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Coexpression cluster:C3042: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3042_optic_cerebellum_temporal_skeletal_occipital_parietal_globus
|full_id=C3042_optic_cerebellum_temporal_skeletal_occipital_parietal_globus
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.00980103585557702!23095$GO:0008088!axon cargo transport!0.00980103585557702!23095$GO:0019894!kinesin binding!0.00980103585557702!23095$GO:0007274!neuromuscular synaptic transmission!0.00980103585557702!23095$GO:0007270!nerve-nerve synaptic transmission!0.016550423946942!23095
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.00980103585557702!23095$GO:0008088!axon cargo transport!0.00980103585557702!23095$GO:0019894!kinesin binding!0.00980103585557702!23095$GO:0007274!neuromuscular synaptic transmission!0.00980103585557702!23095$GO:0007270!nerve-nerve synaptic transmission!0.016550423946942!23095

Revision as of 15:53, 12 September 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
non-terminally differentiated cell1.67e-10180
neurectodermal cell1.00e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.23e-3894
nervous system1.23e-3894
central nervous system3.02e-3782
neural tube7.61e-3457
neural rod7.61e-3457
future spinal cord7.61e-3457
neural keel7.61e-3457
brain1.44e-3269
future brain1.44e-3269
adult organism6.11e-32115
ectoderm7.68e-31173
presumptive ectoderm7.68e-31173
regional part of brain9.96e-3159
neurectoderm4.11e-3090
ectoderm-derived structure4.86e-30169
neural plate1.57e-2986
presumptive neural plate1.57e-2986
anterior neural tube1.07e-2542
head2.23e-25123
regional part of forebrain3.00e-2541
forebrain3.00e-2541
future forebrain3.00e-2541
anterior region of body5.56e-24129
craniocervical region5.56e-24129
organism subdivision3.83e-23365
telencephalon8.77e-2234
gray matter8.88e-2234
brain grey matter8.88e-2234
pre-chordal neural plate1.04e-2161
regional part of telencephalon3.60e-2133
cerebral hemisphere1.81e-2032
multi-cellular organism2.24e-20659
cerebral cortex4.61e-1625
pallium4.61e-1625
regional part of cerebral cortex4.14e-1522
anatomical conduit9.59e-15241
anatomical system1.10e-14625
anatomical group1.76e-14626
cell layer1.95e-14312
epithelium3.22e-14309
multi-tissue structure3.93e-14347
tube5.69e-14194
neocortex6.28e-1420
embryo1.04e-13612
organ2.19e-13511
anatomical cluster3.03e-12286
embryonic structure9.18e-12605
developing anatomical structure9.18e-12605
germ layer1.94e-11604
embryonic tissue1.94e-11604
presumptive structure1.94e-11604
epiblast (generic)1.94e-11604
organ part6.24e-10219
posterior neural tube3.41e-0915
chordal neural plate3.41e-0915
segmental subdivision of nervous system3.86e-0813
segmental subdivision of hindbrain1.82e-0712
hindbrain1.82e-0712
presumptive hindbrain1.82e-0712
nucleus of brain3.50e-079
neural nucleus3.50e-079
basal ganglion4.39e-079
nuclear complex of neuraxis4.39e-079
aggregate regional part of brain4.39e-079
collection of basal ganglia4.39e-079
cerebral subcortex4.39e-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.