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Coexpression cluster:C1637: Difference between revisions

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|full_id=C1637_CD19_Basophils_CD14_CD14CD16_Peripheral_Mast_CD4
|full_id=C1637_CD19_Basophils_CD14_CD14CD16_Peripheral_Mast_CD4
|id=C1637
|id=C1637
|ontology_enrichment_celltype=CL:0000738!7.03e-64!140;CL:0000037!2.32e-60!172;CL:0000566!2.32e-60!172;CL:0000988!5.36e-57!182;CL:0002032!6.47e-56!165;CL:0000837!6.47e-56!165;CL:0002087!1.02e-52!119;CL:0002031!4.13e-51!124;CL:0002057!2.27e-36!42;CL:0000766!3.90e-35!76;CL:0000860!8.70e-34!45;CL:0000763!1.42e-33!112;CL:0000049!1.42e-33!112;CL:0000557!1.49e-32!71;CL:0002009!5.45e-31!65;CL:0002194!2.34e-29!63;CL:0000576!2.34e-29!63;CL:0000040!2.34e-29!63;CL:0000559!2.34e-29!63;CL:0000839!9.04e-29!70;CL:0000134!2.32e-24!358;CL:0002320!2.62e-23!365;CL:0000219!6.81e-20!390;CL:0000542!1.82e-19!53;CL:0000051!1.82e-19!53;CL:0000838!3.36e-19!52;CL:0000048!1.31e-15!430;CL:0000034!3.28e-15!444;CL:0000723!1.10e-14!436;CL:0000945!1.02e-11!24;CL:0000826!1.02e-11!24;CL:0002393!3.96e-10!9;CL:0002397!3.96e-10!9;CL:0000236!3.84e-09!14;CL:0000791!1.78e-08!18;CL:0000789!1.78e-08!18;CL:0002420!1.78e-08!18;CL:0002419!1.78e-08!18;CL:0000790!1.78e-08!18;CL:0000084!4.92e-07!25;CL:0000827!4.92e-07!25
|ontology_enrichment_celltype=CL:0000860!4.18e-83!42;CL:0002057!4.18e-83!42;CL:0000738!2.19e-72!136;CL:0000473!2.20e-71!48;CL:0000234!2.20e-71!48;CL:0000766!4.05e-61!72;CL:0002087!4.72e-60!115;CL:0000557!2.90e-59!67;CL:0002031!4.62e-59!120;CL:0000037!6.50e-58!168;CL:0000566!6.50e-58!168;CL:0000839!4.44e-57!66;CL:0002009!4.21e-56!61;CL:0002194!5.52e-55!59;CL:0000576!5.52e-55!59;CL:0000040!5.52e-55!59;CL:0000559!5.52e-55!59;CL:0000988!3.28e-54!177;CL:0002032!2.89e-50!161;CL:0000837!2.89e-50!161;CL:0000763!4.11e-43!108;CL:0000049!4.11e-43!108;CL:0000325!1.14e-34!87;CL:0002393!3.38e-26!9;CL:0002397!3.38e-26!9;CL:0000134!1.64e-19!354;CL:0002320!7.77e-19!361;CL:0000219!1.85e-16!386;CL:0000034!3.64e-14!441;CL:0000048!1.47e-13!427;CL:0000723!3.70e-13!433;CL:0000767!4.45e-10!3;CL:0000875!9.47e-10!3;CL:0002396!9.47e-10!3;CL:0000226!1.30e-09!3;CL:0000842!1.30e-09!3;CL:0000236!2.87e-09!14;CL:0000838!5.13e-08!52;CL:0000542!8.39e-08!53;CL:0000051!8.39e-08!53;CL:0002242!2.12e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!4.26e-38!102;UBERON:0003061!4.26e-38!102;UBERON:0002193!9.79e-34!112;UBERON:0002371!7.16e-32!80;UBERON:0001474!7.70e-28!86;UBERON:0002384!3.01e-22!375;UBERON:0004765!7.31e-21!101;UBERON:0001434!7.31e-21!101;UBERON:0002405!1.16e-20!115;UBERON:0003081!7.05e-09!216;UBERON:0000178!2.80e-08!15;UBERON:0000179!2.80e-08!15;UBERON:0000463!2.80e-08!15
|ontology_enrichment_uberon=UBERON:0002371!7.94e-54!76;UBERON:0002390!1.17e-53!98;UBERON:0003061!1.17e-53!98;UBERON:0001474!4.31e-49!82;UBERON:0002193!1.49e-47!108;UBERON:0002405!3.61e-44!93;UBERON:0004765!9.37e-44!90;UBERON:0001434!2.81e-38!100;UBERON:0003081!1.53e-19!203;UBERON:0002204!1.61e-18!167;UBERON:0002384!6.47e-18!371;UBERON:0000926!4.96e-09!315;UBERON:0004120!4.96e-09!315;UBERON:0006603!4.96e-09!315
|tf_chipseq_enrich=MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000727842390337103!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252383699564473!POU2F2#5452;3:5.46367443464551:0.0111565009446978:0.0410027026837206!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714002055476568
|tf_chipseq_enrich=MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000727842390337103!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252383699564473!POU2F2#5452;3:5.46367443464551:0.0111565009446978:0.0410027026837206!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714002055476568
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18749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.566117,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.629422,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.893893,0.529713,0.335207,0.434016,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.98236,0.989834,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.431348,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.581874,0.355154,0.730614,0.619037,0.537088,0.603804,0.629445,0.306963,0.206759,0.526495,0.580285,0.550495,0.424482,0.820986,0.610475,0.881697,0.561689,0.672416,0.685628,0.623136,0.708698,0.96913,0.967174,0.0695904,0.70429,0.798758,0.557035,0.427789,0.689998,0.737642,0.886619,0.433702,0.258394,0.644878,0.432123,0.759415,0.661773,0.494975,0.28382,0.392155,0.626931,0.371758,0.91821,0.562417,0.890566,0.85279,0.00339523,0.901563,0.821811,0.680843,0.931136,0.541378,0.922893,0.660884,0.922144,0.898765,0.914902,0.315485,0.311289,0.318577,0.120474,0.389888,0.603509,0.511254,0.0482305,0.0332078,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.108067,0.747776,0.466967,0.283682,0.424668,0.919825,0.797471,0.583101,0.702164,0.477016,0.530902,0.152704,0.792095,0.55798,0.708394,0.932831,0.723248,0.34194,0.226858,0.062406,0.27725,0.89036,0.763919,0.317485,0.633504,0.220564,0.845182,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.490712,0.541363,0.709432,0.583627,0.531474,0.720644,0.562305,0.528646,0.361524,0.31558,0.412744,0.54408,0.62698,0.513592,0.415367,0.815658,0.45585,0.36864,0.538745,0.456862,0.453004,0.680686,0.196391,0.693441,0.382214,0.193207,0.639572,0.68995,0.0655077,0.694478,0.306231,0.0497423,0.646049,0.784543,0.457741,0.641611,0.426239,0.748909,0.289012,0.572661,0.412586,0.534679,0.41502,0.55475,0.66153,0.523749,0.499347,0.307426,0.790204,0.557732,0.490527,0.714189,0.44799,0.236683,0.0571105,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.188453,0.388459,0.321362,0.259785,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.0175269,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.0905116,0.458518,0.282501,0.252005,0.390891,0.238377,0.063694,0.197875,0.287909,0.289389,0.117618,0.0897364,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.128336,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.092937,0.389061,0.0542381,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.0642384,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.133591,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476
}}
}}

