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Coexpression cluster:C705: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!9.98e-77!56;UBERON:0005068!9.98e-77!56;UBERON:0006241!9.98e-77!56;UBERON:0007135!9.98e-77!56;UBERON:0000073!1.26e-76!53;UBERON:0002616!1.26e-76!53;UBERON:0000955!2.67e-68!68;UBERON:0006238!2.67e-68!68;UBERON:0003528!3.01e-64!34;UBERON:0002020!3.01e-64!34;UBERON:0001017!5.02e-63!81;UBERON:0001016!1.01e-62!89;UBERON:0002780!8.61e-62!41;UBERON:0001890!8.61e-62!41;UBERON:0003080!8.61e-62!41;UBERON:0006240!8.61e-62!41;UBERON:0001893!4.61e-59!34;UBERON:0002791!7.63e-58!32;UBERON:0001869!9.48e-58!32;UBERON:0002346!1.75e-53!86;UBERON:0002619!4.49e-52!22;UBERON:0003075!4.57e-50!82;UBERON:0007284!4.57e-50!82;UBERON:0000956!1.54e-45!25;UBERON:0000203!1.54e-45!25;UBERON:0001950!9.31e-45!20;UBERON:0003056!1.17e-39!61;UBERON:0010371!8.08e-38!104;UBERON:0004121!2.50e-32!171;UBERON:0000924!2.50e-32!171;UBERON:0006601!2.50e-32!171;UBERON:0010314!3.92e-30!132;UBERON:0007023!1.79e-29!114;UBERON:0011216!9.70e-23!223;UBERON:0000125!7.92e-20!9;UBERON:0002308!7.92e-20!9;UBERON:0000025!8.69e-17!192;UBERON:0000200!3.08e-16!6;UBERON:0003076!1.07e-15!15;UBERON:0003057!1.07e-15!15;UBERON:0002680!1.80e-15!9;UBERON:0001895!1.80e-15!9;UBERON:0010092!1.80e-15!9;UBERON:0004733!2.09e-15!12;UBERON:0002028!2.09e-15!12;UBERON:0007277!2.09e-15!12;UBERON:0002420!4.99e-15!9;UBERON:0007245!4.99e-15!9;UBERON:0010009!4.99e-15!9;UBERON:0010011!4.99e-15!9;UBERON:0000454!4.99e-15!9;UBERON:0004732!3.82e-14!13;UBERON:0001871!8.27e-14!6;UBERON:0009663!1.54e-13!7;UBERON:0001872!2.42e-13!5;UBERON:0000349!3.77e-13!5;UBERON:0001870!1.21e-12!3;UBERON:0004111!7.95e-12!240;UBERON:0000988!1.18e-11!3;UBERON:0000064!8.05e-11!218;UBERON:0002298!3.29e-10!6;UBERON:0000477!6.64e-10!373;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:0000369!2.73e-09!4;UBERON:0002435!2.73e-09!4;UBERON:0000204!2.73e-09!4;UBERON:0010082!2.73e-09!4;UBERON:0002702!3.47e-09!2;UBERON:0000007!8.35e-09!2;UBERON:0002771!8.69e-09!2;UBERON:0002148!1.97e-08!2;UBERON:0006331!1.97e-08!2;UBERON:0009662!1.97e-08!2;UBERON:0000483!2.65e-08!306;UBERON:0000119!3.81e-08!309;UBERON:0002021!5.48e-08!5;UBERON:0002037!5.16e-07!6;UBERON:0006215!5.16e-07!6
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|tfbs_overrepresentation_for_novel_motifs=0.22923,0.00275938,0.223258,0.345441,0.190185,0.344001,0.411652,0.340819,0.102889,0.0552668,0.317729,0.451026,0.0765797,0.401301,0.553807,0.207465,0.617549,0.148925,0.0839658,0.0292507,0.635173,0.0148753,0.337221,0.546841,0.260754,0.471832,0.0648754,0.335332,0.562141,0.206722,0.298956,0.65246,0.12577,0.268295,0.163884,0.0497783,0.161511,0.345014,0.871544,0.0916487,0.162847,0.285097,0.0815132,0.187953,0.00327556,0.24831,0.412635,0.308385,0.369629,0.192687,0.484909,0.423285,0.0382824,0.725869,0.873575,0.403938,0.570319,0.374657,0.0564659,0.373762,1.65239,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.108268,0.0373297,0.871629,0.0739759,0.237079,0.059808,0.575479,0.639503,0.255642,0.0868483,0.590372,0.4307,1.70185,0.821696,0.180819,0.527748,0.440676,0.508983,1.42111,1.05129,0.795567,1.60439,0.409242,0.190761,0.140087,0.282722,0.709167,0.51326,0.396174,0.446192,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,0.177931,0.232335,0.701175,0.624605,0.325885,1.00416,3.65403,0.104888,0.297931,0.556847,0.132787,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.140769,0.796235,0.301402,0.919079,0.437919,1.06395,19.6857,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.403378,0.0329025,0.0163338,0.796604,0.0978005,0.414334,1.19239,0.494,0.530398,0.260802,0.237047,0.984474,0.778717,0.638755,0.239672,1.38738,0.429983,0.120139,0.410452,0.00249101
}}
}}

