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Coexpression cluster:C3891: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.91e-17!57;UBERON:0005068!1.91e-17!57;UBERON:0006241!1.91e-17!57;UBERON:0007135!1.91e-17!57;UBERON:0000468!2.59e-15!659;UBERON:0002616!1.05e-14!59;UBERON:0000467!1.15e-14!625;UBERON:0000480!1.24e-14!626;UBERON:0001017!1.47e-14!82;UBERON:0005743!9.96e-14!86;UBERON:0003080!9.83e-13!42;UBERON:0002780!2.54e-12!41;UBERON:0001890!2.54e-12!41;UBERON:0006240!2.54e-12!41;UBERON:0002020!2.55e-12!34;UBERON:0003528!2.55e-12!34;UBERON:0000955!5.14e-12!69;UBERON:0006238!5.14e-12!69;UBERON:0002791!1.05e-11!33;UBERON:0001893!1.08e-11!34;UBERON:0003075!1.18e-11!86;UBERON:0007284!1.18e-11!86;UBERON:0000073!1.38e-11!94;UBERON:0001016!1.38e-11!94;UBERON:0001869!5.77e-11!32;UBERON:0002346!1.73e-10!90;UBERON:0000923!2.52e-10!604;UBERON:0005291!2.52e-10!604;UBERON:0006598!2.52e-10!604;UBERON:0002532!2.52e-10!604;UBERON:0002050!2.69e-10!605;UBERON:0005423!2.69e-10!605;UBERON:0000062!3.78e-10!511;UBERON:0000922!4.37e-10!612;UBERON:0004121!1.29e-09!169;UBERON:0004111!3.92e-09!241;UBERON:0000025!5.94e-09!194;UBERON:0000924!6.08e-09!173;UBERON:0006601!6.08e-09!173;UBERON:0000475!6.95e-09!365;UBERON:0000033!1.16e-08!123;UBERON:0000956!1.19e-08!25;UBERON:0000203!1.19e-08!25;UBERON:0003056!2.16e-08!61;UBERON:0007023!6.18e-08!115;UBERON:0000153!8.36e-08!129;UBERON:0007811!8.36e-08!129;UBERON:0002619!1.38e-07!22;UBERON:0000477!4.36e-07!286;UBERON:0000483!6.66e-07!309;UBERON:0001950!9.58e-07!20
|ontology_enrichment_uberon=UBERON:0001049!1.91e-17!57;UBERON:0005068!1.91e-17!57;UBERON:0006241!1.91e-17!57;UBERON:0007135!1.91e-17!57;UBERON:0000468!2.59e-15!659;UBERON:0002616!1.05e-14!59;UBERON:0000467!1.15e-14!625;UBERON:0000480!1.24e-14!626;UBERON:0001017!1.47e-14!82;UBERON:0005743!9.96e-14!86;UBERON:0003080!9.83e-13!42;UBERON:0002780!2.54e-12!41;UBERON:0001890!2.54e-12!41;UBERON:0006240!2.54e-12!41;UBERON:0002020!2.55e-12!34;UBERON:0003528!2.55e-12!34;UBERON:0000955!5.14e-12!69;UBERON:0006238!5.14e-12!69;UBERON:0002791!1.05e-11!33;UBERON:0001893!1.08e-11!34;UBERON:0003075!1.18e-11!86;UBERON:0007284!1.18e-11!86;UBERON:0000073!1.38e-11!94;UBERON:0001016!1.38e-11!94;UBERON:0001869!5.77e-11!32;UBERON:0002346!1.73e-10!90;UBERON:0000923!2.52e-10!604;UBERON:0005291!2.52e-10!604;UBERON:0006598!2.52e-10!604;UBERON:0002532!2.52e-10!604;UBERON:0002050!2.69e-10!605;UBERON:0005423!2.69e-10!605;UBERON:0000062!3.78e-10!511;UBERON:0000922!4.37e-10!612;UBERON:0004121!1.29e-09!169;UBERON:0004111!3.92e-09!241;UBERON:0000025!5.94e-09!194;UBERON:0000924!6.08e-09!173;UBERON:0006601!6.08e-09!173;UBERON:0000475!6.95e-09!365;UBERON:0000033!1.16e-08!123;UBERON:0000956!1.19e-08!25;UBERON:0000203!1.19e-08!25;UBERON:0003056!2.16e-08!61;UBERON:0007023!6.18e-08!115;UBERON:0000153!8.36e-08!129;UBERON:0007811!8.36e-08!129;UBERON:0002619!1.38e-07!22;UBERON:0000477!4.36e-07!286;UBERON:0000483!6.66e-07!309;UBERON:0001950!9.58e-07!20
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.000522123,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.00345589,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.0233668,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.000702541,0.00725252,0.0956287,0.00234531,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0124566,0.000682869,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.00166778,0.155998,0.013844,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0014925,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.00127354,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.00624688,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.000610418,0.169057,0.164202,0.00527533,0.00202722,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.0101199,0.085973,0.00186526,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.000283855,0.163502,0.0249262,0.00117271,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.000253111,0.0802194,0.117027,0.0133783,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.00596775,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.003405,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.131316,0.0691572,0.0821962,0.00163772,0.00879988,0.807281,0.0083957,0.629514,0.261553,0.446302,0.0806291,0.053682,0.147559,0.0619618,0.0914012,0.329568,0.178727,0.0164332,0.00420832,0.292154,0.0964816,0.00183273,0.0582602,0.230901,0.00127255,0.0109219,0.0176124,0.423979,0.109988,0.330894,0.00207312,0.0190732,0.0124294,0.463191,0.00436109,0.528324,0.03861,0.0117562,0.101703,0.0297533,0.253571,0.276829,0.000521481,0.141124,0.316882,0.223503,0.503224,0.0669244,0.00483199,0.314747,0.0567394,0.291709,0.120054,0.0115542,0.102333,0.292835,0.137839,0.00296083,0.0807167,0.056723,0.00280546,5.83227e-05,0.0359955,0.248484,0.747852,0.0419647,0.236471,0.185661,0.346319,0.179399,0.270984,0.258117,0.155555,0.163222,0.0389686,0.000221606,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.000729888,0.217247,0.412837,0.0267008,0.188159,0.00142658,0.448039,0.218623,0.312808,0.00142673,0.0451077,0.0747529,0.229003,0.0222308,0.589326,0.154921,0.294698,0.0671437,0.138202,0.289204,0.327108,0.0295492,0.0428373,0.0263998,0.0193295,0.0282539,6.86797e-05,0.0209597,0.0129079,0.0106166,0.421464,0.141711,0.0181002,0.0374607,0.0150702,0.00836919,0.144809,0.0111455,0.385517,0.376191,0.447325,0.0247309,0.0348837,0.152681,0.0465712,0.137098,0.0369524,1.631e-05,0.0985856,0.00870714,0.293698,0.284593,0.0673219,0.00622965,0.305777,0.601433,0.503082,0.169823,0.284629,0.0379506,0.010587,0.226257,0.016014,0.102469,0.363685,0.130283,0.40841,0.0228979,0.00713629,0.000779217,0.000324942,0.00407232,0.339277,0.00922147,0.281425,0.141758,0.455379,0.520495,0.159617,0.0310416,0.0119179,0.232251,0.0192138,0.0891382,0.0595618,0.00103044,0.0769581,0.0688327,0.00123043,0.00966846,0.475069,0.404569,0.273024,0.262389,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.0223093,0.0216577,0.441735,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.00835866,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.00605613,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.00797323,0.129156,0.210369,0.0200986,0.000971782,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.0268081,0.107043,0.275244,0.00481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3159,0.0457735,0.236464,0.0597546,0.00698179,0.218052,0.0271615,0.11528,0.194982,0.190993,0.000383954,0.283218,0.249955,0.164638,0.224257,0.0935776,0.00776295,0.225752,0.207791,0.0958756,0.0859274,0.00694911,0.0156618,0.0133429,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.0130722,0.215705,0.035048,0.0017212,0.361435
}}
}}

