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Coexpression cluster:C3027: Difference between revisions

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|full_id=C3027_Mammary_keratoacanthoma_Gingival_Prostate_tongue_esophagus_oral
|full_id=C3027_Mammary_keratoacanthoma_Gingival_Prostate_tongue_esophagus_oral
|id=C3027
|id=C3027
|ontology_enrichment_celltype=CL:0002076!4.75e-20!43;CL:0002159!1.44e-13!13;CL:0000223!1.33e-12!59;CL:0002368!1.95e-12!13;CL:0002251!9.69e-12!21;CL:0000622!5.20e-09!5;CL:0000244!1.85e-07!4;CL:0000731!1.85e-07!4;CL:0000154!2.01e-07!6;CL:0002621!2.88e-07!3;CL:0002202!3.89e-07!9;CL:0002632!3.89e-07!9;CL:0000066!4.64e-07!254;CL:0002077!6.43e-07!33
|ontology_enrichment_celltype=CL:0002076!8.55e-17!42;CL:0002621!5.23e-13!3;CL:0002368!5.76e-13!13;CL:0002159!1.89e-12!14;CL:0002328!5.95e-12!3;CL:0000223!3.33e-11!58;CL:0002202!3.86e-10!9;CL:0002632!3.86e-10!9;CL:0002327!1.33e-09!4;CL:0000575!1.18e-08!2
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000166!1.96e-17!21;UBERON:0001004!1.82e-16!72;UBERON:0000165!1.92e-15!28;UBERON:0000930!1.92e-15!28;UBERON:0000161!6.87e-15!35;UBERON:0004119!7.20e-12!169;UBERON:0000925!7.20e-12!169;UBERON:0006595!7.20e-12!169;UBERON:0003102!2.58e-11!95;UBERON:0003408!6.92e-11!10;UBERON:0001044!1.53e-10!6;UBERON:0003293!1.53e-10!6;UBERON:0003294!1.53e-10!6;UBERON:0010047!1.53e-10!6;UBERON:0000167!1.53e-10!6;UBERON:0000078!2.81e-10!18;UBERON:0001444!2.43e-09!48;UBERON:0000974!9.03e-09!10;UBERON:0000153!1.87e-08!129;UBERON:0007811!1.87e-08!129;UBERON:0006562!4.81e-08!11;UBERON:0000065!7.11e-08!53;UBERON:0001007!1.21e-07!155;UBERON:0001555!1.21e-07!155;UBERON:0007026!1.21e-07!155;UBERON:0007196!2.02e-07!14;UBERON:0001558!2.02e-07!14;UBERON:0001949!2.88e-07!3;UBERON:0001042!6.86e-07!10;UBERON:0009145!6.86e-07!10;UBERON:0001723!7.04e-07!3;UBERON:0001033!7.04e-07!3;UBERON:0010056!7.04e-07!3
|ontology_enrichment_uberon=UBERON:0001004!2.26e-21!74;UBERON:0000153!6.65e-20!62;UBERON:0007811!6.65e-20!62;UBERON:0000166!2.54e-19!22;UBERON:0000165!1.19e-16!29;UBERON:0000930!1.19e-16!29;UBERON:0000033!1.09e-15!56;UBERON:0000161!1.57e-15!36;UBERON:0003102!6.69e-15!99;UBERON:0001042!1.36e-13!10;UBERON:0009145!1.36e-13!10;UBERON:0001949!5.23e-13!3;UBERON:0001723!1.69e-12!3;UBERON:0001033!1.69e-12!3;UBERON:0010056!1.69e-12!3;UBERON:0006562!2.71e-12!11;UBERON:0001444!3.17e-12!49;UBERON:0000065!3.77e-12!54;UBERON:0004815!5.95e-12!3;UBERON:0002031!5.95e-12!3;UBERON:0007196!3.52e-11!15;UBERON:0001558!3.52e-11!15;UBERON:0000072!1.01e-10!47;UBERON:0004119!1.44e-10!160;UBERON:0000925!1.44e-10!160;UBERON:0006595!1.44e-10!160;UBERON:0003729!3.25e-10!13;UBERON:0008814!1.10e-09!18;UBERON:0000974!1.32e-09!10;UBERON:0001911!1.33e-09!4;UBERON:0005333!1.33e-09!4;UBERON:0008425!1.33e-09!4;UBERON:0005311!1.33e-09!4;UBERON:0003408!2.41e-09!10;UBERON:0001007!3.37e-09!145;UBERON:0001555!3.37e-09!145;UBERON:0007026!3.37e-09!145;UBERON:0001829!1.13e-08!2;UBERON:0000344!1.40e-08!20;UBERON:0001041!1.52e-08!87;UBERON:0003126!1.59e-08!7;UBERON:0001005!1.59e-08!7;UBERON:0003127!2.60e-08!2;UBERON:0004807!1.13e-07!28;UBERON:0002185!2.44e-07!5;UBERON:0000475!3.65e-07!264;UBERON:0004921!5.23e-07!118;UBERON:0001557!8.00e-07!19
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.0233668,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.0064353,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.000716344,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.0176328,0.178449,0.0356339,0.158844,0.00782633,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.00411171,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.0249262,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.00982118,0.0815104,0.111647,0.372804,0.117027,0.159052,0.00122826,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.00886625,0.584917,0.0381789,0.782949,0.0821962,0.051522,0.252249,0.807281,0.0638737,0.261644,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.39729,0.217139,0.0643874,0.187251,0.362792,0.181715,0.0186051,0.109988,0.330894,0.218329,0.107929,0.376924,0.129235,0.0883629,0.528324,0.168255,0.370782,0.415647,0.484505,0.253571,0.0424424,0.301787,0.141124,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.21363,0.0474194,0.448095,0.576651,0.00229795,0.292835,0.476744,0.439556,0.373868,0.056723,0.0694028,0.18237,0.126021,0.513427,0.747852,0.275351,0.236471,0.185661,0.346319,0.0427964,0.00415948,0.625945,0.0340542,0.513852,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.305671,0.546839,0.00915612,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.0263998,0.000288232,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.0488795,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.00985947,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.522888,0.284629,0.0379506,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.40841,0.206222,0.525396,0.0224921,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.136757,0.404569,0.0204872,0.630264,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.0223093,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,7.53678e-05,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.026047,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,0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}}
}}

