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Coexpression cluster:C2096: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.66e-64!56;UBERON:0005068!3.66e-64!56;UBERON:0006241!3.66e-64!56;UBERON:0007135!3.66e-64!56;UBERON:0001016!3.79e-60!89;UBERON:0000073!1.00e-59!53;UBERON:0002616!1.00e-59!53;UBERON:0001017!9.30e-59!81;UBERON:0000955!9.16e-57!68;UBERON:0006238!9.16e-57!68;UBERON:0002346!1.93e-49!86;UBERON:0003075!3.35e-49!82;UBERON:0007284!3.35e-49!82;UBERON:0002780!7.06e-49!41;UBERON:0001890!7.06e-49!41;UBERON:0003080!7.06e-49!41;UBERON:0006240!7.06e-49!41;UBERON:0007023!5.30e-40!114;UBERON:0003528!2.08e-39!34;UBERON:0002020!2.08e-39!34;UBERON:0001893!3.06e-39!34;UBERON:0002791!1.46e-36!32;UBERON:0001869!2.44e-36!32;UBERON:0010371!5.55e-36!104;UBERON:0003056!1.14e-35!61;UBERON:0002619!3.09e-29!22;UBERON:0010314!1.97e-28!132;UBERON:0004121!8.29e-28!171;UBERON:0000924!8.29e-28!171;UBERON:0006601!8.29e-28!171;UBERON:0000956!5.28e-27!25;UBERON:0000203!5.28e-27!25;UBERON:0011216!1.23e-26!223;UBERON:0001950!1.88e-26!20;UBERON:0003076!8.58e-16!15;UBERON:0003057!8.58e-16!15;UBERON:0000125!6.35e-14!9;UBERON:0002308!6.35e-14!9;UBERON:0002420!7.58e-14!9;UBERON:0007245!7.58e-14!9;UBERON:0010009!7.58e-14!9;UBERON:0010011!7.58e-14!9;UBERON:0000454!7.58e-14!9;UBERON:0000025!9.12e-14!192;UBERON:0000477!3.41e-13!373;UBERON:0004732!3.56e-13!13;UBERON:0004733!9.11e-12!12;UBERON:0002028!9.11e-12!12;UBERON:0007277!9.11e-12!12;UBERON:0009663!3.92e-11!7;UBERON:0001894!6.10e-11!7;UBERON:0006222!6.10e-11!7;UBERON:0002298!8.86e-10!6;UBERON:0000064!2.59e-09!218;UBERON:0000200!2.74e-09!6;UBERON:0000481!4.61e-09!342;UBERON:0004111!1.52e-08!240;UBERON:0000922!1.74e-08!592;UBERON:0000349!2.34e-08!5;UBERON:0002021!2.38e-08!5;UBERON:0001872!2.45e-08!5;UBERON:0005423!2.53e-08!581;UBERON:0001871!5.65e-08!6;UBERON:0002680!6.06e-08!9;UBERON:0001895!6.06e-08!9;UBERON:0010092!6.06e-08!9;UBERON:0000062!7.20e-08!503;UBERON:0000483!7.23e-08!306;UBERON:0000923!9.25e-08!560;UBERON:0010316!9.25e-08!560;UBERON:0005291!9.25e-08!560;UBERON:0006598!9.25e-08!560;UBERON:0010317!9.25e-08!560;UBERON:0002532!9.25e-08!560;UBERON:0000119!1.30e-07!309;UBERON:0002050!1.70e-07!564;UBERON:0002784!2.73e-07!4;UBERON:0000468!6.96e-07!656;UBERON:0000467!7.69e-07!624;UBERON:0000369!7.93e-07!4;UBERON:0002435!7.93e-07!4;UBERON:0000204!7.93e-07!4;UBERON:0010082!7.93e-07!4;UBERON:0000480!8.86e-07!625
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0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.121268,0.500698,0.472542,0.685908,0.747471,0.529642,0.818701,0.483077,0.590496,0.603763,0.184287,0.259354,0.938109,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.215551,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.598945,0.882403,0.464001,0.871271,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.0363436,0.563206,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.210703,0.148933,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.106831,0.254628,0.713293,0.479347,0.102411,0.632833,0.0828233,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.0890097,0.279553,0.25563,0.240967,0.160955,0.036192,0.0432189,0.122439,0.16188,0.0293669,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.0888526,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
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}}
}}

