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Coexpression cluster:C876: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.28e-47!115;UBERON:0001017!8.14e-35!82;UBERON:0001049!9.49e-35!57;UBERON:0005068!9.49e-35!57;UBERON:0006241!9.49e-35!57;UBERON:0007135!9.49e-35!57;UBERON:0005743!3.36e-33!86;UBERON:0000073!3.66e-32!94;UBERON:0001016!3.66e-32!94;UBERON:0002616!3.56e-30!59;UBERON:0000955!1.69e-28!69;UBERON:0006238!1.69e-28!69;UBERON:0003080!2.25e-27!42;UBERON:0002780!4.74e-27!41;UBERON:0001890!4.74e-27!41;UBERON:0006240!4.74e-27!41;UBERON:0003075!5.47e-24!86;UBERON:0007284!5.47e-24!86;UBERON:0001893!3.91e-23!34;UBERON:0002020!4.19e-23!34;UBERON:0003528!4.19e-23!34;UBERON:0002346!4.76e-23!90;UBERON:0002791!1.84e-22!33;UBERON:0001869!9.85e-22!32;UBERON:0003056!3.63e-17!61;UBERON:0000956!4.48e-17!25;UBERON:0000203!4.48e-17!25;UBERON:0002619!3.59e-16!22;UBERON:0000153!3.19e-15!129;UBERON:0007811!3.19e-15!129;UBERON:0000033!3.75e-15!123;UBERON:0001950!9.99e-15!20;UBERON:0004121!6.47e-14!169;UBERON:0000924!1.16e-13!173;UBERON:0006601!1.16e-13!173;UBERON:0000468!1.08e-09!659;UBERON:0000062!2.26e-09!511;UBERON:0000922!4.15e-09!612;UBERON:0003076!1.71e-08!15;UBERON:0003057!1.71e-08!15;UBERON:0002050!1.11e-07!605;UBERON:0005423!1.11e-07!605;UBERON:0002308!1.75e-07!9;UBERON:0000125!1.75e-07!9;UBERON:0000923!1.89e-07!604;UBERON:0005291!1.89e-07!604;UBERON:0006598!1.89e-07!604;UBERON:0002532!1.89e-07!604;UBERON:0000479!1.94e-07!787;UBERON:0002420!1.94e-07!9;UBERON:0007245!1.94e-07!9;UBERON:0010009!1.94e-07!9;UBERON:0010011!1.94e-07!9;UBERON:0000454!1.94e-07!9;UBERON:0000467!3.14e-07!625;UBERON:0000480!4.56e-07!626;UBERON:0004732!4.62e-07!13
|ontology_enrichment_uberon=UBERON:0007023!2.28e-47!115;UBERON:0001017!8.14e-35!82;UBERON:0001049!9.49e-35!57;UBERON:0005068!9.49e-35!57;UBERON:0006241!9.49e-35!57;UBERON:0007135!9.49e-35!57;UBERON:0005743!3.36e-33!86;UBERON:0000073!3.66e-32!94;UBERON:0001016!3.66e-32!94;UBERON:0002616!3.56e-30!59;UBERON:0000955!1.69e-28!69;UBERON:0006238!1.69e-28!69;UBERON:0003080!2.25e-27!42;UBERON:0002780!4.74e-27!41;UBERON:0001890!4.74e-27!41;UBERON:0006240!4.74e-27!41;UBERON:0003075!5.47e-24!86;UBERON:0007284!5.47e-24!86;UBERON:0001893!3.91e-23!34;UBERON:0002020!4.19e-23!34;UBERON:0003528!4.19e-23!34;UBERON:0002346!4.76e-23!90;UBERON:0002791!1.84e-22!33;UBERON:0001869!9.85e-22!32;UBERON:0003056!3.63e-17!61;UBERON:0000956!4.48e-17!25;UBERON:0000203!4.48e-17!25;UBERON:0002619!3.59e-16!22;UBERON:0000153!3.19e-15!129;UBERON:0007811!3.19e-15!129;UBERON:0000033!3.75e-15!123;UBERON:0001950!9.99e-15!20;UBERON:0004121!6.47e-14!169;UBERON:0000924!1.16e-13!173;UBERON:0006601!1.16e-13!173;UBERON:0000468!1.08e-09!659;UBERON:0000062!2.26e-09!511;UBERON:0000922!4.15e-09!612;UBERON:0003076!1.71e-08!15;UBERON:0003057!1.71e-08!15;UBERON:0002050!1.11e-07!605;UBERON:0005423!1.11e-07!605;UBERON:0002308!1.75e-07!9;UBERON:0000125!1.75e-07!9;UBERON:0000923!1.89e-07!604;UBERON:0005291!1.89e-07!604;UBERON:0006598!1.89e-07!604;UBERON:0002532!1.89e-07!604;UBERON:0000479!1.94e-07!787;UBERON:0002420!1.94e-07!9;UBERON:0007245!1.94e-07!9;UBERON:0010009!1.94e-07!9;UBERON:0010011!1.94e-07!9;UBERON:0000454!1.94e-07!9;UBERON:0000467!3.14e-07!625;UBERON:0000480!4.56e-07!626;UBERON:0004732!4.62e-07!13