Revision as of 14:43, 19 October 2012


Full id: C3027_Mammary_keratoacanthoma_Gingival_Prostate_tongue_esophagus_oral



Phase1 CAGE Peaks

Hg19::chr10:5566916..5566932,+p1@CALML3
Hg19::chr10:5567551..5567579,+p@chr10:5567551..5567579
+
Hg19::chr10:5567644..5567657,+p@chr10:5567644..5567657
+


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
respiratory system2.26e-2174
anterior region of body6.65e-2062
craniocervical region6.65e-2062
oral opening2.54e-1922
mouth1.19e-1629
stomodeum1.19e-1629
head1.09e-1556
orifice1.57e-1536
surface structure6.69e-1599
chordate pharynx1.36e-1310
pharyngeal region of foregut1.36e-1310
gingival epithelium5.23e-133
tongue1.69e-123
gustatory system1.69e-123
future tongue1.69e-123
pharynx2.71e-1211
subdivision of head3.17e-1249
respiratory tract3.77e-1254
lower respiratory tract epithelium5.95e-123
epithelium of bronchus5.95e-123
tracheobronchial tree3.52e-1115
lower respiratory tract3.52e-1115
segment of respiratory tract1.01e-1047
endoderm-derived structure1.44e-10160
endoderm1.44e-10160
presumptive endoderm1.44e-10160
mouth mucosa3.25e-1013
pharyngeal arch system1.10e-0918
neck1.32e-0910
mammary gland1.33e-094
mammary bud1.33e-094
mammary ridge1.33e-094
mammary placode1.33e-094
gland of gut2.41e-0910
digestive system3.37e-09145
digestive tract3.37e-09145
primitive gut3.37e-09145
major salivary gland1.13e-082
mucosa1.40e-0820
foregut1.52e-0887
trachea1.59e-087
respiratory airway1.59e-087
open tracheal system trachea2.60e-082
respiratory system epithelium1.13e-0728
bronchus2.44e-075
organism subdivision3.65e-07264
subdivision of digestive tract5.23e-07118
upper respiratory tract8.00e-0719


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

No analysis results for this cluster

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.

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