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Coexpression cluster:C3749: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.70e-78!82;UBERON:0000073!1.90e-76!94;UBERON:0001016!1.90e-76!94;UBERON:0005743!5.03e-76!86;UBERON:0001049!1.26e-74!57;UBERON:0005068!1.26e-74!57;UBERON:0006241!1.26e-74!57;UBERON:0007135!1.26e-74!57;UBERON:0000955!1.40e-64!69;UBERON:0006238!1.40e-64!69;UBERON:0002616!1.72e-62!59;UBERON:0002780!1.74e-59!41;UBERON:0001890!1.74e-59!41;UBERON:0006240!1.74e-59!41;UBERON:0003080!9.26e-58!42;UBERON:0002346!1.65e-55!90;UBERON:0003075!5.47e-53!86;UBERON:0007284!5.47e-53!86;UBERON:0002020!9.99e-50!34;UBERON:0003528!9.99e-50!34;UBERON:0001893!1.40e-49!34;UBERON:0002791!2.93e-48!33;UBERON:0001869!2.94e-46!32;UBERON:0003056!9.86e-42!61;UBERON:0000924!1.06e-41!173;UBERON:0006601!1.06e-41!173;UBERON:0004121!2.23e-39!169;UBERON:0000956!5.41e-36!25;UBERON:0000203!5.41e-36!25;UBERON:0002619!1.65e-32!22;UBERON:0000033!2.02e-32!123;UBERON:0000153!4.66e-30!129;UBERON:0007811!4.66e-30!129;UBERON:0001950!1.21e-29!20;UBERON:0007023!6.93e-27!115;UBERON:0003076!3.22e-17!15;UBERON:0003057!3.22e-17!15;UBERON:0002308!5.82e-15!9;UBERON:0000125!5.82e-15!9;UBERON:0002420!6.52e-15!9;UBERON:0007245!6.52e-15!9;UBERON:0010009!6.52e-15!9;UBERON:0010011!6.52e-15!9;UBERON:0000454!6.52e-15!9;UBERON:0000025!8.05e-15!194;UBERON:0004732!4.02e-14!13;UBERON:0004733!6.86e-13!12;UBERON:0002028!6.86e-13!12;UBERON:0007277!6.86e-13!12;UBERON:0009663!5.56e-12!7;UBERON:0000475!2.20e-11!365;UBERON:0001894!4.84e-11!7;UBERON:0006222!4.84e-11!7;UBERON:0000200!1.38e-10!6;UBERON:0001871!1.74e-10!7;UBERON:0002298!2.74e-10!8;UBERON:0004111!8.99e-10!241;UBERON:0000064!1.45e-09!219;UBERON:0002021!3.16e-09!5;UBERON:0001872!5.45e-09!5;UBERON:0002680!1.06e-08!9;UBERON:0001895!1.06e-08!9;UBERON:0010092!1.06e-08!9;UBERON:0000349!1.17e-08!5;UBERON:0000483!1.25e-07!309;UBERON:0000922!1.35e-07!612;UBERON:0000369!1.91e-07!4;UBERON:0002435!1.91e-07!4;UBERON:0000204!1.91e-07!4;UBERON:0010082!1.91e-07!4;UBERON:0000119!2.13e-07!312;UBERON:0000477!4.00e-07!286;UBERON:0000468!4.23e-07!659
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}}
}}

Revision as of 19:25, 8 August 2012


Full id: C3749_brain_Neurons_parietal_occipital_temporal_cerebellum_medial



Phase1 CAGE Peaks

Hg19::chr19:11562404..11562424,-p@chr19:11562404..11562424
-
Hg19::chr2:27170763..27170781,+p5@DPYSL5
Hg19::chr8:80577410..80577417,+p@chr8:80577410..80577417
+


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neural cell3.63e-1125
neuronal stem cell1.11e-098
neuron4.48e-076
neuroblast4.48e-076
electrically signaling cell4.48e-076
neurectodermal cell9.05e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system2.70e-7882
regional part of nervous system1.90e-7694
nervous system1.90e-7694
neural tube1.26e-7457
neural rod1.26e-7457
future spinal cord1.26e-7457
neural keel1.26e-7457
brain1.40e-6469
future brain1.40e-6469
regional part of brain1.72e-6259
regional part of forebrain1.74e-5941
forebrain1.74e-5941
future forebrain1.74e-5941
anterior neural tube9.26e-5842
neurectoderm1.65e-5590
neural plate5.47e-5386
presumptive neural plate5.47e-5386
gray matter9.99e-5034
brain grey matter9.99e-5034
telencephalon1.40e-4934
regional part of telencephalon2.93e-4833
cerebral hemisphere2.94e-4632
pre-chordal neural plate9.86e-4261
ectoderm1.06e-41173
presumptive ectoderm1.06e-41173
ectoderm-derived structure2.23e-39169
cerebral cortex5.41e-3625
pallium5.41e-3625
regional part of cerebral cortex1.65e-3222
head2.02e-32123
anterior region of body4.66e-30129
craniocervical region4.66e-30129
neocortex1.21e-2920
adult organism6.93e-27115
posterior neural tube3.22e-1715
chordal neural plate3.22e-1715
nucleus of brain5.82e-159
neural nucleus5.82e-159
basal ganglion6.52e-159
nuclear complex of neuraxis6.52e-159
aggregate regional part of brain6.52e-159
collection of basal ganglia6.52e-159
cerebral subcortex6.52e-159
tube8.05e-15194
segmental subdivision of nervous system4.02e-1413
segmental subdivision of hindbrain6.86e-1312
hindbrain6.86e-1312
presumptive hindbrain6.86e-1312
telencephalic nucleus5.56e-127
organism subdivision2.20e-11365
diencephalon4.84e-117
future diencephalon4.84e-117
gyrus1.38e-106
temporal lobe1.74e-107
brainstem2.74e-108
anatomical conduit8.99e-10241
organ part1.45e-09219
occipital lobe3.16e-095
parietal lobe5.45e-095
regional part of metencephalon1.06e-089
metencephalon1.06e-089
future metencephalon1.06e-089
limbic system1.17e-085
epithelium1.25e-07309
embryo1.35e-07612
corpus striatum1.91e-074
striatum1.91e-074
ventral part of telencephalon1.91e-074
future corpus striatum1.91e-074
cell layer2.13e-07312
anatomical cluster4.00e-07286
multi-cellular organism4.23e-07659


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.