|tfbs_overrepresentation=0.379905,0.165882,0.728867,0.136425,0.487545,0.638769,0.123553,0.79935,0.0949833,0.0751516,0.362662,0.535177,0.466136,0.332321,0.383007,0.174443,0.36612,0.266621,0.150322,0.290404,0.465867,0.347332,0.226321,0.258532,0.119603,0.517173,0.505823,0.248219,0.372221,0.254769,0.497451,0.304602,0.0531246,0.503662,0.186593,0.232613,0.462504,0.123445,0.319343,0.187061,0.262412,0.0720324,0.36403,0.4567,0.320656,0.104832,0.109769,0.451673,0.298075,0.321315,0.394657,0.153891,0.196072,0.253845,0.485667,0.110878,0.288967,0.512016,0.217047,0.284457,0.0857174,0.384611,0.291703,0.210978,0.154936,0.143948,0.728252,0.169439,0.236629,0.422102,0.418099,0.189603,0.244032,0.317093,0.0222609,0.0504791,0.262446,0.125439,0.107638,0.0216001,0.260326,0.537952,0.122158,0.306485,0.644092,0.581213,0.18087,0.505147,0.154878,0.176677,0.235838,0.141509,0.259722,0.135495,0.234915,0.306911,0.490977,0.393712,0.25323,0.617548,0.162733,0.620845,0.368092,0.107129,0.523781,0.117829,0.187804,0.351028,0.373254,0.609904,0.453858,0.0985633,0.384904,0.0521236,0.273963,0.0978783,0.0597833,0.160517,0.36177,0.23102,0.421387,0.515724,0.364218,0.235903,0.27674,0.442379,0.248136,0.0437269,0.232332,0.352634,0.168295,0.208122,0.162015,0.0668125,0.331897,0.290508,0.182244,0.156991,0.0958807,0.0118189,0.0667834,0.336046,0.495496,0.398784,0.140562,0.19387,0.268136,0.231997,0.112335,0.320461,0.489241,0.372067,0.450068,0.0776445,0.122732,0.312819,0.207929,0.540588,0.147215,0.0978015,0.539398,0.259477,0.310698,0.381069,0.616518,0.305161,0.115353,0.335504,0.116243,0.309127,0.448004,0.358884,0.0123362,0.153773,0.22114,0.246625,0.364685,0.452289,0.445497,0.103138,0.404846,0.324259,0.0799857,0.308193,0.205269,0.315846,0.454723,0.115749,0.228576,0.435542,0.288225,0.463221,0.325324,0.541351,0.301358,0.134676,0.216866,0.170174,0.189529,0.294254,0.244693,0.17047,0.0896732,0.171015,0.356037,0.593807,0.249119,0.389876,0.499999,0.445315,0.131385,0.281536,0.321205,0.301899,0.675159,0.426262,0.416147,0.273288,0.17733,0.278242,0.368216,0.752859,0.398917,0.409466,0.205617,0.333772,0.361394,0.23638,0.170616,0.16914,0.718804,0.4278,0.120343,0.212398,0.261042,0.254337,0.135096,0.599827,0.414677,0.515899,0.453603,0.368815,0.267103,0.229137,0.309856,0.356902,0.225141,0.298939,0.753277,0.311599,0.405286,0.458984,0.460135,0.266199,0.266349,0.406605,0.288456,0.491561,0.194561,0.486506,0.1745,0.438689,0.414414,0.337164,0.100007,0.22402,0.224264,0.251548,0.314053,0.209873,0.624183,0.178112,0.586128,0.529949,0.237927,0.10985,0.341892,0.928484,0.0860194,0.0935686,0.805397,0.709359,0.268716,0.127137,0.706481,0.572048,0.597321,0.529204,0.409439,0.670395,0.601643,0.700182,0.779492,0.337191,0.402728,0.546909,0.614105,0.645336,0.790175,0.448499,0.735453,0.513143,0.46313,0.741272,0.452085,0.808876,0.295002,0.339338,0.522392,0.497616,0.758108,0.556609,0.206816,0.658492,0.647055,0.750883,0.0804411,0.863015,0.584123,0.621799,0.292795,0.137869,0.681223,0.531812,0.877402,0.524092,0.632518,0.678224,0.478016,0.644668,0.83189,0.259366,0.801657,0.64636