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Coexpression cluster:C4590: Difference between revisions

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|full_id=C4590_Neutrophils_Eosinophils_Whole_embryonic_osteosarcoma_Fibroblast_CD14
|full_id=C4590_Neutrophils_Eosinophils_Whole_embryonic_osteosarcoma_Fibroblast_CD14
|id=C4590
|id=C4590
|ontology_enrichment_celltype=CL:0002371!1.04e-22!591;CL:0000144!3.40e-18!625;CL:0002057!1.14e-15!42;CL:0000222!2.26e-15!119;CL:0000860!3.34e-13!45;CL:0000115!3.43e-12!35;CL:0000766!3.49e-12!76;CL:0000003!5.03e-12!722;CL:0000548!7.01e-12!679;CL:0000004!7.01e-12!679;CL:0000255!7.01e-12!679;CL:0000012!2.37e-11!682;CL:0000723!2.61e-11!436;CL:0000048!4.36e-11!430;CL:0002139!8.77e-11!24;CL:0002078!2.52e-10!44;CL:0000359!4.51e-10!32;CL:0000034!7.67e-10!444;CL:0002194!1.14e-09!63;CL:0000576!1.14e-09!63;CL:0000040!1.14e-09!63;CL:0000559!1.14e-09!63;CL:0000055!1.39e-09!180;CL:0002009!1.65e-09!65;CL:0000192!2.15e-09!42;CL:0000514!2.15e-09!42;CL:0000071!4.13e-09!18;CL:0002546!4.13e-09!18;CL:0000557!6.18e-09!71;CL:0000213!6.47e-09!57;CL:0000215!6.47e-09!57;CL:0000839!3.85e-08!70;CL:0000183!7.86e-08!59;CL:0000680!3.04e-07!57;CL:0000056!3.04e-07!57;CL:0000355!3.04e-07!57;CL:0000187!5.31e-07!54;CL:0000220!6.69e-07!246;CL:0000063!7.53e-07!578
|ontology_enrichment_celltype=CL:0002371!2.25e-24!588;CL:0000222!5.72e-16!121;CL:0000860!5.08e-15!42;CL:0002057!5.08e-15!42;CL:0000473!1.68e-13!48;CL:0000234!1.68e-13!48;CL:0000766!3.82e-13!72;CL:0000548!6.94e-13!679;CL:0000255!6.94e-13!679;CL:0000115!7.48e-13!36;CL:0000723!7.20e-12!433;CL:0000003!1.23e-11!722;CL:0000048!1.53e-11!427;CL:0002139!5.67e-11!24;CL:0002078!6.69e-11!45;CL:0000034!1.82e-10!441;CL:0002194!1.99e-10!59;CL:0000576!1.99e-10!59;CL:0000040!1.99e-10!59;CL:0000559!1.99e-10!59;CL:0000359!2.67e-10!32;CL:0002009!2.82e-10!61;CL:0000192!9.24e-10!43;CL:0000514!9.24e-10!43;CL:0000557!1.41e-09!67;CL:0000213!3.02e-09!58;CL:0000215!3.02e-09!58;CL:0000071!3.08e-09!18;CL:0002546!3.08e-09!18;CL:0000839!1.25e-08!66;CL:0000325!6.27e-08!87;CL:0000183!1.26e-07!59;CL:0000680!1.97e-07!58;CL:0000056!1.97e-07!58;CL:0000355!1.97e-07!58;CL:0002321!2.13e-07!250;CL:0000187!4.71e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!3.37e-29!216;UBERON:0004535!6.09e-23!110;UBERON:0000055!1.75e-22!69;UBERON:0001009!1.22e-21!113;UBERON:0002049!5.80e-21!79;UBERON:0007798!5.80e-21!79;UBERON:0001981!4.38e-20!60;UBERON:0007500!4.38e-20!60;UBERON:0004537!4.38e-20!60;UBERON:0006965!4.38e-20!60;UBERON:0004872!1.44e-17!84;UBERON:0001637!1.83e-16!42;UBERON:0003509!1.83e-16!42;UBERON:0004572!1.83e-16!42;UBERON:0002204!8.10e-14!167;UBERON:0002193!3.59e-13!112;UBERON:0004573!5.29e-13!33;UBERON:0004571!5.29e-13!33;UBERON:0000926!7.03e-12!448;UBERON:0004120!7.03e-12!448;UBERON:0006603!7.03e-12!448;UBERON:0002390!1.81e-10!102;UBERON:0003061!1.81e-10!102;UBERON:0003914!7.08e-10!118;UBERON:0001986!4.13e-09!18;UBERON:0004638!4.13e-09!18;UBERON:0004852!4.13e-09!18;UBERON:0000947!7.78e-09!21;UBERON:0010191!7.78e-09!21;UBERON:0002371!1.44e-08!80;UBERON:0004765!2.87e-08!101;UBERON:0001434!2.87e-08!101;UBERON:0000486!3.95e-08!82;UBERON:0001474!4.25e-08!86;UBERON:0000487!1.60e-07!22;UBERON:0006914!3.99e-07!25;UBERON:0000914!5.19e-07!83;UBERON:0002329!5.19e-07!83;UBERON:0003077!5.19e-07!83;UBERON:0003059!5.19e-07!83;UBERON:0007282!5.19e-07!83;UBERON:0009618!5.19e-07!83;UBERON:0007285!5.19e-07!83;UBERON:0004290!7.82e-07!70;UBERON:0002405!8.28e-07!115
|ontology_enrichment_uberon=UBERON:0003081!2.55e-28!203;UBERON:0000055!1.36e-22!68;UBERON:0000926!4.50e-22!315;UBERON:0004120!4.50e-22!315;UBERON:0006603!4.50e-22!315;UBERON:0004535!9.33e-22!109;UBERON:0002049!3.07e-21!78;UBERON:0007798!3.07e-21!78;UBERON:0001009!2.08e-20!112;UBERON:0007500!4.29e-20!59;UBERON:0001981!4.29e-20!59;UBERON:0004537!4.29e-20!59;UBERON:0006965!4.29e-20!59;UBERON:0004872!6.44e-17!83;UBERON:0001637!1.36e-16!42;UBERON:0003509!1.36e-16!42;UBERON:0004572!1.36e-16!42;UBERON:0002204!2.20e-14!167;UBERON:0004573!5.47e-13!33;UBERON:0004571!5.47e-13!33;UBERON:0002193!6.30e-13!108;UBERON:0002405!1.02e-10!93;UBERON:0002390!3.40e-10!98;UBERON:0003061!3.40e-10!98;UBERON:0003914!6.51e-10!117;UBERON:0004638!3.08e-09!18;UBERON:0001986!3.08e-09!18;UBERON:0004852!3.08e-09!18;UBERON:0002371!7.76e-09!76;UBERON:0000947!7.93e-09!21;UBERON:0010191!7.93e-09!21;UBERON:0001434!1.10e-08!100;UBERON:0004765!1.24e-08!90;UBERON:0001474!3.51e-08!82;UBERON:0000486!4.01e-08!83;UBERON:0007503!6.61e-08!78;UBERON:0000487!1.30e-07!22;UBERON:0006914!4.72e-07!25;UBERON:0002329!7.20e-07!71;UBERON:0003059!7.20e-07!71;UBERON:0007282!7.20e-07!71;UBERON:0004290!7.20e-07!71;UBERON:0009618!7.20e-07!71
