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Coexpression cluster:C2502: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.14e-87!56;UBERON:0005068!2.14e-87!56;UBERON:0006241!2.14e-87!56;UBERON:0007135!2.14e-87!56;UBERON:0000073!2.38e-81!53;UBERON:0002616!2.38e-81!53;UBERON:0001017!4.70e-78!81;UBERON:0001016!1.27e-76!89;UBERON:0002780!9.76e-73!41;UBERON:0001890!9.76e-73!41;UBERON:0003080!9.76e-73!41;UBERON:0006240!9.76e-73!41;UBERON:0002346!8.58e-67!86;UBERON:0003075!4.26e-65!82;UBERON:0007284!4.26e-65!82;UBERON:0000955!4.62e-65!68;UBERON:0006238!4.62e-65!68;UBERON:0003528!1.85e-58!34;UBERON:0002020!1.85e-58!34;UBERON:0001893!6.78e-58!34;UBERON:0001869!1.40e-54!32;UBERON:0002791!3.08e-54!32;UBERON:0003056!7.94e-53!61;UBERON:0010371!1.82e-52!104;UBERON:0002619!1.39e-46!22;UBERON:0004121!2.39e-44!171;UBERON:0000924!2.39e-44!171;UBERON:0006601!2.39e-44!171;UBERON:0001950!3.72e-42!20;UBERON:0000956!2.18e-40!25;UBERON:0000203!2.18e-40!25;UBERON:0010314!9.34e-40!132;UBERON:0007023!5.68e-39!114;UBERON:0011216!1.02e-28!223;UBERON:0002420!1.35e-19!9;UBERON:0007245!1.35e-19!9;UBERON:0010009!1.35e-19!9;UBERON:0010011!1.35e-19!9;UBERON:0000454!1.35e-19!9;UBERON:0000125!2.24e-19!9;UBERON:0002308!2.24e-19!9;UBERON:0000025!1.93e-18!192;UBERON:0001894!5.78e-16!7;UBERON:0006222!5.78e-16!7;UBERON:0003076!7.81e-16!15;UBERON:0003057!7.81e-16!15;UBERON:0009663!2.87e-15!7;UBERON:0000200!2.41e-14!6;UBERON:0004111!3.04e-14!240;UBERON:0000477!3.68e-14!373;UBERON:0002298!6.09e-13!6;UBERON:0001871!1.85e-12!6;UBERON:0002021!1.93e-12!5;UBERON:0001872!2.48e-12!5;UBERON:0000483!2.56e-12!306;UBERON:0000349!2.99e-12!5;UBERON:0000119!4.74e-12!309;UBERON:0000064!1.13e-11!218;UBERON:0004733!9.34e-11!12;UBERON:0002028!9.34e-11!12;UBERON:0007277!9.34e-11!12;UBERON:0002784!2.70e-10!4;UBERON:0000369!5.90e-10!4;UBERON:0002435!5.90e-10!4;UBERON:0000204!5.90e-10!4;UBERON:0010082!5.90e-10!4;UBERON:0003296!7.58e-10!4;UBERON:0010133!7.58e-10!4;UBERON:0004732!8.22e-10!13;UBERON:0005383!4.43e-08!3;UBERON:0005382!4.43e-08!3;UBERON:0001870!4.64e-08!3;UBERON:0000922!4.67e-08!592;UBERON:0000481!7.60e-08!342;UBERON:0000988!1.36e-07!3;UBERON:0002240!2.53e-07!3;UBERON:0005174!2.53e-07!3;UBERON:0001137!2.53e-07!3;UBERON:0001896!5.18e-07!3;UBERON:0005290!5.18e-07!3;UBERON:0010096!5.18e-07!3
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19419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.0237068,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.515487,3.33928e-05,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.0155918,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.758305,0.278645,0.365775,0.155708,0.0336707,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.22476,0.709625,0.265324,0.043404,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.0217469,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.0173373,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.06079,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.61565,0.00312482,0.00683871,0.230477,0.279823,0.295555,0.502112,0.369553,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.163504,0.1267,0.00137171,0.154964,0.296013,0.282366,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.121268,0.500698,0.472542,0.322168,0.399934,0.529642,0.818701,0.483077,0.590496,0.23695,0.541914,0.627201,0.526336,0.293249,0.290703,0.0757071,0.366999,0.478691,0.0744652,0.608176,0.0937029,0.519564,0.365494,0.212703,0.201391,0.364079,0.107716,0.0575699,0.421038,0.0108102,0.328518,0.545608,0.310552,0.324103,0.483764,0.528161,0.453065,0.209437,0.55323,0.161672,0.0651244,0.361291,0.464001,0.336867,0.214786,0.150592,0.278028,0.315519,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.0205071,0.0277366,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.0243103,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.0103854,0.328421,0.137737,0.50338,0.620526,0.404625,0.416164,0.424691,0.357704,0.0286876,0.62689,0.884725,0.274432,0.284496,0.512545,0.512178,0.201413,0.829402,0.321001,0.263302,0.552023,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.0585759,0.226491,0.102502,0.463987,0.627953,0.156131,0.124057,0.0840572,0.483658,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.114247,0.00959742,0.741477,0.385425,0.307816,0.0250382,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.197104,0.608127,0.282281,0.245336,0.2536,0.246827,0.0519643,0.347466,0.387134,0.559969,0.358813,0.303004,0.0554837,0.493455,0.346636,0.457747,0.348802,0.137708,0.579645,0.119749,0.42505,0.254628,0.713293,0.479347,0.416962,0.0806585,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.00789472,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.0445044,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.00348847,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.287598,0.0554083,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.0268645,0.228479,0.127111,0.259989,0.390754,0.355805,0.0433915,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.00984212,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.0164443,0.262778,0.373453,0.362662,0.433518,0.184359,0.0634867,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.0361085,0.362898,0.0510917,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.0331484,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,1.42279,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,1.17228,0.371755,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,1.57574,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,2.28137,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2502_parietal_small_medial_occipital_temporal_pineal_Neurons



