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Coexpression cluster:C1561: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005786!signal recognition particle, endoplasmic reticulum targeting!0.00671140939597315!6729$GO:0048500!signal recognition particle!0.00671140939597315!6729$GO:0045047!protein targeting to ER!0.00671140939597315!6729$GO:0006614!SRP-dependent cotranslational protein targeting to membrane!0.00671140939597315!6729$GO:0008312!7S RNA binding!0.00671140939597315!6729$GO:0006613!cotranslational protein targeting to membrane!0.00735900153067232!6729$GO:0006612!protein targeting to membrane!0.00908311046071554!6729$GO:0016607!nuclear speck!0.0183239138113741!6729$GO:0016604!nuclear body!0.0211939244083363!6729$GO:0006605!protein targeting!0.0385022960084776!6729$GO:0045045!secretory pathway!0.0385344080151568!6729$GO:0032940!secretion by cell!0.0437124690921936!6729
|gostat_on_coexpression_clusters=GO:0005786!signal recognition particle, endoplasmic reticulum targeting!0.00671140939597315!6729$GO:0048500!signal recognition particle!0.00671140939597315!6729$GO:0045047!protein targeting to ER!0.00671140939597315!6729$GO:0006614!SRP-dependent cotranslational protein targeting to membrane!0.00671140939597315!6729$GO:0008312!7S RNA binding!0.00671140939597315!6729$GO:0006613!cotranslational protein targeting to membrane!0.00735900153067232!6729$GO:0006612!protein targeting to membrane!0.00908311046071554!6729$GO:0016607!nuclear speck!0.0183239138113741!6729$GO:0016604!nuclear body!0.0211939244083363!6729$GO:0006605!protein targeting!0.0385022960084776!6729$GO:0045045!secretory pathway!0.0385344080151568!6729$GO:0032940!secretion by cell!0.0437124690921936!6729
|id=C1561
|id=C1561
|ontology_enrichment_celltype=CL:0000037!1.75e-34!172;CL:0000566!1.75e-34!172;CL:0000988!1.52e-33!182;CL:0002032!1.70e-32!165;CL:0000837!1.70e-32!165;CL:0000763!3.33e-31!112;CL:0000049!3.33e-31!112;CL:0000738!1.05e-29!140;CL:0000766!7.06e-27!76;CL:0000034!1.87e-25!444;CL:0000048!2.75e-24!430;CL:0002057!2.99e-24!42;CL:0002031!3.29e-24!124;CL:0000723!1.52e-23!436;CL:0000860!3.63e-23!45;CL:0000839!4.77e-23!70;CL:0000557!6.79e-23!71;CL:0002087!5.45e-21!119;CL:0002009!1.42e-20!65;CL:0000012!5.77e-20!682;CL:0002194!2.00e-19!63;CL:0000576!2.00e-19!63;CL:0000040!2.00e-19!63;CL:0000559!2.00e-19!63;CL:0000134!4.20e-19!358;CL:0000003!6.04e-19!722;CL:0000548!1.41e-18!679;CL:0000004!1.41e-18!679;CL:0000255!1.41e-18!679;CL:0002320!3.01e-17!365;CL:0000144!2.31e-14!625;CL:0000063!3.10e-14!578;CL:0000219!4.45e-14!390;CL:0002371!7.61e-11!591
|ontology_enrichment_celltype=CL:0000766!4.67e-77!72;CL:0000860!8.86e-74!42;CL:0002057!8.86e-74!42;CL:0000557!6.95e-67!67;CL:0000473!4.49e-66!48;CL:0000234!4.49e-66!48;CL:0000839!2.85e-62!66;CL:0002009!5.03e-59!61;CL:0000763!5.53e-56!108;CL:0000049!5.53e-56!108;CL:0002194!1.19e-55!59;CL:0000576!1.19e-55!59;CL:0000040!1.19e-55!59;CL:0000559!1.19e-55!59;CL:0000738!1.88e-53!136;CL:0000037!4.20e-44!168;CL:0000566!4.20e-44!168;CL:0002031!7.59e-44!120;CL:0002032!1.69e-43!161;CL:0000837!1.69e-43!161;CL:0000988!2.23e-42!177;CL:0002087!3.96e-37!115;CL:0000325!2.50e-32!87;CL:0000134!1.82e-16!354;CL:0002320!9.18e-16!361;CL:0002393!2.20e-13!9;CL:0002397!2.20e-13!9;CL:0000219!2.66e-13!386;CL:0000094!2.75e-13!8;CL:0000048!5.31e-12!427;CL:0000081!7.17e-12!11;CL:0000034!1.24e-11!441;CL:0000723!1.47e-11!433;CL:0002274!8.26e-11!5;CL:0000457!8.26e-11!5;CL:0002191!8.26e-11!5;CL:0000097!8.26e-11!5;CL:0000831!8.26e-11!5;CL:0002028!8.26e-11!5;CL:0000767!7.76e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.33e-24!102;UBERON:0003061!1.33e-24!102;UBERON:0002193!1.41e-21!112;UBERON:0002371!2.39e-20!80;UBERON:0001474!7.97e-19!86;UBERON:0002384!1.89e-16!375;UBERON:0003081!4.49e-16!216;UBERON:0004765!6.79e-16!101;UBERON:0001434!6.79e-16!101;UBERON:0002405!2.49e-15!115;UBERON:0002204!9.76e-15!167
