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Coexpression cluster:C1305: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!8.98e-98!56;UBERON:0005068!8.98e-98!56;UBERON:0006241!8.98e-98!56;UBERON:0007135!8.98e-98!56;UBERON:0001017!3.50e-95!81;UBERON:0000073!2.16e-91!53;UBERON:0002616!2.16e-91!53;UBERON:0001016!5.15e-87!89;UBERON:0002780!1.23e-82!41;UBERON:0001890!1.23e-82!41;UBERON:0003080!1.23e-82!41;UBERON:0006240!1.23e-82!41;UBERON:0000955!1.56e-76!68;UBERON:0006238!1.56e-76!68;UBERON:0002346!5.26e-70!86;UBERON:0001893!1.58e-68!34;UBERON:0003528!3.05e-68!34;UBERON:0002020!3.05e-68!34;UBERON:0003075!7.99e-68!82;UBERON:0007284!7.99e-68!82;UBERON:0002791!3.13e-64!32;UBERON:0001869!4.54e-64!32;UBERON:0007023!2.34e-61!114;UBERON:0003056!6.00e-55!61;UBERON:0010371!2.87e-50!104;UBERON:0000956!3.42e-49!25;UBERON:0000203!3.42e-49!25;UBERON:0010314!1.00e-46!132;UBERON:0004121!6.56e-46!171;UBERON:0000924!6.56e-46!171;UBERON:0006601!6.56e-46!171;UBERON:0002619!3.12e-44!22;UBERON:0001950!1.01e-39!20;UBERON:0011216!1.09e-32!223;UBERON:0000025!3.14e-23!192;UBERON:0002420!1.44e-20!9;UBERON:0007245!1.44e-20!9;UBERON:0010009!1.44e-20!9;UBERON:0010011!1.44e-20!9;UBERON:0000454!1.44e-20!9;UBERON:0000125!4.56e-20!9;UBERON:0002308!4.56e-20!9;UBERON:0000477!9.33e-20!373;UBERON:0004111!5.10e-18!240;UBERON:0003076!1.35e-16!15;UBERON:0003057!1.35e-16!15;UBERON:0009663!2.99e-16!7;UBERON:0001894!5.31e-15!7;UBERON:0006222!5.31e-15!7;UBERON:0000200!3.30e-14!6;UBERON:0002298!3.62e-14!6;UBERON:0000349!1.72e-12!5;UBERON:0000483!3.11e-12!306;UBERON:0000119!5.77e-12!309;UBERON:0001871!1.07e-11!6;UBERON:0002021!1.32e-11!5;UBERON:0001872!1.64e-11!5;UBERON:0004733!2.78e-11!12;UBERON:0002028!2.78e-11!12;UBERON:0007277!2.78e-11!12;UBERON:0000481!7.19e-11!342;UBERON:0004732!2.73e-10!13;UBERON:0000369!7.38e-10!4;UBERON:0002435!7.38e-10!4;UBERON:0000204!7.38e-10!4;UBERON:0010082!7.38e-10!4;UBERON:0000064!1.25e-09!218;UBERON:0002784!2.06e-09!4;UBERON:0003296!6.08e-09!4;UBERON:0010133!6.08e-09!4;UBERON:0001896!1.94e-08!3;UBERON:0005290!1.94e-08!3;UBERON:0010096!1.94e-08!3;UBERON:0001870!6.11e-08!3;UBERON:0005383!7.86e-08!3;UBERON:0005382!7.86e-08!3;UBERON:0000922!8.06e-08!592;UBERON:0002240!1.41e-07!3;UBERON:0005174!1.41e-07!3;UBERON:0001137!1.41e-07!3;UBERON:0000988!2.02e-07!3;UBERON:0000923!2.40e-07!560;UBERON:0010316!2.40e-07!560;UBERON:0005291!2.40e-07!560;UBERON:0006598!2.40e-07!560;UBERON:0010317!2.40e-07!560;UBERON:0002532!2.40e-07!560;UBERON:0005423!2.68e-07!581;UBERON:0002050!3.69e-07!564
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}}
}}

