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Coexpression cluster:C1764: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.73e-109!56;UBERON:0005068!3.73e-109!56;UBERON:0006241!3.73e-109!56;UBERON:0007135!3.73e-109!56;UBERON:0000073!1.70e-97!53;UBERON:0002616!1.70e-97!53;UBERON:0001017!1.21e-84!81;UBERON:0000955!3.16e-82!68;UBERON:0006238!3.16e-82!68;UBERON:0002780!4.74e-82!41;UBERON:0001890!4.74e-82!41;UBERON:0003080!4.74e-82!41;UBERON:0006240!4.74e-82!41;UBERON:0003528!1.14e-79!34;UBERON:0002020!1.14e-79!34;UBERON:0001016!1.39e-79!89;UBERON:0001893!2.17e-79!34;UBERON:0003075!1.89e-76!82;UBERON:0007284!1.89e-76!82;UBERON:0002346!1.56e-72!86;UBERON:0002791!4.06e-72!32;UBERON:0001869!1.26e-71!32;UBERON:0007023!2.21e-65!114;UBERON:0010371!1.35e-58!104;UBERON:0003056!2.30e-57!61;UBERON:0002619!3.63e-53!22;UBERON:0010314!5.61e-47!132;UBERON:0000956!1.58e-46!25;UBERON:0000203!1.58e-46!25;UBERON:0001950!8.17e-46!20;UBERON:0004121!8.07e-38!171;UBERON:0000924!8.07e-38!171;UBERON:0006601!8.07e-38!171;UBERON:0000125!8.44e-37!9;UBERON:0002308!8.44e-37!9;UBERON:0011216!4.87e-30!223;UBERON:0009663!5.10e-29!7;UBERON:0002420!6.16e-29!9;UBERON:0007245!6.16e-29!9;UBERON:0010009!6.16e-29!9;UBERON:0010011!6.16e-29!9;UBERON:0000454!6.16e-29!9;UBERON:0003076!1.36e-26!15;UBERON:0003057!1.36e-26!15;UBERON:0000025!4.29e-26!192;UBERON:0002298!7.78e-25!6;UBERON:0000200!6.90e-24!6;UBERON:0004732!1.19e-19!13;UBERON:0004111!3.82e-19!240;UBERON:0000369!1.37e-16!4;UBERON:0002435!1.37e-16!4;UBERON:0000204!1.37e-16!4;UBERON:0010082!1.37e-16!4;UBERON:0004733!2.89e-16!12;UBERON:0002028!2.89e-16!12;UBERON:0007277!2.89e-16!12;UBERON:0000477!2.39e-14!373;UBERON:0000483!3.49e-14!306;UBERON:0002240!4.60e-14!3;UBERON:0005174!4.60e-14!3;UBERON:0001137!4.60e-14!3;UBERON:0000064!4.71e-14!218;UBERON:0000119!5.85e-14!309;UBERON:0002021!9.37e-14!5;UBERON:0001896!1.66e-13!3;UBERON:0005290!1.66e-13!3;UBERON:0010096!1.66e-13!3;UBERON:0000349!1.87e-13!5;UBERON:0000988!4.34e-13!3;UBERON:0001872!5.61e-13!5;UBERON:0005383!6.04e-13!3;UBERON:0005382!6.04e-13!3;UBERON:0001870!8.39e-13!3;UBERON:0000481!1.07e-10!342;UBERON:0001875!4.98e-10!2;UBERON:0006514!4.98e-10!2;UBERON:0001897!6.76e-10!2;UBERON:0010225!6.76e-10!2;UBERON:0005162!8.03e-10!2;UBERON:0000122!8.03e-10!2;UBERON:0001871!1.41e-09!6;UBERON:0002148!1.66e-09!2;UBERON:0006331!1.66e-09!2;UBERON:0009662!1.66e-09!2;UBERON:0001954!1.97e-09!2;UBERON:0003022!1.97e-09!2;UBERON:0002421!1.97e-09!2;UBERON:0002600!1.97e-09!2;UBERON:0001873!2.14e-09!2;UBERON:0010122!2.14e-09!2;UBERON:0002771!2.23e-09!2;UBERON:0002702!3.12e-09!2;UBERON:0000062!3.70e-08!503;UBERON:0002680!1.61e-07!9;UBERON:0001895!1.61e-07!9;UBERON:0010092!1.61e-07!9;UBERON:0000923!5.60e-07!560;UBERON:0010316!5.60e-07!560;UBERON:0005291!5.60e-07!560;UBERON:0006598!5.60e-07!560;UBERON:0010317!5.60e-07!560;UBERON:0002532!5.60e-07!560;UBERON:0002050!7.37e-07!564
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.106358,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.501863,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,1.25074,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,1.72052,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
}}
}}