Revision as of 19:32, 8 August 2012


Full id: C3891_occipital_Osteoblast_Preadipocyte_spinal_leiomyoma_duodenum_Monocytederived



Phase1 CAGE Peaks

Hg19::chr1:160182958..160182971,+p@chr1:160182958..160182971
+
Hg19::chr1:160182997..160183029,+p@chr1:160182997..160183029
+
Hg19::chr1:160183342..160183398,+p6@PEA15


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
non-terminally differentiated cell2.53e-08180
CD14-positive, CD16-negative classical monocyte2.49e-0742
Uber Anatomy
Ontology termp-valuen
neural tube1.91e-1757
neural rod1.91e-1757
future spinal cord1.91e-1757
neural keel1.91e-1757
multi-cellular organism2.59e-15659
regional part of brain1.05e-1459
anatomical system1.15e-14625
anatomical group1.24e-14626
central nervous system1.47e-1482
anterior neural tube9.83e-1342
regional part of forebrain2.54e-1241
forebrain2.54e-1241
future forebrain2.54e-1241
gray matter2.55e-1234
brain grey matter2.55e-1234
brain5.14e-1269
future brain5.14e-1269
regional part of telencephalon1.05e-1133
telencephalon1.08e-1134
neural plate1.18e-1186
presumptive neural plate1.18e-1186
regional part of nervous system1.38e-1194
nervous system1.38e-1194
cerebral hemisphere5.77e-1132
neurectoderm1.73e-1090
germ layer2.52e-10604
embryonic tissue2.52e-10604
presumptive structure2.52e-10604
epiblast (generic)2.52e-10604
embryonic structure2.69e-10605
developing anatomical structure2.69e-10605
organ3.78e-10511
embryo4.37e-10612
ectoderm-derived structure1.29e-09169
anatomical conduit3.92e-09241
tube5.94e-09194
ectoderm6.08e-09173
presumptive ectoderm6.08e-09173
organism subdivision6.95e-09365
head1.16e-08123
cerebral cortex1.19e-0825
pallium1.19e-0825
pre-chordal neural plate2.16e-0861
adult organism6.18e-08115
anterior region of body8.36e-08129
craniocervical region8.36e-08129
regional part of cerebral cortex1.38e-0722
anatomical cluster4.36e-07286
epithelium6.66e-07309
neocortex9.58e-0720


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.