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Coexpression cluster:C3042: Difference between revisions

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}}
}}

Revision as of 15:53, 26 November 2012


Full id: C3042_optic_cerebellum_temporal_skeletal_occipital_parietal_globus



Phase1 CAGE Peaks

Hg19::chr10:735553..735647,-p1@DIP2C
Hg19::chr10:735808..735834,-p2@DIP2C
Hg19::chr1:10270585..10270614,+p2@KIF1B


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 transport0.00980103585557702
GO:0008088axon cargo transport0.00980103585557702
GO:0019894kinesin binding0.00980103585557702
GO:0007274neuromuscular synaptic transmission0.00980103585557702
GO:0007270nerve-nerve synaptic transmission0.016550423946942



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
neurectodermal cell9.06e-0859
Uber Anatomy
Ontology termp-valuen
nervous system9.87e-3889
central nervous system5.97e-3681
neural tube5.91e-3456
neural rod5.91e-3456
future spinal cord5.91e-3456
neural keel5.91e-3456
ectoderm-derived structure1.45e-32171
ectoderm1.45e-32171
presumptive ectoderm1.45e-32171
adult organism2.07e-32114
regional part of nervous system5.02e-3253
regional part of brain5.02e-3253
brain1.43e-3168
future brain1.43e-3168
neurectoderm2.30e-3186
neural plate7.96e-3182
presumptive neural plate7.96e-3182
structure with developmental contribution from neural crest5.45e-26132
regional part of forebrain1.42e-2541
forebrain1.42e-2541
anterior neural tube1.42e-2541
future forebrain1.42e-2541
ecto-epithelium7.57e-25104
brain grey matter6.91e-2234
gray matter6.91e-2234
pre-chordal neural plate6.93e-2261
telencephalon7.77e-2234
regional part of telencephalon1.37e-2032
cerebral hemisphere1.71e-2032
organ system subdivision2.06e-20223
anatomical cluster8.76e-20373
multi-cellular organism1.16e-19656
multi-tissue structure1.03e-16342
cerebral cortex4.51e-1625
pallium4.51e-1625
regional part of cerebral cortex3.57e-1522
anatomical conduit1.10e-14240
anatomical system1.82e-14624
cell layer1.97e-14309
anatomical group3.11e-14625
epithelium3.40e-14306
neocortex5.64e-1420
tube9.31e-14192
embryo2.35e-12592
organ1.36e-11503
developing anatomical structure5.19e-11581
organ part2.33e-10218
germ layer4.77e-10560
germ layer / neural crest4.77e-10560
embryonic tissue4.77e-10560
presumptive structure4.77e-10560
germ layer / neural crest derived structure4.77e-10560
epiblast (generic)4.77e-10560
embryonic structure9.14e-10564
posterior neural tube1.99e-0915
chordal neural plate1.99e-0915
segmental subdivision of nervous system2.56e-0813
segmental subdivision of hindbrain1.22e-0712
hindbrain1.22e-0712
presumptive hindbrain1.22e-0712
neural nucleus2.76e-079
nucleus of brain2.76e-079
basal ganglion3.62e-079
nuclear complex of neuraxis3.62e-079
aggregate regional part of brain3.62e-079
collection of basal ganglia3.62e-079
cerebral subcortex3.62e-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.