Coexpression cluster:C2068: Difference between revisions

Revision as of 15:16, 26 November 2012

Full id: C2068_Fibroblast_Chondrocyte_leiomyoma_spindle_mesenchymal_basal_mesothelioma

Phase1 CAGE Peaks

Hg19::chr10:69834427..69834437,-	p12@HERC4
Hg19::chr10:69834449..69834514,-	p4@HERC4
Hg19::chr10:69834517..69834543,-	p5@HERC4
Hg19::chr10:69834924..69834935,-	p6@HERC4

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data

Cell Type
Ontology term	p-value	n
fibroblast	1.06e-11	76
skin fibroblast	8.35e-10	23
animal cell	4.72e-09	679
eukaryotic cell	4.72e-09	679
vascular associated smooth muscle cell	7.76e-07	32

Uber Anatomy
Ontology term	p-value	n
surface structure	6.25e-09	99
systemic artery	2.82e-07	33
systemic arterial system	2.82e-07	33

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

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

TF	#promoters	Enrichment	p-value	q-value
BCL3#602	4	34.5471028037383	7.01262157705428e-07	3.14465944562461e-05
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106220972792465
EBF1#1879	4	8.906466846569	0.0001588790747201	0.0019929343844214
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101236532054764
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160504213311418
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00389640794081463
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00484293097395095
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00885402843746543
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076634458761076
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00442967079229969
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794030300716048
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321096676660203
TFAP2A#7020	3	12.3889757797837	0.00084694130358843	0.00637871946386904
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114302192747077
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342211619156354

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.14465944562461e-05!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106220972792465!EBF1#1879;4:8.906466846569:0.0001588790747201:0.0019929343844214!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101236532054764!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160504213311418!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389640794081463!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484293097395095!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00885402843746543!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.0076634458761076!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00442967079229969!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794030300716048!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321096676660203!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00637871946386904!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114302192747077!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342211619156354
 |tfbs_overrepresentation=0.191353,0.0774498,0.238232,0.0631091,0.257053,0.363996,0.0569281,0.0358499,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.788552,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.0299044,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.00426281,0.00550137,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.133576,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.355976,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.114558,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.0346699,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,3.11926e-05,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.0616625,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.104555,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.324438,9.68087e-05,0.00232734,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.545829,0.113754,0.0504034,0.169684,0.690367,0.233666,0.000270894,0.389734,0.668426,0.00268757,0.179737,0.420045,0.73391,0.332539,0.186966,0.464128,0.389374,0.594055,0.414547,0.489273,0.413223,0.271656,0.364388,0.34505,0.369161,0.500422,0.49089,0.323639,0.341822,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.279946,0.524104,0.467825,0.563725,0.404903,0.0806606,0.257158,0.460819,0.511459,0.0601683,0.322903,0.350886,0.380582,0.583749,0.398372,0.286293,0.606558,0.127626,0.359128,0.091406,0.683133,0.368633,0.547291,0.109035,0.512763,0.369971,0.578349,0.537928,0.129952,0.683088,0.356005,0.235444,0.0835105,0.402752,0.279301,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.377117,0.0151189,0.250139,0.0774588,0.316925,0.356561,0.0552678,0.211506,0.0883859,0.0962508,0.238465,0.122819,0.571578,0.6873,0.508325,0.773224,0.0907578,0.656755,0.046332,0.280307,0.393583,0.212518,0.0596868,0.0984075,0.293026,0.0537754,0.0326188,0.605423,0.372182,0.0194133,0.214741,0.365653,0.41035,0.0697989,0.35234,0.644643,0.525923,0.291917,0.421082,0.25441,0.202782,0.307342,0.517933,0.584705,0.517001,0.0746589,0.266107,0.419676,0.188259,0.189182,0.138387,0.46699,0.546448,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.283924,0.370995,0.074448,0.429696,0.386216,0.385297,0.346931,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.16264,0.452694,0.565545,0.287542,0.265037,0.261923,0.754776,0.00784981,0.341771,0.106541,0.290547,0.356381,0.184395,0.55524,0.256884,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.261511,0.729876,0.433821,0.64428,0.436806,0.576549,0.499072,0.744662,0.149061,0.0922563,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.540322,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,0.0828344,0.135364,0.0238089,0.383126,0.00107967,0.142001,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.0137555,0.118999,0.0737069,0.357807,0.00325259,0.178782,0.019419,0.0866228,0.27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+|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.80003,2.78539,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,1.55218,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,1.93746,0.344471,1.23824,0.0842336,3.15145,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,1.31558,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,1.49254,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,2.34631,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,2.60183,3.55759,1.37313,0.465545,1.1057,1.14983,1.05974,2.24329,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.97727,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,1.58968,1.24902,0.997363,0.824835,1.65997,0.917558,1.28873,0.632914,4.88132,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,6.53028
 }}

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Coexpression cluster:C2068: Difference between revisions

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Revision as of 15:16, 26 November 2012

Phase1 CAGE Peaks

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