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Coexpression cluster:C2199: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.11e-117!56;UBERON:0005068!1.11e-117!56;UBERON:0006241!1.11e-117!56;UBERON:0007135!1.11e-117!56;UBERON:0000073!1.63e-112!53;UBERON:0002616!1.63e-112!53;UBERON:0002780!3.35e-105!41;UBERON:0001890!3.35e-105!41;UBERON:0003080!3.35e-105!41;UBERON:0006240!3.35e-105!41;UBERON:0003528!1.94e-97!34;UBERON:0002020!1.94e-97!34;UBERON:0001893!2.99e-91!34;UBERON:0001017!6.90e-91!81;UBERON:0001869!1.63e-90!32;UBERON:0002791!5.26e-90!32;UBERON:0000955!1.29e-89!68;UBERON:0006238!1.29e-89!68;UBERON:0003075!4.04e-82!82;UBERON:0007284!4.04e-82!82;UBERON:0001016!3.84e-81!89;UBERON:0002346!6.01e-78!86;UBERON:0003056!4.69e-73!61;UBERON:0002619!1.20e-70!22;UBERON:0007023!7.58e-67!114;UBERON:0010371!4.23e-63!104;UBERON:0001950!6.40e-63!20;UBERON:0000956!6.40e-62!25;UBERON:0000203!6.40e-62!25;UBERON:0010314!2.39e-53!132;UBERON:0004121!9.07e-41!171;UBERON:0000924!9.07e-41!171;UBERON:0006601!9.07e-41!171;UBERON:0002420!4.06e-38!9;UBERON:0007245!4.06e-38!9;UBERON:0010009!4.06e-38!9;UBERON:0010011!4.06e-38!9;UBERON:0000454!4.06e-38!9;UBERON:0000125!1.54e-37!9;UBERON:0002308!1.54e-37!9;UBERON:0009663!2.69e-30!7;UBERON:0011216!2.73e-29!223;UBERON:0000025!1.16e-28!192;UBERON:0000200!3.84e-26!6;UBERON:0002021!2.44e-21!5;UBERON:0000349!3.15e-21!5;UBERON:0004111!3.33e-21!240;UBERON:0000369!1.77e-18!4;UBERON:0002435!1.77e-18!4;UBERON:0000204!1.77e-18!4;UBERON:0010082!1.77e-18!4;UBERON:0002298!2.33e-16!6;UBERON:0000064!4.98e-16!218;UBERON:0003076!7.68e-16!15;UBERON:0003057!7.68e-16!15;UBERON:0000483!9.12e-16!306;UBERON:0000119!1.58e-15!309;UBERON:0001871!2.27e-15!6;UBERON:0000477!6.09e-15!373;UBERON:0001894!6.26e-15!7;UBERON:0006222!6.26e-15!7;UBERON:0005383!1.78e-14!3;UBERON:0005382!1.78e-14!3;UBERON:0001872!2.07e-14!5;UBERON:0001870!5.09e-14!3;UBERON:0000988!1.27e-12!3;UBERON:0000481!3.07e-12!342;UBERON:0004733!2.02e-11!12;UBERON:0002028!2.02e-11!12;UBERON:0007277!2.02e-11!12;UBERON:0004732!1.69e-10!13;UBERON:0001873!2.50e-10!2;UBERON:0010122!2.50e-10!2;UBERON:0001875!4.46e-10!2;UBERON:0006514!4.46e-10!2;UBERON:0002771!5.09e-10!2;UBERON:0002702!6.63e-10!2;UBERON:0001897!1.12e-09!2;UBERON:0010225!1.12e-09!2;UBERON:0001876!1.51e-09!2;UBERON:0001954!2.13e-09!2;UBERON:0003022!2.13e-09!2;UBERON:0002421!2.13e-09!2;UBERON:0002600!2.13e-09!2;UBERON:0002360!3.68e-09!2;UBERON:0000094!3.68e-09!2;UBERON:0010743!3.68e-09!2;UBERON:0002148!5.57e-09!2;UBERON:0006331!5.57e-09!2;UBERON:0009662!5.57e-09!2;UBERON:0000007!5.81e-09!2;UBERON:0000062!1.22e-08!503;UBERON:0000923!1.78e-07!560;UBERON:0010316!1.78e-07!560;UBERON:0005291!1.78e-07!560;UBERON:0006598!1.78e-07!560;UBERON:0010317!1.78e-07!560;UBERON:0002532!1.78e-07!560;UBERON:0002050!2.36e-07!564;UBERON:0002680!2.51e-07!9;UBERON:0001895!2.51e-07!9;UBERON:0010092!2.51e-07!9;UBERON:0005423!7.38e-07!581
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}}
}}

