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Coexpression cluster:C452: Difference between revisions

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|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
|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
|tfbs_overrepresentation_jaspar=MA0003.1;2.47965e-08,MA0004.1;0.158412,MA0006.1;0.523746,MA0007.1;0.146569,MA0009.1;0.526253,MA0014.1;1.18834e-05,MA0017.1;0.0884918,MA0019.1;0.726406,MA0024.1;0.434294,MA0025.1;1.56075,MA0027.1;2.09389,MA0028.1;0.0770177,MA0029.1;0.450974,MA0030.1;0.441064,MA0031.1;0.386141,MA0038.1;0.22896,MA0040.1;1.15521,MA0041.1;0.98026,MA0042.1;0.457543,MA0043.1;0.526535,MA0046.1;0.516541,MA0048.1;0.00505311,MA0050.1;0.458935,MA0051.1;0.22589,MA0052.1;0.459414,MA0055.1;0.000220415,MA0056.1;0,MA0057.1;0.0257204,MA0058.1;0.101748,MA0059.1;0.101051,MA0060.1;0.0258987,MA0061.1;0.0847828,MA0063.1;0,MA0066.1;0.22927,MA0067.1;0.820123,MA0068.1;0.149869,MA0069.1;0.51311,MA0070.1;1.25622,MA0071.1;1.10357,MA0072.1;1.24772,MA0073.1;3.42403e-11,MA0074.1;0.225345,MA0076.1;0.110503,MA0077.1;0.49237,MA0078.1;1.47767,MA0081.1;0.101139,MA0083.1;0.532971,MA0084.1;0.999884,MA0087.1;0.497023,MA0088.1;0.00120138,MA0089.1;0,MA0090.1;0.118716,MA0091.1;0.482932,MA0092.1;1.35462,MA0093.1;0.0708814,MA0095.1;0,MA0098.1;0,MA0100.1;0.239133,MA0101.1;0.0724124,MA0103.1;0.0653004,MA0105.1;0.020431,MA0106.1;0.259598,MA0107.1;0.041912,MA0108.2;0.383574,MA0109.1;0,MA0111.1;0.126618,MA0113.1;0.272101,MA0114.1;0.15638,MA0115.1;0.747865,MA0116.1;0.166035,MA0117.1;0.560027,MA0119.1;0.0925355,MA0122.1;0.583485,MA0124.1;0.70896,MA0125.1;0.631059,MA0130.1;0,MA0131.1;0.315517,MA0132.1;0,MA0133.1;0,MA0135.1;2.33678,MA0136.1;0.234116,MA0139.1;0.0162019,MA0140.1;0.199454,MA0141.1;0.674473,MA0142.1;0.359701,MA0143.1;1.37255,MA0144.1;0.0352516,MA0145.1;0.00165086,MA0146.1;6.28585e-06,MA0147.1;0.0444528,MA0148.1;0.518828,MA0149.1;0.192747,MA0062.2;0.0177333,MA0035.2;0.198962,MA0039.2;5.36166e-08,MA0138.2;0.302079,MA0002.2;0.459473,MA0137.2;0.0801516,MA0104.2;0.0256869,MA0047.2;0.250458,MA0112.2;0.00138028,MA0065.2;0.0401599,MA0150.1;0.115337,MA0151.1;0,MA0152.1;2.47131,MA0153.1;2.53805,MA0154.1;0.0194777,MA0155.1;0.00810476,MA0156.1;0.277694,MA0157.1;0.337287,MA0158.1;0,MA0159.1;0.0446884,MA0160.1;0.543697,MA0161.1;0,MA0162.1;5.0328e-05,MA0163.1;0.00016584,MA0164.1;0.770204,MA0080.2;0.0709213,MA0018.2;0.722038,MA0099.2;0.204301,MA0079.2;8.24982e-14,MA0102.2;1.03595,MA0258.1;0.130743,MA0259.1;0.0476147,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


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)
MA0003.12.47965e-08
MA0004.10.158412
MA0006.10.523746
MA0007.10.146569
MA0009.10.526253
MA0014.11.18834e-05
MA0017.10.0884918
MA0019.10.726406
MA0024.10.434294
MA0025.11.56075
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.11.15521
MA0041.10.98026
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.10.00505311
MA0050.10.458935
MA0051.10.22589
MA0052.10.459414
MA0055.10.000220415
MA0056.10
MA0057.10.0257204
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.0847828
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.149869
MA0069.10.51311
MA0070.11.25622
MA0071.11.10357
MA0072.11.24772
MA0073.13.42403e-11
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.11.47767
MA0081.10.101139
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.00120138
MA0089.10
MA0090.10.118716
MA0091.10.482932
MA0092.11.35462
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.0653004
MA0105.10.020431
MA0106.10.259598
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.10.15638
MA0115.10.747865
MA0116.10.166035
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.12.33678
MA0136.10.234116
MA0139.10.0162019
MA0140.10.199454
MA0141.10.674473
MA0142.10.359701
MA0143.11.37255
MA0144.10.0352516
MA0145.10.00165086
MA0146.16.28585e-06
MA0147.10.0444528
MA0148.10.518828
MA0149.10.192747
MA0062.20.0177333
MA0035.20.198962
MA0039.25.36166e-08
MA0138.20.302079
MA0002.20.459473
MA0137.20.0801516
MA0104.20.0256869
MA0047.20.250458
MA0112.20.00138028
MA0065.20.0401599
MA0150.10.115337
MA0151.10
MA0152.12.47131
MA0153.12.53805
MA0154.10.0194777
MA0155.10.00810476
MA0156.10.277694
MA0157.10.337287
MA0158.10
MA0159.10.0446884
MA0160.10.543697
MA0161.10
MA0162.15.0328e-05
MA0163.10.00016584
MA0164.10.770204
MA0080.20.0709213
MA0018.20.722038
MA0099.20.204301
MA0079.28.24982e-14
MA0102.21.03595
MA0258.10.130743
MA0259.10.0476147
MA0442.10



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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