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Coexpression cluster:C2797: Difference between revisions

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|tf_chipseq_enrich=PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428634976381569!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123873583463688!SMARCC1#6599;2:21.8316796598157:0.00305120745616205:0.0160933819258678
|tf_chipseq_enrich=PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428634976381569!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123873583463688!SMARCC1#6599;2:21.8316796598157:0.00305120745616205:0.0160933819258678
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248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.0757292,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.0159364,0.101893,0.142875,0.0149091,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.267945,0.758305,0.278645,0.365775,0.155708,0.0336707,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.22476,0.499775,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.034089,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.369553,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.0354672,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.509113,0.483077,0.590496,0.603763,0.184287,0.627201,0.938109,0.293249,0.290703,0.622694,0.722684,0.478691,0.360199,0.241059,0.657141,0.519564,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.594773,0.483764,0.528161,0.784052,0.209437,0.284058,0.401218,0.598945,0.169076,0.464001,0.60737,0.579004,0.605327,0.839946,0.586133,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.328421,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.0230743,0.642173,0.284496,0.512545,0.512178,0.563206,0.527709,0.321001,0.263302,0.552023,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.0862349,0.307816,0.461541,0.386339,0.382854,0.232374,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.119749,0.42505,0.254628,0.713293,0.479347,0.416962,0.264955,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.0293669,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.0181825,0.248707,0.31749,0.0121139,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.081972,0.0588457,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.0109327,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.0345639,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,1.33003,1.46495,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,1.75478,1.17228,0.371755,0.493145,0.66492,1.03152,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2797_medulloblastoma_neuroectodermal_peripheral_pineal_carcinoid_neuroepithelioma_small



Phase1 CAGE Peaks

Hg19::chr4:87515454..87515486,+p1@PTPN13
Hg19::chr4:87515493..87515510,+p2@PTPN13
Hg19::chr4:87521610..87521614,+p@chr4:87521610..87521614
+
Hg19::chr4:87526137..87526140,+p@chr4:87526137..87526140
+


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><br>


Cell Type
Ontology termp-valuen
skin fibroblast9.50e-0923
fibroblast2.45e-0776
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure4.68e-26171
ectoderm4.68e-26171
presumptive ectoderm4.68e-26171
nervous system1.00e-1789
surface structure8.78e-1799
central nervous system1.67e-1581
ecto-epithelium2.25e-15104
neurectoderm2.73e-1586
organ system subdivision9.16e-14223
neural tube1.31e-1356
neural rod1.31e-1356
future spinal cord1.31e-1356
neural keel1.31e-1356
structure with developmental contribution from neural crest2.77e-13132
neural plate3.17e-1382
presumptive neural plate3.17e-1382
brain4.07e-1368
future brain4.07e-1368
regional part of forebrain6.03e-1341
forebrain6.03e-1341
anterior neural tube6.03e-1341
future forebrain6.03e-1341
regional part of nervous system8.29e-1353
regional part of brain8.29e-1353
pre-chordal neural plate2.14e-1261
multi-tissue structure1.89e-11342
multi-cellular organism3.23e-10656
brain grey matter9.24e-1034
gray matter9.24e-1034
telencephalon1.28e-0934
anatomical cluster1.89e-09373
regional part of telencephalon4.56e-0932
adult organism8.07e-09114
cerebral hemisphere9.91e-0932
head1.44e-0856
orifice1.59e-0836
mouth1.91e-0829
stomodeum1.91e-0829
skin of body2.18e-0841
subdivision of head3.20e-0849
anterior region of body4.40e-0862
craniocervical region4.40e-0862
integument6.12e-0846
integumental system6.12e-0846
organ part6.99e-08218
organ7.83e-08503
anatomical group7.87e-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)

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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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
PBX3#5090210.95725634337210.01174530180688030.0428634976381569
RFX5#599339.035933120396320.002144561191324070.0123873583463688
SMARCC1#6599221.83167965981570.003051207456162050.0160933819258678



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.