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Coexpression cluster:C452: Difference between revisions

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78005e-05,0.00642154,0.00182162,0.0502562
|tfbs_overrepresentation_for_novel_motifs=0.0942734,0.000416561,0.0904779,0.521108,0.0703126,0.518467,0.226953,0.269959,0.025797,0.00407054,0.155105,0.717665,0.187954,0.218743,0.0696927,0.276011,0.401017,0.17941,0.0183131,0.0575111,1.55615,0.000867372,0.169484,0.240266,0.115011,0.275879,0.0573237,0.168077,0.0717257,0.130724,0.141557,0.432083,0.0360115,0.191773,0.0554298,0.00174623,0.0541423,0.175318,0.172219,0.0212383,1.66188,0.131762,0.0306493,0.243124,0.000552548,0.106689,0.227736,0.148323,0.242675,0.0717847,0.286755,0.236257,0.00469378,0.49846,0.635443,0.220828,0.0737435,0.197918,0.130563,0.197226,0.467239,0.22944,0.025931,0.377975,0.242486,0.349807,0.716956,1.06805,0.423263,0.911622,0.124048,0.281099,0.00448968,1.53163,0.0147578,0.0124209,0.13996,0.364079,1.07834,0.35946,0.086399,0.377089,1.95382,0.511606,0.586887,0.000111344,0.00282308,0.0441419,0.306981,1.1648,0.804514,0.562601,1.13448,1.87436,0.0706505,0.165445,0.0812264,0.483243,0.310601,0.00655811,0.173754,0.441596,0.47839,0.404088,0.340503,0.15226,0.39086,0.216299,0.114869,0.0632414,0.0962642,0.475985,0.0876862,0.161084,0.759328,0.437533,0.00180706,0.140827,0.347912,0.636652,1.51581,1.49196,0.172748,0.698687,0.863933,0.364702,0.633063,0.450719,0.66511,0.0433212,0.563221,0.143305,0.678365,0.248069,0.81669,0.0402326,0.13793,0.168444,0.776656,1.61314,1.21607,0.741657,0.223644,0.480173,0.341918,0.192136,0.328551,1.45545,0.129796,0.0373053,0.00359134,0.00102667,0.563563,0.0236935,0.229091,0.940968,0.799018,0.495466,0.368557,0.0993076,0.740521,0.547006,0.419845,0.101015,0.934619,0.678077,0.0333885,0.641502,6.97337e-07
}}
}}

Revision as of 14:13, 26 November 2012


Full id: C452_hippocampus_locus_middle_pineal_occipital_thalamus_cerebral



Phase1 CAGE Peaks

Hg19::chr13:36348083..36348094,-p@chr13:36348083..36348094
-
Hg19::chr13:42896804..42896815,+p@chr13:42896804..42896815
+
Hg19::chr14:90872343..90872352,+p20@CALM1
Hg19::chr15:25229566..25229589,+p3@PAR5
Hg19::chr15:25231001..25231006,+p@chr15:25231001..25231006
+
Hg19::chr15:25236590..25236600,+p@chr15:25236590..25236600
+
Hg19::chr15:25241034..25241047,+p@chr15:25241034..25241047
+
Hg19::chr15:73852545..73852571,-p@chr15:73852545..73852571
-
Hg19::chr17:44834023..44834067,+p1@AL049276
Hg19::chr20:4681869..4681942,+p@chr20:4681869..4681942
+
Hg19::chr2:44546639..44546676,-p@chr2:44546639..44546676
-
Hg19::chr3:149683046..149683062,-p@chr3:149683046..149683062
-
Hg19::chr4:114303804..114303820,+p7@ANK2
Hg19::chr4:15070456..15070467,+p@chr4:15070456..15070467
+
Hg19::chr5:71503592..71503603,+p3@BC047027
Hg19::chr5:71503633..71503644,+p2@BC047027
Hg19::chr5:71503739..71503750,+p1@BC047027
Hg19::chr5:71504217..71504228,+p37@MAP1B
Hg19::chr6:158733491..158733502,+p5@TULP4
Hg19::chr6:29570683..29570694,-p@chr6:29570683..29570694
-
Hg19::chr6:46190077..46190088,-p@chr6:46190077..46190088
-
Hg19::chrX:70794147..70794220,+p4@OGT


