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Coexpression cluster:C3685: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!5.24e-22!83;UBERON:0002329!5.24e-22!83;UBERON:0003077!5.24e-22!83;UBERON:0003059!5.24e-22!83;UBERON:0007282!5.24e-22!83;UBERON:0009618!5.24e-22!83;UBERON:0007285!5.24e-22!83;UBERON:0004290!6.43e-22!70;UBERON:0001134!6.55e-18!61;UBERON:0002036!6.55e-18!61;UBERON:0003082!6.55e-18!61;UBERON:0002385!7.28e-18!63;UBERON:0001015!7.28e-18!63;UBERON:0000383!7.28e-18!63;UBERON:0000486!3.79e-17!82;UBERON:0002204!5.39e-14!167;UBERON:0002384!4.31e-13!375;UBERON:0005256!1.65e-12!143;UBERON:0002199!1.02e-09!45;UBERON:0002416!1.02e-09!45;UBERON:0004872!7.71e-09!84;UBERON:0002097!7.81e-09!40;UBERON:0000926!2.50e-08!448;UBERON:0004120!2.50e-08!448;UBERON:0006603!2.50e-08!448;UBERON:0003102!3.92e-08!95;UBERON:0000479!4.15e-08!787;UBERON:0001637!4.79e-07!42;UBERON:0003509!4.79e-07!42;UBERON:0004572!4.79e-07!42
|ontology_enrichment_uberon=UBERON:0000914!5.24e-22!83;UBERON:0002329!5.24e-22!83;UBERON:0003077!5.24e-22!83;UBERON:0003059!5.24e-22!83;UBERON:0007282!5.24e-22!83;UBERON:0009618!5.24e-22!83;UBERON:0007285!5.24e-22!83;UBERON:0004290!6.43e-22!70;UBERON:0001134!6.55e-18!61;UBERON:0002036!6.55e-18!61;UBERON:0003082!6.55e-18!61;UBERON:0002385!7.28e-18!63;UBERON:0001015!7.28e-18!63;UBERON:0000383!7.28e-18!63;UBERON:0000486!3.79e-17!82;UBERON:0002204!5.39e-14!167;UBERON:0002384!4.31e-13!375;UBERON:0005256!1.65e-12!143;UBERON:0002199!1.02e-09!45;UBERON:0002416!1.02e-09!45;UBERON:0004872!7.71e-09!84;UBERON:0002097!7.81e-09!40;UBERON:0000926!2.50e-08!448;UBERON:0004120!2.50e-08!448;UBERON:0006603!2.50e-08!448;UBERON:0003102!3.92e-08!95;UBERON:0000479!4.15e-08!787;UBERON:0001637!4.79e-07!42;UBERON:0003509!4.79e-07!42;UBERON:0004572!4.79e-07!42
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321832516779798!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.00062756399572275!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.0043349133084072!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719794030107325!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484229551738379!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613193640689185!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615328641530908
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.00195662,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.000682869,0.0927458,0.0415725,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.0166632,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.00166778,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.00418474,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.000841257,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.00279739,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.00497632,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.713218,0.0691572,0.0821962,0.20128,0.0986134,0.807281,0.335423,0.0185583,0.0376513,0.446302,0.373681,0.309233,0.0313047,0.330703,0.395854,0.329568,0.178727,0.0724671,0.0408801,0.292154,0.405773,0.39729,0.581713,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.129235,0.280025,0.528324,0.00682286,0.0792797,0.0173702,0.484505,0.253571,0.00445889,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.0567394,0.291709,0.448095,0.212757,0.102333,0.292835,0.476744,0.439556,0.373868,0.213592,0.0694028,0.18237,0.0359955,0.248484,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.0772647,0.503058,0.163222,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0027389,0.184794,0.596648,0.421596,0.217247,0.412837,0.305671,0.546839,0.551561,0.448039,0.218623,0.312808,0.000236487,0.0451077,0.0747529,0.229003,0.28275,0.223844,0.50215,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.085507,0.108847,0.228096,0.336314,0.0209597,0.15631,0.20495,0.0182254,0.141711,0.104399,0.516462,0.311758,0.335105,0.000567622,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.0450006,0.343734,0.0526965,0.305777,0.0144637,0.503082,0.0391885,0.284629,0.0379506,0.0741332,0.226257,0.405955,0.41707,0.363685,0.130283,0.0538047,0.206222,0.03988,0.651524,0.437176,0.269226,0.00872205,0.0479524,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.0688327,0.182325,0.34988,0.475069,0.404569,0.273024,0.0793778,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.00387172,0.15983,0.107111,0.000976405,0.00389058,0.123593,0.129156,0.210369,0.0200986,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.062811,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.00853267,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526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}}
}}

Revision as of 12:31, 5 September 2012


Full id: C3685_Fibroblast_Pericytes_Mesenchymal_Meningeal_Trabecular_Adipocyte_Saos2



Phase1 CAGE Peaks

Hg19::chr17:75315534..75315612,+p4@SEPT9
Hg19::chr17:75315994..75316022,+p7@SEPT9
Hg19::chr17:75316024..75316071,+p16@SEPT9


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>


Uber Anatomy
Ontology termp-valuen
somite5.24e-2283
paraxial mesoderm5.24e-2283
presomitic mesoderm5.24e-2283
presumptive segmental plate5.24e-2283
trunk paraxial mesoderm5.24e-2283
presumptive paraxial mesoderm5.24e-2283
dermomyotome6.43e-2270
skeletal muscle tissue6.55e-1861
striated muscle tissue6.55e-1861
myotome6.55e-1861
muscle tissue7.28e-1863
musculature7.28e-1863
musculature of body7.28e-1863
multilaminar epithelium3.79e-1782
musculoskeletal system5.39e-14167
connective tissue4.31e-13375
trunk mesenchyme1.65e-12143
integument1.02e-0945
integumental system1.02e-0945
splanchnic layer of lateral plate mesoderm7.71e-0984
skin of body7.81e-0940
mesoderm2.50e-08448
mesoderm-derived structure2.50e-08448
presumptive mesoderm2.50e-08448
surface structure3.92e-0895
tissue4.15e-08787
artery4.79e-0742
arterial blood vessel4.79e-0742
arterial system4.79e-0742


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
E2F6#187635.017155731697390.00791769806886330.0321832516779798
GTF2B#2959331.94382993432423.06634405746243e-050.00062756399572275
GTF2F1#2962312.73966087675770.0004835525047438590.0043349133084072
MXI1#460139.96157162875930.001011470541259020.00719794030107325
RFX5#5993312.04791082719510.0005717246050312580.00484229551738379
TCF7L2#6934310.77017656313730.0008003181298398380.00613193640689185
TFAP2C#7022310.80922860986020.0007916746575753130.00615328641530908



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.