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Coexpression cluster:C4377: Difference between revisions

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|full_id=C4377_migratory_Dendritic_smooth_aorta_heart_skeletal_immature
|full_id=C4377_migratory_Dendritic_smooth_aorta_heart_skeletal_immature
|id=C4377
|id=C4377
|ontology_enrichment_celltype=CL:0000057!1.20e-07!75
|ontology_enrichment_celltype=CL:0000057!5.27e-08!76
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000062!3.07e-08!511;UBERON:0000926!6.27e-07!448;UBERON:0004120!6.27e-07!448;UBERON:0006603!6.27e-07!448
|ontology_enrichment_uberon=UBERON:0000926!5.74e-09!315;UBERON:0004120!5.74e-09!315;UBERON:0006603!5.74e-09!315;UBERON:0000062!5.08e-07!503
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326844521630542!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900392283366662!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000372041670778366!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295558023703392!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174570402201423!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203623549900937!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024908520481006!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617811473978242!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109781097599868
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326844521630542!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900392283366662!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000372041670778366!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295558023703392!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174570402201423!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203623549900937!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024908520481006!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617811473978242!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109781097599868
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.000235346,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.000522123,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.0472875,0.251834,0.064341,0.0235519,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.00788672,0.228812,0.00660014,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.00135672,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.00377835,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0119747,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0121776,0.0619218,0.0163125,0.163376,0.0085789,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.003405,0.446759,0.0865903,0.0380459,0.130174,0.00212189,0.000318664,0.00102762,0.0821962,0.563047,1.42797e-05,5.636e-05,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.0724671,0.271958,0.292154,0.0964816,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.0883629,0.528324,0.03861,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,5.12277e-05,0.283727,0.314747,0.000273712,0.291709,0.448095,0.212757,0.102333,0.292835,0.00439271,0.439556,0.373868,0.056723,0.0154652,0.18237,0.126021,0.00847576,0.747852,0.275351,0.236471,0.185661,0.346319,0.0427964,0.270984,0.625945,0.503058,1.07519e-05,0.0389686,0.248634,0.000383048,0.472384,0.163244,0.0670502,0.0730934,0.184794,4.58399e-05,0.00365572,0.217247,0.412837,0.671377,0.546839,0.551561,0.448039,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.00449125,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.109738,0.278044,9.1744e-06,0.108847,0.228096,0.336314,0.19763,0.15631,0.0530502,0.421464,0.48267,0.420626,0.516462,6.80909e-06,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.0348837,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.0741332,0.226257,0.016014,0.41707,0.363685,0.130283,0.00320894,0.206222,0.171685,1.49063e-05,0.00288466,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.0385377,0.159617,0.238587,9.51685e-06,0.232251,0.189515,0.0891382,0.0595618,1.31517e-05,0.0769581,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.0223093,0.0216577,0.441735,0.191777,0.111931,0.0051519,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.0684384,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187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}}
}}

Revision as of 15:54, 19 October 2012


Full id: C4377_migratory_Dendritic_smooth_aorta_heart_skeletal_immature



Phase1 CAGE Peaks

Hg19::chr4:148653206..148653219,+p2@ARHGAP10
Hg19::chr4:148653221..148653295,+p1@ARHGAP10
Hg19::chr4:148653296..148653307,+p3@ARHGAP10


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
fibroblast5.27e-0876
Uber Anatomy
Ontology termp-valuen
mesoderm5.74e-09315
mesoderm-derived structure5.74e-09315
presumptive mesoderm5.74e-09315
organ5.08e-07503


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
E2F1#186934.907389214879320.008460985347239390.0326844521630542
FOS#235338.99795530889440.001372499272417130.00900392283366662
FOSL1#8061339.7135797163731.59554825631833e-050.000372041670778366
MYC#460935.22228187160940.007020843755740150.0295558023703392
NANOG#79923219.49651898734180.003427255648501020.0174570402201423
SMARCB1#6598318.25271578115740.000164397760679890.00203623549900937
TFAP2A#7020316.5186343730450.0002218033880766340.0024908520481006
TFAP2C#7022310.80922860986020.0007916746575753130.00617811473978242
ZNF263#1012738.221841637010680.001799043925565870.0109781097599868



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.