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:0007584response to nutrient0.0018146241377
GO:0031667response to nutrient levels0.0018146241377
GO:0009991response to extracellular stimulus0.0018146241377
GO:0005737cytoplasm0.0190233746672385
GO:0001578microtubule bundle formation0.0302789522840798
GO:0016358dendrite development0.0310607224280252
GO:0004176ATP-dependent peptidase activity0.0310607224280252
GO:0005829cytosol0.0310607224280252
GO:0042221response to chemical stimulus0.0310607224280252
GO:0044267cellular protein metabolic process0.0310607224280252
GO:0007026negative regulation of microtubule depolymerization0.0310607224280252
GO:0031114regulation of microtubule depolymerization0.0310607224280252
GO:0044260cellular macromolecule metabolic process0.0310607224280252
GO:0009605response to external stimulus0.0310607224280252
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0310607224280252
GO:0007019microtubule depolymerization0.0310607224280252
GO:0019538protein metabolic process0.0329272534405792
GO:0031110regulation of microtubule polymerization or depolymerization0.0341029829548606
GO:0006493protein amino acid O-linked glycosylation0.0341029829548606
GO:0031109microtubule polymerization or depolymerization0.0345536204345278
GO:0008375acetylglucosaminyltransferase activity0.0451180952332877
GO:0051261protein depolymerization0.0451180952332877
GO:0051129negative regulation of cellular component organization and biogenesis0.0487683090769321
GO:0044424intracellular part0.0494291388539985



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube1.37e-8256
neural rod1.37e-8256
future spinal cord1.37e-8256
neural keel1.37e-8256
regional part of nervous system2.60e-7653
regional part of brain2.60e-7653
adult organism7.02e-72114
central nervous system9.97e-6581
regional part of forebrain1.86e-6341
forebrain1.86e-6341
anterior neural tube1.86e-6341
future forebrain1.86e-6341
neural plate6.47e-6282
presumptive neural plate6.47e-6282
brain3.93e-6168
future brain3.93e-6168
nervous system2.11e-5989
neurectoderm2.49e-5886
brain grey matter2.11e-5434
gray matter2.11e-5434
telencephalon2.65e-5334
regional part of telencephalon3.37e-5032
cerebral hemisphere4.55e-5032
ecto-epithelium1.35e-45104
structure with developmental contribution from neural crest3.94e-44132
pre-chordal neural plate5.05e-4461
regional part of cerebral cortex2.64e-4222
neocortex7.71e-3820
cerebral cortex1.30e-3625
pallium1.30e-3625
ectoderm-derived structure1.70e-28171
ectoderm1.70e-28171
presumptive ectoderm1.70e-28171
tube8.20e-24192
organ system subdivision7.78e-23223
anatomical conduit3.64e-20240
basal ganglion2.39e-199
nuclear complex of neuraxis2.39e-199
aggregate regional part of brain2.39e-199
collection of basal ganglia2.39e-199
cerebral subcortex2.39e-199
posterior neural tube2.48e-1915
chordal neural plate2.48e-1915
neural nucleus2.66e-199
nucleus of brain2.66e-199
anatomical cluster3.49e-17373
segmental subdivision of nervous system1.29e-1513
telencephalic nucleus3.68e-157
epithelium2.05e-14306
multi-tissue structure3.05e-14342
cell layer4.13e-14309
segmental subdivision of hindbrain1.01e-1312
hindbrain1.01e-1312
presumptive hindbrain1.01e-1312
gyrus2.73e-136
brainstem3.10e-136
limbic system9.66e-125
temporal lobe1.33e-116
organ part2.07e-11218
diencephalon2.91e-117
future diencephalon2.91e-117
parietal lobe3.04e-115
occipital lobe4.96e-115
regional part of diencephalon7.01e-104
corpus striatum2.65e-094
striatum2.65e-094
ventral part of telencephalon2.65e-094
future corpus striatum2.65e-094
embryo8.48e-09592
regional part of metencephalon1.55e-089
metencephalon1.55e-089
future metencephalon1.55e-089
embryonic structure3.88e-08564
caudate-putamen7.20e-083
dorsal striatum7.20e-083
germ layer8.28e-08560
germ layer / neural crest8.28e-08560
embryonic tissue8.28e-08560
presumptive structure8.28e-08560
germ layer / neural crest derived structure8.28e-08560
epiblast (generic)8.28e-08560
organ8.87e-08503
developing anatomical structure8.92e-08581
spinal cord1.15e-073
dorsal region element1.15e-073
dorsum1.15e-073
frontal cortex1.53e-073
pons1.74e-073
medulla oblongata2.07e-073
myelencephalon2.07e-073
future myelencephalon2.07e-073
male genital duct6.37e-073
internal male genitalia6.37e-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.

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