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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1414_Wilms_cerebellum_parietal_hippocampus_medial_caudate_middle
|full_id=C1414_Wilms_cerebellum_parietal_hippocampus_medial_caudate_middle
|gostat_on_coexpression_clusters=GO:0043121!neurotrophin binding!0.00853644177557988!4916
|gostat_on_coexpression_clusters=GO:0043121!neurotrophin binding!0.00853644177557988!4916

Revision as of 13:57, 12 September 2012


Full id: C1414_Wilms_cerebellum_parietal_hippocampus_medial_caudate_middle



Phase1 CAGE Peaks

Hg19::chr15:88740321..88740326,-p@chr15:88740321..88740326
-
Hg19::chr15:88799384..88799430,-p3@NTRK3
Hg19::chr15:88799702..88799755,-p5@NTRK3
Hg19::chr15:88799926..88799941,-p2@NTRK3
Hg19::chr15:88799948..88799977,-p1@NTRK3
Hg19::chr7:54609955..54609962,+p13@VSTM2A


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:0043121neurotrophin binding0.00853644177557988



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
adult organism4.03e-50115
central nervous system7.22e-4782
regional part of nervous system1.08e-4394
nervous system1.08e-4394
neural tube6.03e-4257
neural rod6.03e-4257
future spinal cord6.03e-4257
neural keel6.03e-4257
regional part of brain3.29e-4159
brain1.41e-3969
future brain1.41e-3969
neural plate9.03e-3586
presumptive neural plate9.03e-3586
neurectoderm2.92e-3390
anterior neural tube5.67e-3242
regional part of forebrain1.55e-3141
forebrain1.55e-3141
future forebrain1.55e-3141
gray matter2.18e-2734
brain grey matter2.18e-2734
telencephalon2.60e-2734
regional part of telencephalon1.49e-2633
cerebral hemisphere4.73e-2632
ectoderm-derived structure1.72e-25169
ectoderm6.17e-25173
presumptive ectoderm6.17e-25173
anterior region of body4.57e-23129
craniocervical region4.57e-23129
pre-chordal neural plate1.72e-2261
head4.63e-22123
cerebral cortex1.07e-2025
pallium1.07e-2025
regional part of cerebral cortex5.30e-1922
neocortex2.01e-1720
tube1.83e-13194
anatomical cluster6.19e-11286
posterior neural tube7.04e-1115
chordal neural plate7.04e-1115
anatomical conduit8.60e-10241
segmental subdivision of nervous system1.52e-0913
segmental subdivision of hindbrain7.08e-0912
hindbrain7.08e-0912
presumptive hindbrain7.08e-0912
organ7.94e-09511
organism subdivision1.18e-08365
basal ganglion2.76e-089
nuclear complex of neuraxis2.76e-089
aggregate regional part of brain2.76e-089
collection of basal ganglia2.76e-089
cerebral subcortex2.76e-089
nucleus of brain4.14e-089
neural nucleus4.14e-089
organ part6.43e-08219
temporal lobe1.35e-077
multi-cellular organism3.14e-07659
cell layer6.88e-07312
regional part of metencephalon7.93e-079
metencephalon7.93e-079
future metencephalon7.93e-079
brainstem9.45e-078


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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