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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}

Revision as of 17:04, 8 August 2012


Full id: C1259_Neurons_parietal_occipital_temporal_brain_duodenum_glioblastoma



Phase1 CAGE Peaks

Hg19::chr20:62009349..62009358,-p10@CHRNA4
Hg19::chr2:104423528..104423529,-p@chr2:104423528..104423529
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Hg19::chr4:176734316..176734327,-p25@GPM6A
Hg19::chr4:176734368..176734405,-p19@GPM6A
Hg19::chr9:100199546..100199572,-p@chr9:100199546..100199572
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Hg19::chr9:100199913..100199937,-p@chr9:100199913..100199937
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Hg19::chr9:100199938..100199951,-p@chr9:100199938..100199951
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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:0035094response to nicotine0.0116780462456223
GO:0043279response to alkaloid0.0116780462456223
GO:0014070response to organic cyclic substance0.0116780462456223
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0116780462456223
GO:0015464acetylcholine receptor activity0.0116780462456223
GO:0042166acetylcholine binding0.0116780462456223
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0116780462456223
GO:0005887integral to plasma membrane0.0116780462456223
GO:0031226intrinsic to plasma membrane0.0116780462456223
GO:0043176amine binding0.0172001288703765
GO:0001666response to hypoxia0.0172001288703765
GO:0010033response to organic substance0.0203612309968446
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0216421112045033
GO:0044459plasma membrane part0.0216421112045033
GO:0043235receptor complex0.0280579879925454
GO:0005230extracellular ligand-gated ion channel activity0.0280579879925454
GO:0030594neurotransmitter receptor activity0.0280579879925454
GO:0042165neurotransmitter binding0.0280579879925454
GO:0009986cell surface0.0280579879925454
GO:0045211postsynaptic membrane0.0280579879925454
GO:0044456synapse part0.0280579879925454
GO:0015276ligand-gated ion channel activity0.0280579879925454
GO:0022834ligand-gated channel activity0.0280579879925454
GO:0005886plasma membrane0.0352157565233113
GO:0007268synaptic transmission0.0455607017688047
GO:0019226transmission of nerve impulse0.0498214260109094



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 cell2.07e-088
neural cell1.01e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.22e-5582
regional part of nervous system6.86e-5194
nervous system6.86e-5194
telencephalon1.61e-4734
gray matter1.64e-4734
brain grey matter1.64e-4734
cerebral hemisphere2.43e-4732
regional part of forebrain3.07e-4741
forebrain3.07e-4741
future forebrain3.07e-4741
brain3.72e-4769
future brain3.72e-4769
regional part of cerebral cortex5.48e-4622
anterior neural tube6.31e-4642
regional part of telencephalon3.05e-4533
neural tube2.62e-4457
neural rod2.62e-4457
future spinal cord2.62e-4457
neural keel2.62e-4457
cerebral cortex5.83e-4425
pallium5.83e-4425
regional part of brain1.76e-4259
neocortex1.89e-4120
neural plate1.65e-3186
presumptive neural plate1.65e-3186
neurectoderm1.22e-2990
pre-chordal neural plate4.47e-2961
adult organism1.36e-26115
ectoderm-derived structure1.91e-26169
ectoderm1.60e-25173
presumptive ectoderm1.60e-25173
head2.89e-23123
anterior region of body5.85e-23129
craniocervical region5.85e-23129
gyrus5.20e-166
temporal lobe9.22e-167
parietal lobe1.67e-135
tube1.74e-10194
middle temporal gyrus7.30e-093
occipital lobe1.55e-085
limbic system1.55e-085
pons1.19e-073


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.