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190985625952663!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.00013045438385249!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918731365727576!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322231757268761!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764899861253661!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278094505085945!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203889534825401!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140825918113724!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110038271474187
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190985625952663!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.00013045438385249!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918731365727576!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322231757268761!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764899861253661!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278094505085945!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203889534825401!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140825918113724!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110038271474187
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526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.00956472,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.00502301,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,0.655293,0.21727,0.00514993,0.000310064,0.192475,0.177967,0.0465298,0.057571,0.047591,0.00174134,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.000919297,0.0611073,0.206454,0.218192,0.108277,0.0673484,0.00613985,0.0494066,0.0958493,0.00171529,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.00326415,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,6.78596e-05,0.0360851,0.0168763,0.131093,0.0434602,0.00935312,0.103051,0.36927,0.449036,0.407369,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.0107863,0.0966095,0.381071,0.057779,0.643768,0.432035,0.366326,0.390366,0.48809,0.50058,0.117158,0.0391928,0.000322406,0.0572701,0.227104,0.518585,0.250246,0.38649,0.284625,0.504757,0.55194,0.375373,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,0.00846715,0.000498078,0.258219,0.119142,0.243383,5.59455e-07,0.390974,0.0115792,0.000194132,0.161598,0.751174,0.277094,0.496032,0.0239796,0.37357,8.87042e-08,4.38605e-07,3.25586e-05,0.0132585,5.84732e-08,0.20342,8.73915e-05,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.000835245,0.230581,0.120226,0.28424,2.54652e-05,0.00677385,0.181415,0.00475227,0.00465874,0.00047615,0.408413,0.516511,0.322213,0.0234043,0.33942,0.0156581,0.387276,0.169614,0.481611,0.537348,0.222037,0.416621,0.416292,0.462712,0.0457685,0.215157,0.204817,0.452428,0.138871,3.08861e-07,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.0980968,0.0111982,0.534741,0.39088,0.0109626,0.236011,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,9.35975e-06,0.00623664,0.303709,0.15059,0.386538,0.159081,0.250964,0.383276,0.457886,0.0344603,0.220231,0.00608438,0.196976,0.191517,0.463751,0.0145214,0.307334,0.0246928,0.283463,0.0102434,0.135386,0.399569,0.273281,0.368095,0.275089,0.384593,0.0283414,0.0740334,0.339729,0.197805,0.24107,0.387069,0.332774,0.52832,0.299887,0.634365,0.00170684,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.0139199,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.000508432,0.197112,0.240478,0.156465,0.13108,0.00350063,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.0012829,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.0136582,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0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}}
}}

