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Coexpression cluster:C4589: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!3.98e-09!39;DOID:2531!5.00e-09!51;DOID:0060083!5.00e-09!51;DOID:8692!6.64e-08!31
|ontology_enrichment_disease=DOID:1240!3.98e-09!39;DOID:2531!5.00e-09!51;DOID:0060083!5.00e-09!51;DOID:8692!6.64e-08!31
|ontology_enrichment_uberon=UBERON:0002193!3.76e-26!112;UBERON:0002390!6.63e-24!102;UBERON:0003061!6.63e-24!102;UBERON:0003081!1.48e-23!216;UBERON:0002384!1.99e-16!375;UBERON:0002371!2.46e-15!80;UBERON:0002405!2.98e-15!115;UBERON:0001474!2.56e-13!86;UBERON:0004535!3.26e-11!110;UBERON:0000055!1.35e-10!69;UBERON:0001009!1.59e-10!113;UBERON:0004765!5.74e-10!101;UBERON:0001434!5.74e-10!101;UBERON:0001981!9.98e-10!60;UBERON:0007500!9.98e-10!60;UBERON:0004537!9.98e-10!60;UBERON:0006965!9.98e-10!60;UBERON:0002049!1.35e-08!79;UBERON:0007798!1.35e-08!79;UBERON:0001986!1.80e-08!18;UBERON:0004638!1.80e-08!18;UBERON:0004852!1.80e-08!18;UBERON:0002204!4.05e-08!167;UBERON:0004872!2.93e-07!84;UBERON:0000178!3.77e-07!15;UBERON:0000179!3.77e-07!15;UBERON:0000463!3.77e-07!15;UBERON:0001637!6.87e-07!42;UBERON:0003509!6.87e-07!42;UBERON:0004572!6.87e-07!42
|ontology_enrichment_uberon=UBERON:0002193!3.76e-26!112;UBERON:0002390!6.63e-24!102;UBERON:0003061!6.63e-24!102;UBERON:0003081!1.48e-23!216;UBERON:0002384!1.99e-16!375;UBERON:0002371!2.46e-15!80;UBERON:0002405!2.98e-15!115;UBERON:0001474!2.56e-13!86;UBERON:0004535!3.26e-11!110;UBERON:0000055!1.35e-10!69;UBERON:0001009!1.59e-10!113;UBERON:0004765!5.74e-10!101;UBERON:0001434!5.74e-10!101;UBERON:0001981!9.98e-10!60;UBERON:0007500!9.98e-10!60;UBERON:0004537!9.98e-10!60;UBERON:0006965!9.98e-10!60;UBERON:0002049!1.35e-08!79;UBERON:0007798!1.35e-08!79;UBERON:0001986!1.80e-08!18;UBERON:0004638!1.80e-08!18;UBERON:0004852!1.80e-08!18;UBERON:0002204!4.05e-08!167;UBERON:0004872!2.93e-07!84;UBERON:0000178!3.77e-07!15;UBERON:0000179!3.77e-07!15;UBERON:0000463!3.77e-07!15;UBERON:0001637!6.87e-07!42;UBERON:0003509!6.87e-07!42;UBERON:0004572!6.87e-07!42
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322219417370731!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464644445489243!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270701995563322!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140818371981577
|tfbs_overrepresentation=0.147255,0.0586687,1.02437e-07,0.0477154,0.199763,0.287811,0.0430074,6.15996e-09,0.03272,0.0257057,0.000504333,0.225367,0.0190579,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.0108656,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.0175714,0.111283,0.121201,0.154071,0.0541794,0.0701653,3.49836e-06,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,6.43194e-06,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.00234531,0.0425,0.114846,3.03235e-05,0.0347684,0.064341,0.00180443,5.63916e-05,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.000351844,0.141874,0.0370665,0.219088,0.0409286,0.0669887,4.81991e-06,0.144217,1.01392e-06,0.0177901,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.00424238,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.000366242,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.0128549,2.83261e-10,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.00660878,0.179689,0.137725,0.00384591,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.00360981,0.27358,0.15185,0.00173038,0.178359,0.0458667,0.104357,0.121154,0.1129,0.00664287,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,9.54774e-06,0.000717242,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.000150753,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,8.66121e-07,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.0133783,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0024791,3.59546e-05,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.003405,0.119261,0.0865903,0.0380459,0.130174,3.7536e-05,8.22817e-07,0.00102762,1.22251e-07,0.00163772,6.36653e-11,0.0263372,0.335423,0.00355277,0.0376513,2.19052e-07,0.0806291,0.053682,0.0313047,0.00800846,0.0914012,0.061507,0.0078057,5.07235e-10,0.271958,3.08112e-05,0.000206884,0.00183273,0.581713,0.00244849,0.187251,0.000106625,0.181715,0.423979,0.109988,0.00802393,0.0257868,0.00257817,0.0124294,0.129235,0.000107655,0.0407001,2.65956e-11,6.06726e-07,0.101703,0.142924,0.253571,0.276829,0.301787,4.83115e-07,0.00695027,0.000139476,7.66237e-07,0.000394966,1.44183e-06,0.00679651,6.42143e-13,0.0474194,0.448095,3.25755e-05,0.102333,0.292835,5.90455e-05,2.61417e-06,0.373868,3.33907e-07,6.73349e-07,0.18237,7.24085e-10,1.33224e-05,2.89198e-09,0.0419647,0.236471,0.185661,0.00934251,0.000147221,0.0405716,0.258117,2.58387e-10,0.00637776,0.169228,0.00314692,0.00471332,0.00419907,0.163244,0.0670502,0.0730934,0.184794,0.0641718,4.18938e-12,0.0121151,0.1002,2.66372e-06,0.000174153,2.10734e-05,0.448039,0.218623,0.000612438,0.00142673,0.0451077,0.0747529,0.0284893,0.28275,0.00223439,0.154921,0.0054714,7.73492e-05,0.477304,0.289204,0.327108,0.000194033,0.278044,2.93451e-10,0.00262586,0.228096,0.0642385,0.19763,0.000720848,2.65121e-07,0.000260039,0.000601045,0.0181002,0.00654277,4.47404e-13,2.62112e-07,0.144809,0.145539,0.00159233,0.0818086,0.119597,0.459928,1.35811e-05,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.00133722,0.293698,0.284593,0.343734,0.306556,0.0524121,0.00257275,0.000782215,0.00696513,0.0450125,1.69523e-05,0.010587,0.00232369,0.000207442,0.00230458,0.363685,0.464871,0.0142811,0.206222,1.22049e-06,1.70901e-08,0.113671,4.50581e-08,0.00872205,0.0479524,0.281425,0.141758,0.455379,1.10215e-06,0.159617,0.00275523,0.000124053,0.232251,0.0192138,0.0891382,0.0595618,0.171389,7.42877e-05,0.347298,7.49248e-10,0.00966846,0.00431743,0.0958562,1.27454e-08,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,3.38013e-05,0.0214618,0.191777,0.111931,0.0051519,0.0435386,0.303336,0.126478,0.134852,0.10689,0.00427764,0.0627924,0.381386,0.0179103,0.00605613,0.279795,0.00168854,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,8.14289e-05,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383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}}
}}