Phase1 CAGE Peaks

Hg19::chr19:54461858..54461872,+p@chr19:54461858..54461872
+
Hg19::chr2:166538795..166538813,+p@chr2:166538795..166538813
+
Hg19::chr2:166538815..166538832,+p@chr2:166538815..166538832
+
Hg19::chr2:210574692..210574711,+p19@MAP2


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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
embryonic stem cell1.33e-095
neuronal stem cell2.90e-078
Uber Anatomy
Ontology termp-valuen
neural tube2.14e-8756
neural rod2.14e-8756
future spinal cord2.14e-8756
neural keel2.14e-8756
regional part of nervous system2.38e-8153
regional part of brain2.38e-8153
central nervous system4.70e-7881
nervous system1.27e-7689
regional part of forebrain9.76e-7341
forebrain9.76e-7341
anterior neural tube9.76e-7341
future forebrain9.76e-7341
neurectoderm8.58e-6786
neural plate4.26e-6582
presumptive neural plate4.26e-6582
brain4.62e-6568
future brain4.62e-6568
brain grey matter1.85e-5834
gray matter1.85e-5834
telencephalon6.78e-5834
cerebral hemisphere1.40e-5432
regional part of telencephalon3.08e-5432
pre-chordal neural plate7.94e-5361
ecto-epithelium1.82e-52104
regional part of cerebral cortex1.39e-4622
ectoderm-derived structure2.39e-44171
ectoderm2.39e-44171
presumptive ectoderm2.39e-44171
neocortex3.72e-4220
cerebral cortex2.18e-4025
pallium2.18e-4025
structure with developmental contribution from neural crest9.34e-40132
adult organism5.68e-39114
organ system subdivision1.02e-28223
basal ganglion1.35e-199
nuclear complex of neuraxis1.35e-199
aggregate regional part of brain1.35e-199
collection of basal ganglia1.35e-199
cerebral subcortex1.35e-199
neural nucleus2.24e-199
nucleus of brain2.24e-199
tube1.93e-18192
diencephalon5.78e-167
future diencephalon5.78e-167
posterior neural tube7.81e-1615
chordal neural plate7.81e-1615
telencephalic nucleus2.87e-157
gyrus2.41e-146
anatomical conduit3.04e-14240
anatomical cluster3.68e-14373
brainstem6.09e-136
temporal lobe1.85e-126
occipital lobe1.93e-125
parietal lobe2.48e-125
epithelium2.56e-12306
limbic system2.99e-125
cell layer4.74e-12309
organ part1.13e-11218
segmental subdivision of hindbrain9.34e-1112
hindbrain9.34e-1112
presumptive hindbrain9.34e-1112
regional part of diencephalon2.70e-104
corpus striatum5.90e-104
striatum5.90e-104
ventral part of telencephalon5.90e-104
future corpus striatum5.90e-104
gland of diencephalon7.58e-104
neuroendocrine gland7.58e-104
segmental subdivision of nervous system8.22e-1013
caudate-putamen4.43e-083
dorsal striatum4.43e-083
frontal cortex4.64e-083
embryo4.67e-08592
multi-tissue structure7.60e-08342
pons1.36e-073
spinal cord2.53e-073
dorsal region element2.53e-073
dorsum2.53e-073
medulla oblongata5.18e-073
myelencephalon5.18e-073
future myelencephalon5.18e-073
Disease
Ontology termp-valuen
neuroectodermal tumor5.15e-0710


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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