Personal tools

Coexpression cluster:C729

From FANTOM5_SSTAR

Revision as of 18:25, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C729_diencephalon_corpus_thalamus_occipital_brain_medulla_frontal



Phase1 CAGE Peaks

Hg19::chr10:98104208..98104212,-p@chr10:98104208..98104212
-
Hg19::chr10:98119004..98119021,-p6@OPALIN
Hg19::chr14:91199850..91199861,-p@chr14:91199850..91199861
-
Hg19::chr15:29362934..29362952,+p12@APBA2
Hg19::chr17:40120071..40120085,+p15@CNP
Hg19::chr1:102830819..102830832,-p@chr1:102830819..102830832
-
Hg19::chr5:161277768..161277782,+p8@GABRA1
Hg19::chr6:154589029..154589034,-p@chr6:154589029..154589034
-
Hg19::chr7:124391226..124391235,-p@chr7:124391226..124391235
-
Hg19::chr8:27336724..27336740,-p2@CHRNA2
Hg19::chr8:27336747..27336786,-p1@CHRNA2


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:0005230extracellular ligand-gated ion channel activity0.00218984226483319
GO:0030594neurotransmitter receptor activity0.00218984226483319
GO:0042165neurotransmitter binding0.00218984226483319
GO:0045211postsynaptic membrane0.00218984226483319
GO:0044456synapse part0.00218984226483319
GO:0015276ligand-gated ion channel activity0.00218984226483319
GO:0022834ligand-gated channel activity0.00218984226483319
GO:00041132',3'-cyclic-nucleotide 3'-phosphodiesterase activity0.00290422436151884
GO:0009214cyclic nucleotide catabolic process0.00290422436151884
GO:0030054cell junction0.0104193408310402
GO:0022836gated channel activity0.0130906880856879
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0141512183731324
GO:0005216ion channel activity0.0158057161306655
GO:0022838substrate specific channel activity0.0158057161306655
GO:0022803passive transmembrane transporter activity0.0158057161306655
GO:0015267channel activity0.0158057161306655
GO:0015464acetylcholine receptor activity0.0158057161306655
GO:0042166acetylcholine binding0.0158057161306655
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0158057161306655
GO:0009166nucleotide catabolic process0.0161635391315681
GO:0007214gamma-aminobutyric acid signaling pathway0.0161635391315681
GO:0004890GABA-A receptor activity0.0231299660486301
GO:0043176amine binding0.0245209602058705
GO:0016917GABA receptor activity0.0245209602058705
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0245209602058705
GO:0009187cyclic nucleotide metabolic process0.025079492031823
GO:0006810transport0.0250847393240961
GO:0051234establishment of localization0.0259695966312425
GO:0043168anion binding0.0260711541028255
GO:0031404chloride ion binding0.0260711541028255
GO:0051179localization0.0277142115861157
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0277142115861157
GO:0015075ion transmembrane transporter activity0.0277142115861157
GO:0005887integral to plasma membrane0.0277142115861157
GO:0031226intrinsic to plasma membrane0.0277142115861157
GO:0006811ion transport0.0277142115861157
GO:0005254chloride channel activity0.0277142115861157
GO:0048770pigment granule0.0277142115861157
GO:0042470melanosome0.0277142115861157
GO:0006821chloride transport0.0283185860774372
GO:0022891substrate-specific transmembrane transporter activity0.0306335778602095
GO:0005253anion channel activity0.0309822963045119
GO:0043235receptor complex0.0328343825739733
GO:0022857transmembrane transporter activity0.0328343825739733
GO:0022892substrate-specific transporter activity0.0371058061679059
GO:0007154cell communication0.0371058061679059
GO:0008081phosphoric diester hydrolase activity0.0381430120006649
GO:0004888transmembrane receptor activity0.045364967461019



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
conventional dendritic cell2.06e-078
Uber Anatomy
Ontology termp-valuen
neural tube7.06e-3257
neural rod7.06e-3257
future spinal cord7.06e-3257
neural keel7.06e-3257
central nervous system1.02e-2982
regional part of nervous system2.97e-2794
nervous system2.97e-2794
adult organism3.62e-27115
regional part of brain1.59e-2659
brain2.54e-2669
future brain2.54e-2669
regional part of forebrain9.72e-2441
forebrain9.72e-2441
future forebrain9.72e-2441
telencephalon1.61e-2334
gray matter2.08e-2334
brain grey matter2.08e-2334
anterior neural tube8.01e-2342
regional part of telencephalon1.48e-2233
cerebral hemisphere1.22e-2132
neural plate9.30e-2086
presumptive neural plate9.30e-2086
neurectoderm5.76e-1890
regional part of cerebral cortex1.36e-1722
neocortex3.93e-1620
cerebral cortex1.33e-1525
pallium1.33e-1525
pre-chordal neural plate6.98e-1561
anterior region of body2.47e-12129
craniocervical region2.47e-12129
head1.01e-11123
ectoderm-derived structure2.37e-10169
posterior neural tube3.85e-1015
chordal neural plate3.85e-1015
ectoderm1.29e-09173
presumptive ectoderm1.29e-09173
nucleus of brain1.56e-099
neural nucleus1.56e-099
basal ganglion2.41e-099
nuclear complex of neuraxis2.41e-099
aggregate regional part of brain2.41e-099
collection of basal ganglia2.41e-099
cerebral subcortex2.41e-099
tube1.59e-08194
segmental subdivision of hindbrain8.84e-0812
hindbrain8.84e-0812
presumptive hindbrain8.84e-0812
telencephalic nucleus1.14e-077
gyrus3.12e-076
segmental subdivision of nervous system6.48e-0713


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.