Revision as of 15:21, 26 November 2012


Full id: C2199_caudate_parietal_occipital_middle_medial_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr12:19358228..19358248,+p7@PLEKHA5
Hg19::chr2:152527863..152527893,-p4@NEB
Hg19::chr2:3050387..3050399,-p@chr2:3050387..3050399
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Hg19::chr9:138594018..138594036,+p4@KCNT1


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:0007525somatic muscle development0.027319432152077
GO:0030018Z disc0.027319432152077
GO:0031674I band0.027319432152077
GO:0005545phosphatidylinositol binding0.027319432152077
GO:0015269calcium-activated potassium channel activity0.027319432152077
GO:0022839ion gated channel activity0.027319432152077
GO:0005227calcium activated cation channel activity0.027319432152077
GO:0008307structural constituent of muscle0.027319432152077
GO:0030832regulation of actin filament length0.027319432152077
GO:0032535regulation of cellular component size0.027319432152077
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.027319432152077
GO:0030017sarcomere0.027319432152077
GO:0030016myofibril0.027319432152077
GO:0051493regulation of cytoskeleton organization and biogenesis0.027319432152077
GO:0033043regulation of organelle organization and biogenesis0.027319432152077
GO:0044449contractile fiber part0.027438161099036
GO:0043292contractile fiber0.0275425165044705
GO:0051128regulation of cellular component organization and biogenesis0.0406012548667762



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 tube1.11e-11756
neural rod1.11e-11756
future spinal cord1.11e-11756
neural keel1.11e-11756
regional part of nervous system1.63e-11253
regional part of brain1.63e-11253
regional part of forebrain3.35e-10541
forebrain3.35e-10541
anterior neural tube3.35e-10541
future forebrain3.35e-10541
brain grey matter1.94e-9734
gray matter1.94e-9734
telencephalon2.99e-9134
central nervous system6.90e-9181
cerebral hemisphere1.63e-9032
regional part of telencephalon5.26e-9032
brain1.29e-8968
future brain1.29e-8968
neural plate4.04e-8282
presumptive neural plate4.04e-8282
nervous system3.84e-8189
neurectoderm6.01e-7886
pre-chordal neural plate4.69e-7361
regional part of cerebral cortex1.20e-7022
adult organism7.58e-67114
ecto-epithelium4.23e-63104
neocortex6.40e-6320
cerebral cortex6.40e-6225
pallium6.40e-6225
structure with developmental contribution from neural crest2.39e-53132
ectoderm-derived structure9.07e-41171
ectoderm9.07e-41171
presumptive ectoderm9.07e-41171
basal ganglion4.06e-389
nuclear complex of neuraxis4.06e-389
aggregate regional part of brain4.06e-389
collection of basal ganglia4.06e-389
cerebral subcortex4.06e-389
neural nucleus1.54e-379
nucleus of brain1.54e-379
telencephalic nucleus2.69e-307
organ system subdivision2.73e-29223
tube1.16e-28192
gyrus3.84e-266
occipital lobe2.44e-215
limbic system3.15e-215
anatomical conduit3.33e-21240
corpus striatum1.77e-184
striatum1.77e-184
ventral part of telencephalon1.77e-184
future corpus striatum1.77e-184
brainstem2.33e-166
organ part4.98e-16218
posterior neural tube7.68e-1615
chordal neural plate7.68e-1615
epithelium9.12e-16306
cell layer1.58e-15309
temporal lobe2.27e-156
anatomical cluster6.09e-15373
diencephalon6.26e-157
future diencephalon6.26e-157
caudate-putamen1.78e-143
dorsal striatum1.78e-143
parietal lobe2.07e-145
frontal cortex5.09e-143
pons1.27e-123
multi-tissue structure3.07e-12342
segmental subdivision of hindbrain2.02e-1112
hindbrain2.02e-1112
presumptive hindbrain2.02e-1112
segmental subdivision of nervous system1.69e-1013
caudate nucleus2.50e-102
future caudate nucleus2.50e-102
globus pallidus4.46e-102
pallidum4.46e-102
middle temporal gyrus5.09e-102
middle frontal gyrus6.63e-102
dorsal plus ventral thalamus1.12e-092
thalamic complex1.12e-092
amygdala1.51e-092
Ammon's horn2.13e-092
lobe parts of cerebral cortex2.13e-092
hippocampal formation2.13e-092
limbic lobe2.13e-092
meninx3.68e-092
membrane organ3.68e-092
meningeal cluster3.68e-092
locus ceruleus5.57e-092
brainstem nucleus5.57e-092
hindbrain nucleus5.57e-092
pituitary gland5.81e-092
organ1.22e-08503
germ layer1.78e-07560
germ layer / neural crest1.78e-07560
embryonic tissue1.78e-07560
presumptive structure1.78e-07560
germ layer / neural crest derived structure1.78e-07560
epiblast (generic)1.78e-07560
embryonic structure2.36e-07564
regional part of metencephalon2.51e-079


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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