Revision as of 15:05, 26 November 2012


Full id: C1764_occipital_optic_spinal_diencephalon_thalamus_globus_substantia



Phase1 CAGE Peaks

Hg19::chr16:57295953..57295964,-p@chr16:57295953..57295964
-
Hg19::chrX:103041626..103041634,+p@chrX:103041626..103041634
+
Hg19::chrX:103042721..103042782,+p5@PLP1
Hg19::chrX:103046089..103046096,+p@chrX:103046089..103046096
+
Hg19::chrX:103046153..103046162,+p@chrX:103046153..103046162
+


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 tube3.73e-10956
neural rod3.73e-10956
future spinal cord3.73e-10956
neural keel3.73e-10956
regional part of nervous system1.70e-9753
regional part of brain1.70e-9753
central nervous system1.21e-8481
brain3.16e-8268
future brain3.16e-8268
regional part of forebrain4.74e-8241
forebrain4.74e-8241
anterior neural tube4.74e-8241
future forebrain4.74e-8241
brain grey matter1.14e-7934
gray matter1.14e-7934
nervous system1.39e-7989
telencephalon2.17e-7934
neural plate1.89e-7682
presumptive neural plate1.89e-7682
neurectoderm1.56e-7286
regional part of telencephalon4.06e-7232
cerebral hemisphere1.26e-7132
adult organism2.21e-65114
ecto-epithelium1.35e-58104
pre-chordal neural plate2.30e-5761
regional part of cerebral cortex3.63e-5322
structure with developmental contribution from neural crest5.61e-47132
cerebral cortex1.58e-4625
pallium1.58e-4625
neocortex8.17e-4620
ectoderm-derived structure8.07e-38171
ectoderm8.07e-38171
presumptive ectoderm8.07e-38171
neural nucleus8.44e-379
nucleus of brain8.44e-379
organ system subdivision4.87e-30223
telencephalic nucleus5.10e-297
basal ganglion6.16e-299
nuclear complex of neuraxis6.16e-299
aggregate regional part of brain6.16e-299
collection of basal ganglia6.16e-299
cerebral subcortex6.16e-299
posterior neural tube1.36e-2615
chordal neural plate1.36e-2615
tube4.29e-26192
brainstem7.78e-256
gyrus6.90e-246
segmental subdivision of nervous system1.19e-1913
anatomical conduit3.82e-19240
corpus striatum1.37e-164
striatum1.37e-164
ventral part of telencephalon1.37e-164
future corpus striatum1.37e-164
segmental subdivision of hindbrain2.89e-1612
hindbrain2.89e-1612
presumptive hindbrain2.89e-1612
anatomical cluster2.39e-14373
epithelium3.49e-14306
spinal cord4.60e-143
dorsal region element4.60e-143
dorsum4.60e-143
organ part4.71e-14218
cell layer5.85e-14309
occipital lobe9.37e-145
medulla oblongata1.66e-133
myelencephalon1.66e-133
future myelencephalon1.66e-133
limbic system1.87e-135
pons4.34e-133
parietal lobe5.61e-135
caudate-putamen6.04e-133
dorsal striatum6.04e-133
frontal cortex8.39e-133
multi-tissue structure1.07e-10342
globus pallidus4.98e-102
pallidum4.98e-102
dorsal plus ventral thalamus6.76e-102
thalamic complex6.76e-102
multi cell component structure8.03e-102
neuron projection bundle8.03e-102
temporal lobe1.41e-096
locus ceruleus1.66e-092
brainstem nucleus1.66e-092
hindbrain nucleus1.66e-092
Ammon's horn1.97e-092
lobe parts of cerebral cortex1.97e-092
hippocampal formation1.97e-092
limbic lobe1.97e-092
caudate nucleus2.14e-092
future caudate nucleus2.14e-092
middle temporal gyrus2.23e-092
middle frontal gyrus3.12e-092
organ3.70e-08503
regional part of metencephalon1.61e-079
metencephalon1.61e-079
future metencephalon1.61e-079
germ layer5.60e-07560
germ layer / neural crest5.60e-07560
embryonic tissue5.60e-07560
presumptive structure5.60e-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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