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Coexpression cluster:C2579: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.80e-57!114;UBERON:0001049!1.70e-44!56;UBERON:0005068!1.70e-44!56;UBERON:0006241!1.70e-44!56;UBERON:0007135!1.70e-44!56;UBERON:0000073!2.51e-41!53;UBERON:0002616!2.51e-41!53;UBERON:0001017!1.45e-36!81;UBERON:0002780!3.11e-36!41;UBERON:0001890!3.11e-36!41;UBERON:0003080!3.11e-36!41;UBERON:0006240!3.11e-36!41;UBERON:0000955!4.34e-35!68;UBERON:0006238!4.34e-35!68;UBERON:0003075!1.63e-33!82;UBERON:0007284!1.63e-33!82;UBERON:0002346!5.92e-33!86;UBERON:0001016!1.06e-31!89;UBERON:0003528!9.10e-30!34;UBERON:0002020!9.10e-30!34;UBERON:0001893!1.18e-29!34;UBERON:0002791!6.98e-28!32;UBERON:0001869!7.90e-28!32;UBERON:0003056!5.78e-25!61;UBERON:0010371!7.80e-23!104;UBERON:0000956!1.95e-22!25;UBERON:0000203!1.95e-22!25;UBERON:0002619!2.29e-21!22;UBERON:0001950!1.46e-19!20;UBERON:0010314!3.16e-17!132;UBERON:0011216!1.09e-13!223;UBERON:0004121!3.29e-13!171;UBERON:0000924!3.29e-13!171;UBERON:0006601!3.29e-13!171;UBERON:0003076!1.75e-09!15;UBERON:0003057!1.75e-09!15;UBERON:0002420!7.17e-09!9;UBERON:0007245!7.17e-09!9;UBERON:0010009!7.17e-09!9;UBERON:0010011!7.17e-09!9;UBERON:0000454!7.17e-09!9;UBERON:0000125!9.92e-09!9;UBERON:0002308!9.92e-09!9;UBERON:0001894!6.15e-08!7;UBERON:0006222!6.15e-08!7;UBERON:0001871!9.12e-08!6;UBERON:0004732!2.18e-07!13;UBERON:0000200!3.62e-07!6;UBERON:0000025!5.64e-07!192;UBERON:0002298!5.73e-07!6;UBERON:0009663!6.64e-07!7;UBERON:0004733!9.89e-07!12;UBERON:0002028!9.89e-07!12;UBERON:0007277!9.89e-07!12
|ontology_enrichment_uberon=UBERON:0007023!2.80e-57!114;UBERON:0001049!1.70e-44!56;UBERON:0005068!1.70e-44!56;UBERON:0006241!1.70e-44!56;UBERON:0007135!1.70e-44!56;UBERON:0000073!2.51e-41!53;UBERON:0002616!2.51e-41!53;UBERON:0001017!1.45e-36!81;UBERON:0002780!3.11e-36!41;UBERON:0001890!3.11e-36!41;UBERON:0003080!3.11e-36!41;UBERON:0006240!3.11e-36!41;UBERON:0000955!4.34e-35!68;UBERON:0006238!4.34e-35!68;UBERON:0003075!1.63e-33!82;UBERON:0007284!1.63e-33!82;UBERON:0002346!5.92e-33!86;UBERON:0001016!1.06e-31!89;UBERON:0003528!9.10e-30!34;UBERON:0002020!9.10e-30!34;UBERON:0001893!1.18e-29!34;UBERON:0002791!6.98e-28!32;UBERON:0001869!7.90e-28!32;UBERON:0003056!5.78e-25!61;UBERON:0010371!7.80e-23!104;UBERON:0000956!1.95e-22!25;UBERON:0000203!1.95e-22!25;UBERON:0002619!2.29e-21!22;UBERON:0001950!1.46e-19!20;UBERON:0010314!3.16e-17!132;UBERON:0011216!1.09e-13!223;UBERON:0004121!3.29e-13!171;UBERON:0000924!3.29e-13!171;UBERON:0006601!3.29e-13!171;UBERON:0003076!1.75e-09!15;UBERON:0003057!1.75e-09!15;UBERON:0002420!7.17e-09!9;UBERON:0007245!7.17e-09!9;UBERON:0010009!7.17e-09!9;UBERON:0010011!7.17e-09!9;UBERON:0000454!7.17e-09!9;UBERON:0000125!9.92e-09!9;UBERON:0002308!9.92e-09!9;UBERON:0001894!6.15e-08!7;UBERON:0006222!6.15e-08!7;UBERON:0001871!9.12e-08!6;UBERON:0004732!2.18e-07!13;UBERON:0000200!3.62e-07!6;UBERON:0000025!5.64e-07!192;UBERON:0002298!5.73e-07!6;UBERON:0009663!6.64e-07!7;UBERON:0004733!9.89e-07!12;UBERON:0002028!9.89e-07!12;UBERON:0007277!9.89e-07!12
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,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,4.35854e-13,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.818701,0.483077,0.061678,0.603763,0.541914,0.627201,0.938109,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.598945,0.882403,0.464001,0.871271,0.0118057,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,4.55261e-10,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.512178,0.563206,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.0181825,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,23.6677,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,5.64555,7.83934,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2579_spinal_cerebellum_amygdala_occipital_pineal_medial_CD4



Phase1 CAGE Peaks

Hg19::chr1:26093536..26093557,+p@chr1:26093536..26093557
+
Hg19::chr1:26093961..26094017,+p@chr1:26093961..26094017
+
Hg19::chr1:26094071..26094085,+p@chr1:26094071..26094085
+
Hg19::chr1:26094142..26094180,+p@chr1:26094142..26094180
+


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
adult organism2.80e-57114
neural tube1.70e-4456
neural rod1.70e-4456
future spinal cord1.70e-4456
neural keel1.70e-4456
regional part of nervous system2.51e-4153
regional part of brain2.51e-4153
central nervous system1.45e-3681
regional part of forebrain3.11e-3641
forebrain3.11e-3641
anterior neural tube3.11e-3641
future forebrain3.11e-3641
brain4.34e-3568
future brain4.34e-3568
neural plate1.63e-3382
presumptive neural plate1.63e-3382
neurectoderm5.92e-3386
nervous system1.06e-3189
brain grey matter9.10e-3034
gray matter9.10e-3034
telencephalon1.18e-2934
regional part of telencephalon6.98e-2832
cerebral hemisphere7.90e-2832
pre-chordal neural plate5.78e-2561
ecto-epithelium7.80e-23104
cerebral cortex1.95e-2225
pallium1.95e-2225
regional part of cerebral cortex2.29e-2122
neocortex1.46e-1920
structure with developmental contribution from neural crest3.16e-17132
organ system subdivision1.09e-13223
ectoderm-derived structure3.29e-13171
ectoderm3.29e-13171
presumptive ectoderm3.29e-13171
posterior neural tube1.75e-0915
chordal neural plate1.75e-0915
basal ganglion7.17e-099
nuclear complex of neuraxis7.17e-099
aggregate regional part of brain7.17e-099
collection of basal ganglia7.17e-099
cerebral subcortex7.17e-099
neural nucleus9.92e-099
nucleus of brain9.92e-099
diencephalon6.15e-087
future diencephalon6.15e-087
temporal lobe9.12e-086
segmental subdivision of nervous system2.18e-0713
gyrus3.62e-076
tube5.64e-07192
brainstem5.73e-076
telencephalic nucleus6.64e-077
segmental subdivision of hindbrain9.89e-0712
hindbrain9.89e-0712
presumptive hindbrain9.89e-0712


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)

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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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