Revision as of 16:04, 19 October 2012


Full id: C4590_Neutrophils_Eosinophils_Whole_embryonic_osteosarcoma_Fibroblast_CD14



Phase1 CAGE Peaks

Hg19::chr6:30654342..30654353,-p11@PPP1R18
Hg19::chr6:30654376..30654395,-p5@PPP1R18
Hg19::chr6:30654401..30654477,-p1@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><br>

Cell Type
Ontology termp-valuen
somatic cell2.25e-24588
mesodermal cell5.72e-16121
classical monocyte5.08e-1542
CD14-positive, CD16-negative classical monocyte5.08e-1542
defensive cell1.68e-1348
phagocyte1.68e-1348
myeloid leukocyte3.82e-1372
animal cell6.94e-13679
eukaryotic cell6.94e-13679
endothelial cell7.48e-1336
somatic stem cell7.20e-12433
native cell1.23e-11722
multi fate stem cell1.53e-11427
endothelial cell of vascular tree5.67e-1124
meso-epithelial cell6.69e-1145
stem cell1.82e-10441
monopoietic cell1.99e-1059
monocyte1.99e-1059
monoblast1.99e-1059
promonocyte1.99e-1059
vascular associated smooth muscle cell2.67e-1032
macrophage dendritic cell progenitor2.82e-1061
smooth muscle cell9.24e-1043
smooth muscle myoblast9.24e-1043
granulocyte monocyte progenitor cell1.41e-0967
lining cell3.02e-0958
barrier cell3.02e-0958
blood vessel endothelial cell3.08e-0918
embryonic blood vessel endothelial progenitor cell3.08e-0918
myeloid lineage restricted progenitor cell1.25e-0866
stuff accumulating cell6.27e-0887
contractile cell1.26e-0759
muscle precursor cell1.97e-0758
myoblast1.97e-0758
multi-potent skeletal muscle stem cell1.97e-0758
embryonic cell2.13e-07250
muscle cell4.71e-0755
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm2.55e-28203
vessel1.36e-2268
mesoderm4.50e-22315
mesoderm-derived structure4.50e-22315
presumptive mesoderm4.50e-22315
cardiovascular system9.33e-22109
vasculature3.07e-2178
vascular system3.07e-2178
circulatory system2.08e-20112
epithelial tube open at both ends4.29e-2059
blood vessel4.29e-2059
blood vasculature4.29e-2059
vascular cord4.29e-2059
splanchnic layer of lateral plate mesoderm6.44e-1783
artery1.36e-1642
arterial blood vessel1.36e-1642
arterial system1.36e-1642
musculoskeletal system2.20e-14167
systemic artery5.47e-1333
systemic arterial system5.47e-1333
hemolymphoid system6.30e-13108
immune system1.02e-1093
hematopoietic system3.40e-1098
blood island3.40e-1098
epithelial tube6.51e-10117
blood vessel endothelium3.08e-0918
endothelium3.08e-0918
cardiovascular system endothelium3.08e-0918
bone marrow7.76e-0976
aorta7.93e-0921
aortic system7.93e-0921
skeletal system1.10e-08100
skeletal element1.24e-0890
bone element3.51e-0882
multilaminar epithelium4.01e-0883
epithelial vesicle6.61e-0878
simple squamous epithelium1.30e-0722
squamous epithelium4.72e-0725
somite7.20e-0771
presomitic mesoderm7.20e-0771
presumptive segmental plate7.20e-0771
dermomyotome7.20e-0771
trunk paraxial mesoderm7.20e-0771


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
CCNT2#90536.336201576962630.003930750035764890.0190985625952663
CTBP2#1488362.71700033932814.049570681927e-060.00013045438385249
EBF1#187938.9064668465690.00141523283560980.00918731365727576
EGR1#195834.988179094810140.008056488137383440.0322231757268761
ETS1#211339.728760922202340.001085840092584840.00764899861253661
SIN3A#2594235.408884726815140.006318961977991520.0278094505085945
SMARCB1#6598318.25271578115740.000164397760679890.00203889534825401
ZBTB7A#5134137.35190930787590.002516255860282270.0140825918113724
ZNF263#1012738.221841637010680.001799043925565870.0110038271474187



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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