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Coexpression cluster:C2130: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0015459!potassium channel regulator activity!0.0476617645314093!7881$GO:0016247!channel regulator activity!0.0476617645314093!7881
|gostat_on_coexpression_clusters=GO:0015459!potassium channel regulator activity!0.0476617645314093!7881$GO:0016247!channel regulator activity!0.0476617645314093!7881
|id=C2130
|id=C2130
|ontology_enrichment_celltype=CL:0002319!2.74e-07!25;CL:0000047!6.40e-07!8
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.95e-53!82;UBERON:0005743!2.75e-51!86;UBERON:0001049!2.98e-50!57;UBERON:0005068!2.98e-50!57;UBERON:0006241!2.98e-50!57;UBERON:0007135!2.98e-50!57;UBERON:0000073!4.97e-48!94;UBERON:0001016!4.97e-48!94;UBERON:0000955!1.13e-42!69;UBERON:0006238!1.13e-42!69;UBERON:0002616!2.50e-41!59;UBERON:0002780!1.27e-39!41;UBERON:0001890!1.27e-39!41;UBERON:0006240!1.27e-39!41;UBERON:0002346!6.36e-39!90;UBERON:0003075!2.45e-38!86;UBERON:0007284!2.45e-38!86;UBERON:0003080!2.86e-38!42;UBERON:0007023!6.16e-34!115;UBERON:0002020!1.70e-33!34;UBERON:0003528!1.70e-33!34;UBERON:0001893!1.85e-33!34;UBERON:0002791!1.96e-32!33;UBERON:0001869!1.54e-31!32;UBERON:0003056!7.58e-29!61;UBERON:0000924!6.90e-27!173;UBERON:0006601!6.90e-27!173;UBERON:0004121!4.81e-26!169;UBERON:0000153!3.06e-25!129;UBERON:0007811!3.06e-25!129;UBERON:0000033!7.52e-25!123;UBERON:0002619!1.97e-24!22;UBERON:0000956!5.48e-24!25;UBERON:0000203!5.48e-24!25;UBERON:0001950!2.87e-22!20;UBERON:0000025!7.57e-18!194;UBERON:0004111!1.86e-13!241;UBERON:0003076!9.96e-13!15;UBERON:0003057!9.96e-13!15;UBERON:0000477!2.73e-12!286;UBERON:0002420!4.20e-11!9;UBERON:0007245!4.20e-11!9;UBERON:0010009!4.20e-11!9;UBERON:0010011!4.20e-11!9;UBERON:0000454!4.20e-11!9;UBERON:0002308!6.33e-11!9;UBERON:0000125!6.33e-11!9;UBERON:0004732!9.23e-11!13;UBERON:0000475!1.80e-10!365;UBERON:0000483!3.61e-10!309;UBERON:0000119!4.19e-10!312;UBERON:0004733!6.22e-10!12;UBERON:0002028!6.22e-10!12;UBERON:0007277!6.22e-10!12;UBERON:0000481!1.41e-09!347;UBERON:0001871!1.65e-09!7;UBERON:0009663!5.66e-09!7;UBERON:0000922!2.17e-08!612;UBERON:0000064!1.07e-07!219;UBERON:0001894!1.73e-07!7;UBERON:0006222!1.73e-07!7;UBERON:0000200!1.84e-07!6;UBERON:0002680!2.84e-07!9;UBERON:0001895!2.84e-07!9;UBERON:0010092!2.84e-07!9;UBERON:0000349!5.79e-07!5;UBERON:0000062!8.19e-07!511;UBERON:0002298!8.33e-07!8;UBERON:0002050!8.60e-07!605;UBERON:0005423!8.60e-07!605
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}}
}}

Revision as of 12:06, 19 October 2012


Full id: C2130_brain_putamen_temporal_diencephalon_caudate_amygdala_occipital



Phase1 CAGE Peaks

Hg19::chr11:41244377..41244381,-p@chr11:41244377..41244381
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Hg19::chr19:46928841..46928843,-p@chr19:46928841..46928843
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Hg19::chr1:33359121..33359137,+p5@HPCA
Hg19::chr3:156009131..156009143,+p20@KCNAB1


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

GO IDGO nameFDR corrected p-value
GO:0015459potassium channel regulator activity0.0476617645314093
GO:0016247channel regulator activity0.0476617645314093



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 tube7.15e-10056
neural rod7.15e-10056
future spinal cord7.15e-10056
neural keel7.15e-10056
central nervous system5.51e-9581
regional part of nervous system5.37e-9353
regional part of brain5.37e-9353
nervous system4.97e-8489
brain5.72e-7968
future brain5.72e-7968
regional part of forebrain1.23e-7141
forebrain1.23e-7141
anterior neural tube1.23e-7141
future forebrain1.23e-7141
neural plate3.53e-6982
presumptive neural plate3.53e-6982
neurectoderm2.73e-6586
brain grey matter4.77e-6534
gray matter4.77e-6534
telencephalon5.44e-6534
cerebral hemisphere8.80e-6132
regional part of telencephalon1.39e-6032
adult organism1.02e-51114
ecto-epithelium1.81e-51104
pre-chordal neural plate6.81e-5061
regional part of cerebral cortex8.42e-4722
structure with developmental contribution from neural crest3.85e-46132
cerebral cortex1.62e-4425
pallium1.62e-4425
neocortex4.18e-4220
ectoderm-derived structure2.04e-39171
ectoderm2.04e-39171
presumptive ectoderm2.04e-39171
organ system subdivision7.23e-35223
posterior neural tube8.38e-2815
chordal neural plate8.38e-2815
tube1.94e-23192
basal ganglion4.18e-229
nuclear complex of neuraxis4.18e-229
aggregate regional part of brain4.18e-229
collection of basal ganglia4.18e-229
cerebral subcortex4.18e-229
neural nucleus7.82e-229
nucleus of brain7.82e-229
segmental subdivision of hindbrain1.95e-2112
hindbrain1.95e-2112
presumptive hindbrain1.95e-2112
segmental subdivision of nervous system1.39e-1913
anatomical cluster3.36e-19373
telencephalic nucleus1.59e-177
temporal lobe6.36e-176
anatomical conduit1.18e-16240
regional part of metencephalon1.23e-159
metencephalon1.23e-159
future metencephalon1.23e-159
brainstem1.17e-136
limbic system2.82e-135
epithelium1.48e-12306
cell layer2.72e-12309
organ part2.77e-12218
occipital lobe3.10e-125
parietal lobe4.10e-125
multi-tissue structure5.79e-12342
corpus striatum3.45e-114
striatum3.45e-114
ventral part of telencephalon3.45e-114
future corpus striatum3.45e-114
embryo1.40e-10592
gyrus2.06e-106
cerebellum1.20e-096
rhombic lip1.20e-096
embryonic structure1.23e-09564
regional part of diencephalon1.35e-094
organ2.20e-09503
developing anatomical structure2.40e-09581
germ layer3.02e-09560
germ layer / neural crest3.02e-09560
embryonic tissue3.02e-09560
presumptive structure3.02e-09560
germ layer / neural crest derived structure3.02e-09560
epiblast (generic)3.02e-09560
caudate-putamen7.95e-093
dorsal striatum7.95e-093
diencephalon1.92e-087
future diencephalon1.92e-087
spinal cord4.28e-083
dorsal region element4.28e-083
dorsum4.28e-083
pons8.28e-083
multi-cellular organism1.37e-07656
medulla oblongata1.62e-073
myelencephalon1.62e-073
future myelencephalon1.62e-073
anatomical system2.43e-07624
anatomical group2.68e-07625


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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