,0.307913,0.518181,0.75453,0.729812,0.940187,0.453399,0.0796735,0.0793808,0.592113,0.619475,0.554881,0.459973,0.720683,0.899843,0.612555,0.34158,0.61983,0.0232233,0.381293,0.575816,0.26133,0.57139,0.414137,0.187965,0.203643,0.458246,0.291171,0.0323865,0.485492,0.474216,0.24446,0.906941,0.90982,0.264787,0.522931,0.675485,0.477117,0.129311,0.207912,0.541692,0.0999005,0.279275,0.618419,0.649146,0.134145,0.579255,0.0205021,0.695325,0.264835,0.0761872,0.0644202,0.00175199,0.540073,0.70766,0.483435,0.399451,0.45982,0.227488,0.317159,0.487071,0.886944,0.238565,0.706059,0.374554,0.376154,0.767978,0.757252,0.530872,0.282307,0.0121198,0.391668,0.133308,0.357482,0.227597,0.35231,0.267558,0.422549,0.647652,0.63385,0.134581,0.666547,0.665423,0.520871,0.877297,0.650282,0.633904,0.59893,0.737186,0.536776,0.790368,0.22158,0.742357,0.846759,0.247202,0.499854,0.654077,0.823852,0.514283,0.609745,0.711558,0.433169,0.628964,0.367837,0.543971,0.0730383,0.406484,0.558571,0.165775,0.54746,0.467603,0.244286,0.168254,0.892826,0.34044,0.721936,0.675012,0.725223,0.575685,0.788897,0.592665,0.349385,0.315651,0.195042,0.157921,0.473551,0.216218,0.162951,0.373485,0.531611,0.494987,0.257347,0.255702,0.47205,0.29961,0.64109,0.125012,0.66188,0.333468,0.352452,0.287616,0.616277,0.176796,0.176452,0.0527744,0.296191,0.626433,0.77346,0.00927449,0.427392,0.305866,0.282022,0.246314,0.238193,0.406937,0.288143,0.125904,0.0116264,0.32684,0.339579,0.507652,0.475759,0.720751,0.14256,0.228642,0.187038,0.453028,0.298062,0.524321,0.703005,0.479486,0.346481,0.13098,0.137686,0.487944,0.462936,0.336393,0.440086,0.457632,0.426628,0.240557,0.259353,0.0333885,0.529873,0.287981,0.619307,0.0143703,0.435843,0.077275,0.50994,0.0875223,0.345012,0.127712,0.149004,0.504834,0.392756,0.220778,0.264715,0.407611,0.326688,0.248037,0.158248,0.0796495,0.887822,0.358005,0.0431634,0.184427,0.160618,0.526429,0.22169,0.210572,0.411099,0.474863,0.155833,0.21615,0.159259,0.120131,0.100087,0.112146,0.585964,0.4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}}
}}

Revision as of 20:55, 8 August 2012


Full id: C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital



Phase1 CAGE Peaks

Hg19::chr10:94001015..94001051,-p@chr10:94001015..94001051
-
Hg19::chr15:93632396..93632407,-p3@RGMA
Hg19::chr1:160103394..160103410,+p@chr1:160103394..160103410
+
Hg19::chr1:160103559..160103576,+p@chr1:160103559..160103576
+
Hg19::chr1:160103656..160103669,+p@chr1:160103656..160103669
+
Hg19::chr1:160103687..160103724,+p@chr1:160103687..160103724
+
Hg19::chr1:160103733..160103769,+p@chr1:160103733..160103769
+
Hg19::chr1:160107625..160107629,+p@chr1:160107625..160107629
+
Hg19::chrX:135849340..135849399,-p6@ARHGEF6


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:0001843neural tube closure0.010383953248564
GO:0014020primary neural tube formation0.010383953248564
GO:0001839neural plate morphogenesis0.010383953248564
GO:0001841neural tube formation0.010383953248564
GO:0001840neural plate development0.010383953248564
GO:0001838embryonic epithelial tube formation0.010383953248564
GO:0021915neural tube development0.010383953248564