Revision as of 14:48, 26 November 2012


Full id: C1305_neuroectodermal_medulla_retina_peripheral_hippocampus_caudate_pituitary



Phase1 CAGE Peaks

Hg19::chr10:18240899..18240911,+p3@SLC39A12
Hg19::chr12:20848282..20848305,+p6@SLCO1C1
Hg19::chr12:20848316..20848349,+p3@SLCO1C1
Hg19::chr12:20848377..20848399,+p5@SLCO1C1
Hg19::chr12:20848404..20848452,+p2@SLCO1C1
Hg19::chr12:20848471..20848483,+p8@SLCO1C1


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:0006829zinc ion transport0.0185258703232524
GO:0006811ion transport0.0185258703232524
GO:0000041transition metal ion transport0.0459694753598906



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
neuronal stem cell5.18e-098
Uber Anatomy
Ontology termp-valuen
neural tube8.98e-9856
neural rod8.98e-9856
future spinal cord8.98e-9856
neural keel8.98e-9856
central nervous system3.50e-9581
regional part of nervous system2.16e-9153
regional part of brain2.16e-9153
nervous system5.15e-8789
regional part of forebrain1.23e-8241
forebrain1.23e-8241
anterior neural tube1.23e-8241
future forebrain1.23e-8241
brain1.56e-7668
future brain1.56e-7668
neurectoderm5.26e-7086
telencephalon1.58e-6834
brain grey matter3.05e-6834
gray matter3.05e-6834
neural plate7.99e-6882
presumptive neural plate7.99e-6882
regional part of telencephalon3.13e-6432
cerebral hemisphere4.54e-6432
adult organism2.34e-61114
pre-chordal neural plate6.00e-5561
ecto-epithelium2.87e-50104
cerebral cortex3.42e-4925
pallium3.42e-4925
structure with developmental contribution from neural crest1.00e-46132
ectoderm-derived structure6.56e-46171
ectoderm6.56e-46171
presumptive ectoderm6.56e-46171
regional part of cerebral cortex3.12e-4422
neocortex1.01e-3920
organ system subdivision1.09e-32223
tube3.14e-23192
basal ganglion1.44e-209
nuclear complex of neuraxis1.44e-209
aggregate regional part of brain1.44e-209
collection of basal ganglia1.44e-209
cerebral subcortex1.44e-209
neural nucleus4.56e-209
nucleus of brain4.56e-209
anatomical cluster9.33e-20373
anatomical conduit5.10e-18240
posterior neural tube1.35e-1615
chordal neural plate1.35e-1615
telencephalic nucleus2.99e-167
diencephalon5.31e-157
future diencephalon5.31e-157
gyrus3.30e-146
brainstem3.62e-146
limbic system1.72e-125
epithelium3.11e-12306
cell layer5.77e-12309
temporal lobe1.07e-116
occipital lobe1.32e-115
parietal lobe1.64e-115
segmental subdivision of hindbrain2.78e-1112
hindbrain2.78e-1112
presumptive hindbrain2.78e-1112
multi-tissue structure7.19e-11342
segmental subdivision of nervous system2.73e-1013
corpus striatum7.38e-104
striatum7.38e-104
ventral part of telencephalon7.38e-104
future corpus striatum7.38e-104
organ part1.25e-09218
regional part of diencephalon2.06e-094
gland of diencephalon6.08e-094
neuroendocrine gland6.08e-094
medulla oblongata1.94e-083
myelencephalon1.94e-083
future myelencephalon1.94e-083
frontal cortex6.11e-083
caudate-putamen7.86e-083
dorsal striatum7.86e-083
embryo8.06e-08592
spinal cord1.41e-073
dorsal region element1.41e-073
dorsum1.41e-073
pons2.02e-073
germ layer2.40e-07560
germ layer / neural crest2.40e-07560
embryonic tissue2.40e-07560
presumptive structure2.40e-07560
germ layer / neural crest derived structure2.40e-07560
epiblast (generic)2.40e-07560
developing anatomical structure2.68e-07581
embryonic structure3.69e-07564


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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