Revision as of 14:33, 5 September 2012


Full id: C4589_Neutrophils_Eosinophils_acute_CD8_Whole_thymus_CD4



Phase1 CAGE Peaks

Hg19::chr6:30652445..30652456,-p14@PPP1R18
Hg19::chr6:30652466..30652492,-p8@PPP1R18
Hg19::chr6:30652497..30652508,-p13@PPP1R18


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell8.80e-52172
angioblastic mesenchymal cell8.80e-52172
hematopoietic cell1.15e-50182
hematopoietic oligopotent progenitor cell1.54e-48165
hematopoietic multipotent progenitor cell1.54e-48165
leukocyte1.18e-42140
nongranular leukocyte6.66e-36119
hematopoietic lineage restricted progenitor cell5.58e-34124
myeloid cell3.69e-29112
common myeloid progenitor3.69e-29112
myeloid leukocyte3.51e-2376
multi fate stem cell1.93e-19430
mesenchymal cell8.08e-19358
somatic stem cell1.00e-18436
stem cell3.39e-18444
granulocyte monocyte progenitor cell5.19e-1871
connective tissue cell9.95e-18365
myeloid lineage restricted progenitor cell2.31e-1770
lymphoid lineage restricted progenitor cell3.11e-1752
lymphocyte3.83e-1753
common lymphoid progenitor3.83e-1753
monopoietic cell6.21e-1763
monocyte6.21e-1763
monoblast6.21e-1763
promonocyte6.21e-1763
macrophage dendritic cell progenitor4.69e-1665
CD14-positive, CD16-negative classical monocyte2.63e-1542
classical monocyte1.36e-1245
motile cell2.57e-12390
endothelial cell5.30e-1135
T cell1.09e-1025
pro-T cell1.09e-1025
endothelial cell of vascular tree4.97e-1024
mature alpha-beta T cell8.78e-1018
alpha-beta T cell8.78e-1018
immature T cell8.78e-1018
mature T cell8.78e-1018
immature alpha-beta T cell8.78e-1018
blood vessel endothelial cell1.80e-0818
embryonic blood vessel endothelial progenitor cell1.80e-0818
somatic cell3.28e-08591
CD8-positive, alpha-beta T cell5.16e-0811
meso-epithelial cell2.10e-0744
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.76e-26112
hematopoietic system6.63e-24102
blood island6.63e-24102
lateral plate mesoderm1.48e-23216
connective tissue1.99e-16375
bone marrow2.46e-1580
immune system2.98e-15115
bone element2.56e-1386
cardiovascular system3.26e-11110
vessel1.35e-1069
circulatory system1.59e-10113
skeletal element5.74e-10101
skeletal system5.74e-10101
blood vessel9.98e-1060
epithelial tube open at both ends9.98e-1060
blood vasculature9.98e-1060
vascular cord9.98e-1060
vasculature1.35e-0879
vascular system1.35e-0879
endothelium1.80e-0818
blood vessel endothelium1.80e-0818
cardiovascular system endothelium1.80e-0818
musculoskeletal system4.05e-08167
splanchnic layer of lateral plate mesoderm2.93e-0784
blood3.77e-0715
haemolymphatic fluid3.77e-0715
organism substance3.77e-0715
artery6.87e-0742
arterial blood vessel6.87e-0742
arterial system6.87e-0742
Disease
Ontology termp-valuen
leukemia3.98e-0939
hematologic cancer5.00e-0951
immune system cancer5.00e-0951
myeloid leukemia6.64e-0831


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
EGR1#195834.988179094810140.008056488137383440.0322219417370731
ELF1#199734.258097958807540.01295179875054610.0464644445489243
NFKB1#479035.488063424193840.006049381815655430.0270701995563322
ZBTB7A#5134137.35190930787590.002516255860282270.0140818371981577



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.