Revision as of 11:31, 19 October 2012


Full id: C1637_CD19_Basophils_CD14_CD14CD16_Peripheral_Mast_CD4



Phase1 CAGE Peaks

Hg19::chr11:60157065..60157091,-p@chr11:60157065..60157091
-
Hg19::chr17:7036237..7036263,-p@chr17:7036237..7036263
-
Hg19::chr3:42108875..42108907,-p@chr3:42108875..42108907
-
Hg19::chr6:25006945..25006954,-p@chr6:25006945..25006954
-
Hg19::chr9:27572810..27572824,+p@chr9:27572810..27572824
+


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
classical monocyte4.18e-8342
CD14-positive, CD16-negative classical monocyte4.18e-8342
leukocyte2.19e-72136
defensive cell2.20e-7148
phagocyte2.20e-7148
myeloid leukocyte4.05e-6172
nongranular leukocyte4.72e-60115
granulocyte monocyte progenitor cell2.90e-5967
hematopoietic lineage restricted progenitor cell4.62e-59120
hematopoietic stem cell6.50e-58168
angioblastic mesenchymal cell6.50e-58168
myeloid lineage restricted progenitor cell4.44e-5766
macrophage dendritic cell progenitor4.21e-5661
monopoietic cell5.52e-5559
monocyte5.52e-5559
monoblast5.52e-5559
promonocyte5.52e-5559
hematopoietic cell3.28e-54177
hematopoietic oligopotent progenitor cell2.89e-50161
hematopoietic multipotent progenitor cell2.89e-50161
myeloid cell4.11e-43108
common myeloid progenitor4.11e-43108
stuff accumulating cell1.14e-3487
intermediate monocyte3.38e-269
CD14-positive, CD16-positive monocyte3.38e-269
mesenchymal cell1.64e-19354
connective tissue cell7.77e-19361
motile cell1.85e-16386
stem cell3.64e-14441
multi fate stem cell1.47e-13427
somatic stem cell3.70e-13433
basophil4.45e-103
non-classical monocyte9.47e-103
CD14-low, CD16-positive monocyte9.47e-103
single nucleate cell1.30e-093
mononuclear cell1.30e-093
B cell2.87e-0914
lymphoid lineage restricted progenitor cell5.13e-0852
lymphocyte8.39e-0853
common lymphoid progenitor8.39e-0853
nucleate cell2.12e-0755
Uber Anatomy
Ontology termp-valuen
bone marrow7.94e-5476
hematopoietic system1.17e-5398
blood island1.17e-5398
bone element4.31e-4982
hemolymphoid system1.49e-47108
immune system3.61e-4493
skeletal element9.37e-4490
skeletal system2.81e-38100
lateral plate mesoderm1.53e-19203
musculoskeletal system1.61e-18167
connective tissue6.47e-18371
mesoderm4.96e-09315
mesoderm-derived structure4.96e-09315
presumptive mesoderm4.96e-09315


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
MEF2A#4205414.99458472771523.876195075647e-050.000727842390337103
MEF2C#4208216.52454179704960.005579850077982050.0252383699564473
POU2F2#545235.463674434645510.01115650094469780.0410027026837206
SPI1#668846.563458806818180.0009957429636454020.00714002055476568



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.