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Coexpression cluster:C1259: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0035094!response to nicotine!0.0116780462456223!1137$GO:0043279!response to alkaloid!0.0116780462456223!1137$GO:0014070!response to organic cyclic substance!0.0116780462456223!1137$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!0.0116780462456223!1137$GO:0015464!acetylcholine receptor activity!0.0116780462456223!1137$GO:0042166!acetylcholine binding!0.0116780462456223!1137$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.0116780462456223!1137$GO:0005887!integral to plasma membrane!0.0116780462456223!1137;2823$GO:0031226!intrinsic to plasma membrane!0.0116780462456223!1137;2823$GO:0043176!amine binding!0.0172001288703765!1137$GO:0001666!response to hypoxia!0.0172001288703765!1137$GO:0010033!response to organic substance!0.0203612309968446!1137$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0216421112045033!1137$GO:0044459!plasma membrane part!0.0216421112045033!1137;2823$GO:0043235!receptor complex!0.0280579879925454!1137$GO:0005230!extracellular ligand-gated ion channel activity!0.0280579879925454!1137$GO:0030594!neurotransmitter receptor activity!0.0280579879925454!1137$GO:0042165!neurotransmitter binding!0.0280579879925454!1137$GO:0009986!cell surface!0.0280579879925454!2823$GO:0045211!postsynaptic membrane!0.0280579879925454!1137$GO:0044456!synapse part!0.0280579879925454!1137$GO:0015276!ligand-gated ion channel activity!0.0280579879925454!1137$GO:0022834!ligand-gated channel activity!0.0280579879925454!1137$GO:0005886!plasma membrane!0.0352157565233113!1137;2823$GO:0007268!synaptic transmission!0.0455607017688047!1137$GO:0019226!transmission of nerve impulse!0.0498214260109094!1137
|gostat_on_coexpression_clusters=GO:0035094!response to nicotine!0.0116780462456223!1137$GO:0043279!response to alkaloid!0.0116780462456223!1137$GO:0014070!response to organic cyclic substance!0.0116780462456223!1137$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!0.0116780462456223!1137$GO:0015464!acetylcholine receptor activity!0.0116780462456223!1137$GO:0042166!acetylcholine binding!0.0116780462456223!1137$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.0116780462456223!1137$GO:0005887!integral to plasma membrane!0.0116780462456223!1137;2823$GO:0031226!intrinsic to plasma membrane!0.0116780462456223!1137;2823$GO:0043176!amine binding!0.0172001288703765!1137$GO:0001666!response to hypoxia!0.0172001288703765!1137$GO:0010033!response to organic substance!0.0203612309968446!1137$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0216421112045033!1137$GO:0044459!plasma membrane part!0.0216421112045033!1137;2823$GO:0043235!receptor complex!0.0280579879925454!1137$GO:0005230!extracellular ligand-gated ion channel activity!0.0280579879925454!1137$GO:0030594!neurotransmitter receptor activity!0.0280579879925454!1137$GO:0042165!neurotransmitter binding!0.0280579879925454!1137$GO:0009986!cell surface!0.0280579879925454!2823$GO:0045211!postsynaptic membrane!0.0280579879925454!1137$GO:0044456!synapse part!0.0280579879925454!1137$GO:0015276!ligand-gated ion channel activity!0.0280579879925454!1137$GO:0022834!ligand-gated channel activity!0.0280579879925454!1137$GO:0005886!plasma membrane!0.0352157565233113!1137;2823$GO:0007268!synaptic transmission!0.0455607017688047!1137$GO:0019226!transmission of nerve impulse!0.0498214260109094!1137
|id=C1259
|id=C1259
|ontology_enrichment_celltype=CL:0000047!2.07e-08!8;CL:0002319!1.01e-07!25
|ontology_enrichment_celltype=CL:0000540!4.90e-38!6;CL:0000031!4.90e-38!6;CL:0000404!4.90e-38!6;CL:0000047!9.31e-29!8;CL:0002319!4.87e-09!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.22e-55!82;UBERON:0005743!1.72e-52!86;UBERON:0000073!6.86e-51!94;UBERON:0001016!6.86e-51!94;UBERON:0001893!1.61e-47!34;UBERON:0002020!1.64e-47!34;UBERON:0003528!1.64e-47!34;UBERON:0001869!2.43e-47!32;UBERON:0002780!3.07e-47!41;UBERON:0001890!3.07e-47!41;UBERON:0006240!3.07e-47!41;UBERON:0000955!3.72e-47!69;UBERON:0006238!3.72e-47!69;UBERON:0002619!5.48e-46!22;UBERON:0003080!6.31e-46!42;UBERON:0002791!3.05e-45!33;UBERON:0001049!2.62e-44!57;UBERON:0005068!2.62e-44!57;UBERON:0006241!2.62e-44!57;UBERON:0007135!2.62e-44!57;UBERON:0000956!5.83e-44!25;UBERON:0000203!5.83e-44!25;UBERON:0002616!1.76e-42!59;UBERON:0001950!1.89e-41!20;UBERON:0003075!1.65e-31!86;UBERON:0007284!1.65e-31!86;UBERON:0002346!1.22e-29!90;UBERON:0003056!4.47e-29!61;UBERON:0007023!1.36e-26!115;UBERON:0004121!1.91e-26!169;UBERON:0000924!1.60e-25!173;UBERON:0006601!1.60e-25!173;UBERON:0000033!2.89e-23!123;UBERON:0000153!5.85e-23!129;UBERON:0007811!5.85e-23!129;UBERON:0000200!5.20e-16!6;UBERON:0001871!9.22e-16!7;UBERON:0001872!1.67e-13!5;UBERON:0000025!1.74e-10!194;UBERON:0002771!7.30e-09!3;UBERON:0002021!1.55e-08!5;UBERON:0000349!1.55e-08!5;UBERON:0000988!1.19e-07!3
|ontology_enrichment_uberon=UBERON:0001017!1.14e-14!81;UBERON:0001016!3.06e-13!89;UBERON:0001950!2.90e-11!20;UBERON:0002619!2.41e-10!22;UBERON:0002114!1.67e-09!2;UBERON:0000956!3.16e-09!25;UBERON:0000203!3.16e-09!25;UBERON:0002791!2.12e-07!32;UBERON:0001869!2.12e-07!32;UBERON:0003528!5.19e-07!34;UBERON:0002020!5.19e-07!34;UBERON:0001893!5.19e-07!34;UBERON:0004121!5.71e-07!171;UBERON:0000924!5.71e-07!171;UBERON:0006601!5.71e-07!171;UBERON:0011216!6.23e-07!223
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}}
}}

Revision as of 11:02, 19 October 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
-


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
neuron4.90e-386
neuroblast4.90e-386
electrically signaling cell4.90e-386
neuronal stem cell9.31e-298
neural cell4.87e-0925
Uber Anatomy
Ontology termp-valuen
central nervous system1.14e-1481
nervous system3.06e-1389
neocortex2.90e-1120
regional part of cerebral cortex2.41e-1022
duodenum1.67e-092
cerebral cortex3.16e-0925
pallium3.16e-0925
regional part of telencephalon2.12e-0732
cerebral hemisphere2.12e-0732
brain grey matter5.19e-0734
gray matter5.19e-0734
telencephalon5.19e-0734
ectoderm-derived structure5.71e-07171
ectoderm5.71e-07171
presumptive ectoderm5.71e-07171
organ system subdivision6.23e-07223


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.