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Coexpression cluster:C729

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Full id: C729_diencephalon_corpus_thalamus_occipital_brain_medulla_frontal



Phase1 CAGE Peaks

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


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
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 clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data


Uber Anatomy
Ontology termp-valuen
neural tube3.01e-8156
neural rod3.01e-8156
future spinal cord3.01e-8156
neural keel3.01e-8156
regional part of nervous system7.24e-8053
regional part of brain7.24e-8053
regional part of forebrain1.42e-7441
forebrain1.42e-7441
anterior neural tube1.42e-7441
future forebrain1.42e-7441
brain1.44e-7068
future brain1.44e-7068
telencephalon1.90e-6734
brain grey matter5.41e-6734
gray matter5.41e-6734
central nervous system4.74e-6381
cerebral hemisphere1.04e-5732
regional part of telencephalon1.93e-5732
nervous system2.19e-5689
neural plate3.01e-5482
presumptive neural plate3.01e-5482
neurectoderm1.59e-5186
pre-chordal neural plate4.43e-4961
neocortex6.89e-4820
adult organism1.32e-44114
regional part of cerebral cortex1.65e-4322
ecto-epithelium7.88e-42104
cerebral cortex3.36e-3825
pallium3.36e-3825
structure with developmental contribution from neural crest1.43e-34132
neural nucleus1.05e-329
nucleus of brain1.05e-329
ectoderm-derived structure2.26e-27171
ectoderm2.26e-27171
presumptive ectoderm2.26e-27171
gyrus1.03e-256
basal ganglion5.24e-249
nuclear complex of neuraxis5.24e-249
aggregate regional part of brain5.24e-249
collection of basal ganglia5.24e-249
cerebral subcortex5.24e-249
telencephalic nucleus7.09e-227
organ system subdivision2.13e-21223
tube2.05e-20192
pons2.58e-193
brainstem4.15e-176
anatomical conduit2.65e-15240
temporal lobe2.81e-146
dorsal plus ventral thalamus1.12e-132
thalamic complex1.12e-132
globus pallidus1.74e-132
pallidum1.74e-132
locus ceruleus2.24e-132
brainstem nucleus2.24e-132
hindbrain nucleus2.24e-132
middle temporal gyrus3.71e-132
occipital lobe2.64e-125
parietal lobe4.17e-125
epithelium7.19e-11306
cell layer1.03e-10309
anatomical cluster1.07e-10373
organ part1.59e-10218
posterior neural tube2.74e-1015
chordal neural plate2.74e-1015
frontal cortex3.54e-093
multi-tissue structure3.89e-09342
diencephalon7.08e-097
future diencephalon7.08e-097
segmental subdivision of hindbrain1.26e-0812
hindbrain1.26e-0812
presumptive hindbrain1.26e-0812
corpus callosum4.57e-081
central nervous system cell part cluster4.57e-081
axon tract4.57e-081
intercerebral commissure4.57e-081
dorsal telencephalic commissure4.57e-081
brain white matter4.57e-081
brain commissure4.57e-081
white matter4.57e-081
nervous system commissure4.57e-081
cerebral hemisphere white matter4.57e-081
occipital pole5.22e-081
pole of cerebral hemisphere5.22e-081
segmental subdivision of nervous system5.73e-0813
postcentral gyrus6.80e-081
paracentral gyrus8.28e-081
nucleus accumbens1.01e-071
ventral striatum1.01e-071
insula1.22e-071
olfactory region1.48e-071
primary subdivision of skull1.48e-071
cranium1.48e-071
neurocranium1.48e-071
chondrocranium1.48e-071
cartilaginous neurocranium1.48e-071
head paraxial mesoderm1.48e-071
putamen2.47e-071
substantia nigra2.63e-071
midbrain nucleus2.63e-071
regional part of midbrain2.63e-071


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0148593
MA0004.10.349539
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.10.0481212
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.11.6617
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.895841
MA0043.10.790919
MA0046.10.779945
MA0048.10.41425
MA0050.10.338274
MA0051.10.439895
MA0052.11.70446
MA0055.11.04456
MA0056.10
MA0057.10.397382
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.0112492
MA0074.10.439193
MA0076.10.278993
MA0077.11.78038
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.11.44338
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.277793
MA0146.10.0109959
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.00136845
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.260758
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.11.05873
MA0153.10.887528
MA0154.10.634487
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.0158063
MA0164.11.2703
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.27.51746e-05
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.