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Difference between revisions of "Coexpression cluster:C4613"

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191047842044513!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032747437321388!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324128437054725!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322318163026313!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464724262104746!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0402119341006885!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154768457133618!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128682328375769!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270771605642325!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770983393128985!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278141387457098!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054544567994726!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390343178658938!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618597258435644!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422930581693203!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140856110731639!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.01100576080964
 
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191047842044513!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032747437321388!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324128437054725!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322318163026313!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464724262104746!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0402119341006885!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154768457133618!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128682328375769!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270771605642325!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770983393128985!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278141387457098!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054544567994726!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390343178658938!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618597258435644!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422930581693203!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140856110731639!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.01100576080964
 
|tfbs_overrepresentation=0.147255,0.0586687,0.00192761,0.0477154,0.199763,0.287811,0.0430074,0.0022397,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.0472875,0.00327964,0.064341,0.209032,0.0154619,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,5.12341e-06,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.000642566,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.0151713,0.164202,0.100942,0.062995,0.10299,0.14193,0.0800546,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.0249262,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.00102968,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.131316,0.0691572,0.0821962,0.20128,0.0986134,2.6703e-09,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.0164332,0.271958,0.292154,0.405773,0.0921263,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.101703,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.0567394,0.291709,0.448095,0.576651,0.416816,0.0478086,0.476744,0.439556,0.373868,0.57762,0.241757,0.18237,0.126021,0.00847576,1.43819e-05,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.503058,0.513852,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.671377,0.546839,0.551561,0.120021,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.294698,0.34331,0.138202,0.289204,0.327108,0.00650617,0.278044,0.0015747,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,2.91338e-09,0.335105,0.144809,0.145539,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.522888,0.0450125,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.753577,0.206222,0.03988,0.0905337,0.020698,0.269226,0.339277,0.552319,0.281425,0.141758,0.124432,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.0397695,0.0769581,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.000578907,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.00151445,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.0268081,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906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 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,2.63304,0.388328,0.795576,1.21459,1.3235,0.439574,6.19641,1.36391,1.45286,0.855276,0.567465,2.05816,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,2.33699,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,2.87582,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,10.6662,0.303648,0.381882,1.053,2.0169,1.63834,3.03421,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,4.59952,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,5.4618
 
}}
 
}}

Revision as of 07:51, 26 November 2012


Full id: C4613_pleomorphic_Fibroblast_mesodermal_Nucleus_Smooth_thyroid_hepatic



Phase1 CAGE Peaks

  Short description
Hg19::chr6:52441770..52441784,- p2@TRAM2
Hg19::chr6:52441791..52441804,- p3@TRAM2
Hg19::chr6:52441810..52441865,- p1@TRAM2


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


Uber Anatomy
Ontology termp-valuen
epithelial vesicle9.18e-1978
somite1.35e-1871
presomitic mesoderm1.35e-1871
presumptive segmental plate1.35e-1871
dermomyotome1.35e-1871
trunk paraxial mesoderm1.35e-1871
unilaminar epithelium2.43e-18148
dense mesenchyme tissue4.22e-1873
paraxial mesoderm8.78e-1872
presumptive paraxial mesoderm8.78e-1872
trunk mesenchyme3.76e-17122
multilaminar epithelium8.99e-1783
mesenchyme2.92e-16160
entire embryonic mesenchyme2.92e-16160
vasculature4.33e-1678
vascular system4.33e-1678
splanchnic layer of lateral plate mesoderm2.70e-1483
skeletal muscle tissue3.05e-1462
striated muscle tissue3.05e-1462
myotome3.05e-1462
muscle tissue3.98e-1464
musculature3.98e-1464
musculature of body3.98e-1464
vessel1.07e-1268
epithelial tube2.54e-12117
organism subdivision2.86e-12264
trunk2.79e-11199
epithelial tube open at both ends3.18e-1159
blood vessel3.18e-1159
blood vasculature3.18e-1159
vascular cord3.18e-1159
cardiovascular system5.62e-11109
circulatory system1.43e-10112
integument1.83e-1046
integumental system1.83e-1046
artery4.95e-1042
arterial blood vessel4.95e-1042
arterial system4.95e-1042
skin of body3.50e-0941
organ component layer5.28e-0966
surface structure6.04e-0999
systemic artery1.92e-0833
systemic arterial system1.92e-0833
mesoderm1.30e-07315
mesoderm-derived structure1.30e-07315
presumptive mesoderm1.30e-07315
cell layer3.07e-07309
multi-tissue structure4.30e-07342


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#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0191047842044513
E2F1#186934.907389214879320.008460985347239390.032747437321388
E2F6#187635.017155731697390.00791769806886330.0324128437054725
EGR1#195834.988179094810140.008056488137383440.0322318163026313
ELF1#199734.258097958807540.01295179875054610.0464724262104746
ELK4#2005210.8237877723120.01091284719516480.0402119341006885
GABPB1#255337.067683836182170.002832212825417420.0154768457133618
IRF1#365937.63716375356390.002244692747297240.0128682328375769
NFKB1#479035.488063424193840.006049381815655430.0270771605642325
REST#597839.650028716128020.001112636247114590.00770983393128985
SIN3A#2594235.408884726815140.006318961977991520.0278141387457098
TAF7#6879311.43306940492390.0006690181981945830.0054544567994726
TFAP2A#7020211.01242291536330.01054990655215560.0390343178658938
TFAP2C#7022310.80922860986020.0007916746575753130.00618597258435644
USF2#7392312.99219738506960.0004558979393427810.00422930581693203
ZBTB7A#5134137.35190930787590.002516255860282270.0140856110731639
ZNF263#1012738.221841637010680.001799043925565870.01100576080964



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.