Revision as of 15:17, 26 November 2012


Full id: C2096_cerebellum_thalamus_substantia_globus_occipital_brain_optic



Phase1 CAGE Peaks

Hg19::chr11:112834886..112834890,+p@chr11:112834886..112834890
+
Hg19::chr1:171904935..171904938,+p@chr1:171904935..171904938
+
Hg19::chr1:172001694..172001701,+p@chr1:172001694..172001701
+
Hg19::chr2:25288238..25288242,+p@chr2:25288238..25288242
+


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

No GOStat results

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 tube3.66e-6456
neural rod3.66e-6456
future spinal cord3.66e-6456
neural keel3.66e-6456
nervous system3.79e-6089
regional part of nervous system1.00e-5953
regional part of brain1.00e-5953
central nervous system9.30e-5981
brain9.16e-5768
future brain9.16e-5768
neurectoderm1.93e-4986
neural plate3.35e-4982
presumptive neural plate3.35e-4982
regional part of forebrain7.06e-4941
forebrain7.06e-4941
anterior neural tube7.06e-4941
future forebrain7.06e-4941
adult organism5.30e-40114
brain grey matter2.08e-3934
gray matter2.08e-3934
telencephalon3.06e-3934
regional part of telencephalon1.46e-3632
cerebral hemisphere2.44e-3632
ecto-epithelium5.55e-36104
pre-chordal neural plate1.14e-3561
regional part of cerebral cortex3.09e-2922
structure with developmental contribution from neural crest1.97e-28132
ectoderm-derived structure8.29e-28171
ectoderm8.29e-28171
presumptive ectoderm8.29e-28171
cerebral cortex5.28e-2725
pallium5.28e-2725
organ system subdivision1.23e-26223
neocortex1.88e-2620
posterior neural tube8.58e-1615
chordal neural plate8.58e-1615
neural nucleus6.35e-149
nucleus of brain6.35e-149
basal ganglion7.58e-149
nuclear complex of neuraxis7.58e-149
aggregate regional part of brain7.58e-149
collection of basal ganglia7.58e-149
cerebral subcortex7.58e-149
tube9.12e-14192
anatomical cluster3.41e-13373
segmental subdivision of nervous system3.56e-1313
segmental subdivision of hindbrain9.11e-1212
hindbrain9.11e-1212
presumptive hindbrain9.11e-1212
telencephalic nucleus3.92e-117
diencephalon6.10e-117
future diencephalon6.10e-117
brainstem8.86e-106
organ part2.59e-09218
gyrus2.74e-096
multi-tissue structure4.61e-09342
anatomical conduit1.52e-08240
embryo1.74e-08592
limbic system2.34e-085
occipital lobe2.38e-085
parietal lobe2.45e-085
developing anatomical structure2.53e-08581
temporal lobe5.65e-086
regional part of metencephalon6.06e-089
metencephalon6.06e-089
future metencephalon6.06e-089
organ7.20e-08503
epithelium7.23e-08306
germ layer9.25e-08560
germ layer / neural crest9.25e-08560
embryonic tissue9.25e-08560
presumptive structure9.25e-08560
germ layer / neural crest derived structure9.25e-08560
epiblast (generic)9.25e-08560
cell layer1.30e-07309
embryonic structure1.70e-07564
regional part of diencephalon2.73e-074
multi-cellular organism6.96e-07656
anatomical system7.69e-07624
corpus striatum7.93e-074
striatum7.93e-074
ventral part of telencephalon7.93e-074
future corpus striatum7.93e-074
anatomical group8.86e-07625


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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