Revision as of 14:25, 26 November 2012


Full id: C705_small_cerebellum_parietal_occipital_temporal_amygdala_olfactory



Phase1 CAGE Peaks

Hg19::chr17:47653077..47653091,+p3@NXPH3
Hg19::chr20:30573367..30573378,+p@chr20:30573367..30573378
+
Hg19::chr20:30574743..30574753,+p@chr20:30574743..30574753
+
Hg19::chr20:30574762..30574771,+p@chr20:30574762..30574771
+
Hg19::chr6:102297713..102297717,+p@chr6:102297713..102297717
+
Hg19::chr6:102357270..102357274,+p@chr6:102357270..102357274
+
Hg19::chr6:102358656..102358697,+p@chr6:102358656..102358697
+
Hg19::chr6:102365472..102365475,+p@chr6:102365472..102365475
+
Hg19::chr6:102367060..102367078,+p@chr6:102367060..102367078
+
Hg19::chr6:102368618..102368631,+p@chr6:102368618..102368631
+
Hg19::chr6:102374094..102374097,+p@chr6:102374094..102374097
+
Hg19::chr7:29274566..29274570,+p@chr7:29274566..29274570
+


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 tube9.98e-7756
neural rod9.98e-7756
future spinal cord9.98e-7756
neural keel9.98e-7756
regional part of nervous system1.26e-7653
regional part of brain1.26e-7653
brain2.67e-6868
future brain2.67e-6868
brain grey matter3.01e-6434
gray matter3.01e-6434
central nervous system5.02e-6381
nervous system1.01e-6289
regional part of forebrain8.61e-6241
forebrain8.61e-6241
anterior neural tube8.61e-6241
future forebrain8.61e-6241
telencephalon4.61e-5934
regional part of telencephalon7.63e-5832
cerebral hemisphere9.48e-5832
neurectoderm1.75e-5386
regional part of cerebral cortex4.49e-5222
neural plate4.57e-5082
presumptive neural plate4.57e-5082
cerebral cortex1.54e-4525
pallium1.54e-4525
neocortex9.31e-4520
pre-chordal neural plate1.17e-3961
ecto-epithelium8.08e-38104
ectoderm-derived structure2.50e-32171
ectoderm2.50e-32171
presumptive ectoderm2.50e-32171
structure with developmental contribution from neural crest3.92e-30132
adult organism1.79e-29114
organ system subdivision9.70e-23223
neural nucleus7.92e-209
nucleus of brain7.92e-209
tube8.69e-17192
gyrus3.08e-166
posterior neural tube1.07e-1515
chordal neural plate1.07e-1515
regional part of metencephalon1.80e-159
metencephalon1.80e-159
future metencephalon1.80e-159
segmental subdivision of hindbrain2.09e-1512
hindbrain2.09e-1512
presumptive hindbrain2.09e-1512
basal ganglion4.99e-159
nuclear complex of neuraxis4.99e-159
aggregate regional part of brain4.99e-159
collection of basal ganglia4.99e-159
cerebral subcortex4.99e-159
segmental subdivision of nervous system3.82e-1413
temporal lobe8.27e-146
telencephalic nucleus1.54e-137
parietal lobe2.42e-135
limbic system3.77e-135
frontal cortex1.21e-123
anatomical conduit7.95e-12240
pons1.18e-113
organ part8.05e-11218
brainstem3.29e-106
anatomical cluster6.64e-10373
Ammon's horn1.97e-092
lobe parts of cerebral cortex1.97e-092
hippocampal formation1.97e-092
limbic lobe1.97e-092
corpus striatum2.73e-094
striatum2.73e-094
ventral part of telencephalon2.73e-094
future corpus striatum2.73e-094
middle frontal gyrus3.47e-092
pituitary gland8.35e-092
middle temporal gyrus8.69e-092
locus ceruleus1.97e-082
brainstem nucleus1.97e-082
hindbrain nucleus1.97e-082
epithelium2.65e-08306
cell layer3.81e-08309
occipital lobe5.48e-085
cerebellum5.16e-076
rhombic lip5.16e-076


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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