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Coexpression cluster:C2205: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172913923170336!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160617833121619!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234573032002976!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466016451109103!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488631271882188!MEF2C#4208;3:30.983515869468:5.56692972943475e-05:0.00094108865978057!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186279161889552!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434796034381259!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765508003634847!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321417612868759!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162724385139232!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482829870435937!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107160628354989!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342298484345972
|tf_chipseq_enrich=CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172913923170336!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160617833121619!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234573032002976!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466016451109103!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488631271882188!MEF2C#4208;3:30.983515869468:5.56692972943475e-05:0.00094108865978057!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186279161889552!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434796034381259!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765508003634847!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321417612868759!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162724385139232!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482829870435937!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107160628354989!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342298484345972
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5411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.000354369,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.22476,0.307186,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.0501465,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.0368787,0.459091,0.54832,0.502211,0.296013,0.282366,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.153911,0.472542,0.322168,0.399934,0.529642,0.509113,0.483077,0.590496,0.603763,0.541914,0.259354,0.0237007,0.293249,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.00190736,0.56318,0.364079,0.680099,0.579886,0.421038,0.0108102,0.328518,0.545608,0.310552,0.324103,0.483764,0.103928,0.784052,0.209437,0.0404917,0.748403,0.598945,0.169076,0.464001,0.336867,0.579004,0.870272,0.839946,0.586133,0.261575,0.00354463,0.264245,0.379063,0.0602936,0.522925,0.436016,0.0277366,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.301684,0.39549,0.234254,0.357409,0.599068,0.137737,0.50338,0.0746831,0.404625,0.416164,0.424691,0.715362,0.479581,0.077723,0.884725,0.642173,0.284496,0.512545,0.512178,0.201413,0.829402,0.684899,0.0381838,0.552023,0.180735,0.189249,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.187223,0.438176,0.349112,0.741477,0.385425,0.307816,0.0250382,0.386339,0.382854,0.598787,0.478745,0.24434,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.210703,0.493455,0.346636,0.457747,0.0694762,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.0806585,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.0331645,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.0713545,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.0641033,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.0571822,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,2.74508,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,1.63433,1.09415,0.433165,0.344471,1.23824,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,1.6033,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,8.38231,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,1.63159,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,5.81307,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
}}
}}

Revision as of 15:21, 26 November 2012


Full id: C2205_teratocarcinoma_Natural_CD8_mycosis_cord_diffuse_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:4378920..4378934,+p@chr12:4378920..4378934
+
Hg19::chr12:4378938..4378957,+p@chr12:4378938..4378957
+
Hg19::chr12:4378971..4378986,+p@chr12:4378971..4378986
+
Hg19::chr2:98330332..98330376,+p@chr2:98330332..98330376
+


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
leukocyte5.22e-35136
nongranular leukocyte6.21e-33115
hematopoietic lineage restricted progenitor cell2.35e-31120
hematopoietic stem cell1.05e-30168
angioblastic mesenchymal cell1.05e-30168
hematopoietic cell1.53e-30177
hematopoietic oligopotent progenitor cell3.67e-27161
hematopoietic multipotent progenitor cell3.67e-27161
lymphoid lineage restricted progenitor cell8.08e-2552
lymphocyte5.21e-2453
common lymphoid progenitor5.21e-2453
nucleate cell1.74e-2255
mature alpha-beta T cell1.60e-1618
alpha-beta T cell1.60e-1618
immature T cell1.60e-1618
mature T cell1.60e-1618
immature alpha-beta T cell1.60e-1618
classical monocyte1.43e-1442
CD14-positive, CD16-negative classical monocyte1.43e-1442
T cell2.18e-1425
pro-T cell2.18e-1425
defensive cell2.63e-1148
phagocyte2.63e-1148
CD8-positive, alpha-beta T cell4.55e-1111
myeloid leukocyte6.20e-1072
macrophage dendritic cell progenitor7.83e-1061
granulocyte monocyte progenitor cell9.34e-1067
lymphocyte of B lineage3.67e-0924
pro-B cell3.67e-0924
monopoietic cell6.20e-0959
monocyte6.20e-0959
monoblast6.20e-0959
promonocyte6.20e-0959
myeloid lineage restricted progenitor cell1.40e-0866
myeloid cell3.66e-08108
common myeloid progenitor3.66e-08108
circulating cell3.19e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.18e-21108
hematopoietic system1.19e-2098
blood island1.19e-2098
blood3.45e-1315
haemolymphatic fluid3.45e-1315
organism substance3.45e-1315
immune system1.58e-1293
bone marrow1.49e-0876
bone element4.52e-0782
hemopoietic organ8.16e-077
immune organ8.16e-077
skeletal element8.86e-0790


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


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

TF#promotersEnrichmentp-valueq-value
CHD2#110637.758017125587640.003351522464536340.0172913923170336
ELF1#199744.258097958807540.003041525565781240.0160617833121619
FOS#235336.74846648167080.005032452776317940.0234573032002976
MAX#414934.839416631755340.01315737137836840.0466016451109103
MEF2A#4205314.0574231822330.0005830038854186610.00488631271882188
MEF2C#4208330.9835158694685.56692972943475e-050.00094108865978057
MXI1#460137.471178721569470.003741314738550960.0186279161889552
PAX5#507935.002174148383370.01196533174786410.0434796034381259
SMC3#9126311.28369963369960.001115802366868050.00765508003634847
TAF1#687243.343046285745290.008005664898701650.0321417612868759
TCF12#693837.975848676639820.003090920396013070.0162724385139232
USF1#739134.771124457905970.01370465887188020.0482829870435937
USF2#739239.74414803880220.001718341848410070.0107160628354989
ZBTB7A#5134135.513931980906920.009038352821081090.0342298484345972



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.