!5.83e-08!7;UBERON:0005383!2.39e-07!3;UBERON:0005382!2.39e-07!3;UBERON:0000349!2.64e-07!5;UBERON:0001950!5.43e-07!20;UBERON:0011216!7.43e-07!223
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,1.14971,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,3.9962,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,1.58259,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.251545,31.1376,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,1.76107,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,15.5521,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,2.74749,0.87256,2.09294,0.577088,0.953361,0.526389,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,1.35505,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 15:15, 26 November 2012


Full id: C2027_cerebellum_middle_pineal_occipital_medial_parietal_medulla



Phase1 CAGE Peaks

Hg19::chrX:1480354..1480394,-p@chrX:1480354..1480394
-
Hg19::chrX:1534966..1534978,+p@chrX:1534966..1534978
+
Hg19::chrX:1535807..1535821,+p@chrX:1535807..1535821
+
Hg19::chrX:1535840..1535859,+p@chrX:1535840..1535859
+
Hg19::chrX:1535864..1535880,+p@chrX:1535864..1535880
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube1.43e-2656
neural rod1.43e-2656
future spinal cord1.43e-2656
neural keel1.43e-2656
regional part of nervous system2.70e-2453
regional part of brain2.70e-2453
central nervous system9.78e-2281
brain5.25e-2168
future brain5.25e-2168
regional part of forebrain1.36e-1941
forebrain1.36e-1941
anterior neural tube1.36e-1941
future forebrain1.36e-1941
nervous system1.47e-1889
brain grey matter1.01e-1734
gray matter1.01e-1734
neural plate1.30e-1682
presumptive neural plate1.30e-1682
neurectoderm1.49e-1686
regional part of telencephalon5.34e-1532
basal ganglion1.85e-149
nuclear complex of neuraxis1.85e-149
aggregate regional part of brain1.85e-149
collection of basal ganglia1.85e-149
cerebral subcortex1.85e-149
neural nucleus2.46e-149
nucleus of brain2.46e-149
telencephalon7.47e-1434
adult organism1.78e-13114
cerebral hemisphere4.30e-1332
ecto-epithelium4.67e-13104
pre-chordal neural plate2.10e-1261
telencephalic nucleus8.59e-117
uterine cervix1.70e-106
neck of organ1.70e-106
structure with developmental contribution from neural crest7.57e-10132
regional part of diencephalon1.93e-094
regional part of cerebral cortex1.98e-0922
posterior neural tube3.83e-0815
chordal neural plate3.83e-0815
ectoderm-derived structure3.90e-08171
ectoderm3.90e-08171
presumptive ectoderm3.90e-08171
cerebral cortex5.06e-0825
pallium5.06e-0825
diencephalon5.83e-087
future diencephalon5.83e-087
caudate-putamen2.39e-073
dorsal striatum2.39e-073
limbic system2.64e-075
neocortex5.43e-0720
organ system subdivision7.43e-07223
Disease
Ontology termp-valuen
cervical cancer2.70e-095


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)

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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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