GO:0016331morphogenesis of embryonic epithelium0.0105201195496108
GO:0002009morphogenesis of an epithelium0.0236325170582736
GO:0007254JNK cascade0.0236325170582736
GO:0031098stress-activated protein kinase signaling pathway0.0236325170582736
GO:0035239tube morphogenesis0.0242021142259976
GO:0048598embryonic morphogenesis0.0242021142259976
GO:0009792embryonic development ending in birth or egg hatching0.0242021142259976
GO:0043009chordate embryonic development0.0242021142259976
GO:0035295tube development0.0274244371401497
GO:0048503GPI anchor binding0.0274244371401497
GO:0009986cell surface0.0274244371401497
GO:0000165MAPKKK cascade0.0274244371401497
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0035023regulation of Rho protein signal transduction0.0274244371401497
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0032502developmental process0.0274244371401497
GO:0007266Rho protein signal transduction0.0298931627822005
GO:0009790embryonic development0.0358469119443389
GO:0035091phosphoinositide binding0.0368062548747997
GO:0005085guanyl-nucleotide exchange factor activity0.0435957043134591
GO:0005543phospholipid binding0.0441627868691779
GO:0016337cell-cell adhesion0.0441627868691779
GO:0005096GTPase activator activity0.0441627868691779
GO:0046578regulation of Ras protein signal transduction0.044715327201792
GO:0007243protein kinase cascade0.044715327201792
GO:0007265Ras protein signal transduction0.049776947180899



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
adult organism2.28e-47115
central nervous system8.14e-3582
neural tube9.49e-3557
neural rod9.49e-3557
future spinal cord9.49e-3557
neural keel9.49e-3557
regional part of nervous system3.66e-3294
nervous system3.66e-3294
regional part of brain3.56e-3059
brain1.69e-2869
future brain1.69e-2869
anterior neural tube2.25e-2742
regional part of forebrain4.74e-2741
forebrain4.74e-2741
future forebrain4.74e-2741
neural plate5.47e-2486
presumptive neural plate5.47e-2486
telencephalon3.91e-2334
gray matter4.19e-2334
brain grey matter4.19e-2334
neurectoderm4.76e-2390
regional part of telencephalon1.84e-2233
cerebral hemisphere9.85e-2232
pre-chordal neural plate3.63e-1761
cerebral cortex4.48e-1725
pallium4.48e-1725
regional part of cerebral cortex3.59e-1622
anterior region of body3.19e-15129
craniocervical region3.19e-15129
head3.75e-15123
neocortex9.99e-1520
ectoderm-derived structure6.47e-14169
ectoderm1.16e-13173
presumptive ectoderm1.16e-13173
multi-cellular organism1.08e-09659
organ2.26e-09511
embryo4.15e-09612
posterior neural tube1.71e-0815
chordal neural plate1.71e-0815
embryonic structure1.11e-07605
developing anatomical structure1.11e-07605
nucleus of brain1.75e-079
neural nucleus1.75e-079
germ layer1.89e-07604
embryonic tissue1.89e-07604
presumptive structure1.89e-07604
epiblast (generic)1.89e-07604
tissue1.94e-07787
basal ganglion1.94e-079
nuclear complex of neuraxis1.94e-079
aggregate regional part of brain1.94e-079
collection of basal ganglia1.94e-079
cerebral subcortex1.94e-079
anatomical system3.14e-07625
anatomical group4.56e-07626
segmental subdivision of nervous system4.62e-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.