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Coexpression cluster:C3841: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3841_cerebellum_skeletal_insula_paracentral_frontal_occipital_parietal
|full_id=C3841_cerebellum_skeletal_insula_paracentral_frontal_occipital_parietal
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.010993053729904!23095$GO:0008088!axon cargo transport!0.010993053729904!23095$GO:0019894!kinesin binding!0.010993053729904!23095$GO:0007274!neuromuscular synaptic transmission!0.010993053729904!23095$GO:0007270!nerve-nerve synaptic transmission!0.0185633133458944!23095
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.010993053729904!23095$GO:0008088!axon cargo transport!0.010993053729904!23095$GO:0019894!kinesin binding!0.010993053729904!23095$GO:0007274!neuromuscular synaptic transmission!0.010993053729904!23095$GO:0007270!nerve-nerve synaptic transmission!0.0185633133458944!23095

Revision as of 16:49, 12 September 2012


Full id: C3841_cerebellum_skeletal_insula_paracentral_frontal_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr1:10270644..10270651,+p4@KIF1B
Hg19::chr1:53192114..53192150,+p1@ZYG11B
Hg19::chr2:170683942..170683972,+p1@UBR3


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:0008089anterograde axon cargo transport0.010993053729904
GO:0008088axon cargo transport0.010993053729904
GO:0019894kinesin binding0.010993053729904
GO:0007274neuromuscular synaptic transmission0.010993053729904
GO:0007270nerve-nerve synaptic transmission0.0185633133458944



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 organism2.35e-46115
central nervous system3.09e-2982
neural tube8.04e-2957
neural rod8.04e-2957
future spinal cord8.04e-2957
neural keel8.04e-2957
brain5.35e-2869
future brain5.35e-2869
regional part of brain1.36e-2659
anterior neural tube1.06e-2542
regional part of forebrain2.69e-2541
forebrain2.69e-2541
future forebrain2.69e-2541
regional part of nervous system3.15e-2594
nervous system3.15e-2594
telencephalon1.75e-2134
gray matter2.61e-2134
brain grey matter2.61e-2134
head3.34e-21123
anterior region of body3.53e-21129
craniocervical region3.53e-21129
regional part of telencephalon8.46e-2133
neural plate1.84e-2086
presumptive neural plate1.84e-2086
cerebral hemisphere3.08e-2032
neurectoderm2.45e-1990
ectoderm-derived structure6.65e-19169
ectoderm2.56e-18173
presumptive ectoderm2.56e-18173
cerebral cortex5.51e-1625
pallium5.51e-1625
regional part of cerebral cortex1.52e-1522
pre-chordal neural plate1.92e-1561
neocortex2.08e-1420
organ1.09e-12511
multi-cellular organism1.96e-10659
anatomical system1.66e-09625
anatomical group1.97e-09626
organism subdivision1.77e-08365
basal ganglion7.85e-079
nuclear complex of neuraxis7.85e-079
aggregate regional part of brain7.85e-079
collection of basal ganglia7.85e-079
cerebral subcortex7.85e-079
nucleus of brain8.82e-079
neural nucleus8.82e-079
embryo9.08e-07612


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0190057223604282
IRF1#365937.63716375356390.002244692747297240.0128098719105501
SIN3A#2594235.408884726815140.006318961977991520.0276799794488489
YY1#752834.911170749853860.008441455341808260.0329428725223493



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.