|ontology_enrichment_uberon=UBERON:0002390!9.36e-70!98;UBERON:0003061!9.36e-70!98;UBERON:0002193!1.19e-61!108;UBERON:0002371!1.34e-59!76;UBERON:0001474!3.80e-54!82;UBERON:0002405!7.59e-50!93;UBERON:0004765!5.30e-48!90;UBERON:0001434!1.52e-43!100;UBERON:0003081!8.19e-28!203;UBERON:0002204!3.74e-23!167;UBERON:0000926!5.68e-15!315;UBERON:0004120!5.68e-15!315;UBERON:0006603!5.68e-15!315;UBERON:0002384!8.30e-15!371;UBERON:0000178!7.13e-12!15;UBERON:0000179!7.13e-12!15;UBERON:0000463!7.13e-12!15
|tf_chipseq_enrich=EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432232303717668!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447195496364511!ELK4#2005;3:9.74140899508082:0.0021255865657434:0.0122852316181337!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542247360674225
|tf_chipseq_enrich=EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432232303717668!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447195496364511!ELK4#2005;3:9.74140899508082:0.0021255865657434:0.0122852316181337!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542247360674225
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39826,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.00398358,0.312064,0.080156,0.274185,0.180885,0.0545112,0.160961,0.33844,0.0649137,0.0974216,0.0137454,0.195675,0.174786,0.176557,0.0917509,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.566117,0.36304,0.0196869,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.131825,0.0789618,0.084895,0.160115,0.0819954,0.10091,0.122658,0.0120484,0.228398,0.056055,0.120552,0.41771,0.189229,0.262721,0.335207,0.434016,0.190688,0.299739,0.278645,0.381281,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.0227103,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.00864115,0.672453,0.0576826,0.336512,0.173868,0.109708,0.0162151,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.110025,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.32673,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.0850129,0.432408,0.190404,0.135865,0.145815,0.18137,0.180609,0.291283,0.0415219,0.0123556,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.431348,0.262486,0.0482841,0.131936,0.288826,0.246621,0.463617,0.119485,0.0965376,0.0822869,0.279263,0.0643411,0.35463,0.581771,0.47901,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.1798,0.629713,0.581874,0.355154,0.145569,0.619037,0.537088,0.236988,0.629445,0.0528459,0.569605,0.526495,0.0119447,0.191067,0.764863,0.248142,0.0700912,0.167927,0.200159,0.306829,0.111362,0.0759172,0.708698,0.139489,0.663441,0.349068,0.344004,0.217481,0.196345,0.427789,0.689998,0.386595,0.0700328,0.433702,0.258394,0.644878,0.432123,0.172498,0.09639,0.149969,0.0903515,0.392155,0.259088,0.371758,0.109303,0.20076,0.183098,0.0137162,0.254547,0.204391,0.249366,0.316342,0.133485,0.541378,0.117335,0.0958693,0.469682,0.198685,0.104059,0.315485,0.311289,0.00707421,0.120474,0.389888,0.236714,0.511254,0.193221,0.246387,0.224252,0.22199,0.155054,0.466978,0.166402,0.257848,0.0717012,0.192234,0.427276,0.400353,0.466967,0.283682,0.424668,0.0148534,0.474058,0.218352,0.341421,0.138015,0.530902,0.033063,0.209091,0.55798,0.0366436,0.137174,0.0415773,0.34194,0.592696,0.226514,0.0212338,0.182727,0.177129,0.317485,0.633504,0.220564,0.119459,0.262394,0.307462,0.135076,0.469588,0.298027,0.274593,0.490712,0.541363,0.0369687,0.218812,0.0415974,0.720644,0.562305,0.528646,0.361524,0.31558,0.412744,0.00853264,0.259136,0.513592,0.415367,0.815658,0.45585,0.36864,0.538745,0.456862,0.0234438,0.680686,0.557093,0.330982,0.382214,0.553161,0.271769,0.326875,0.339393,0.694478,0.306231,0.298354,0.278436,0.199987,0.457741,0.641611,0.426239,0.0517097,0.0234011,0.572661,0.412586,0.178696,0.41502,0.55475,0.66153,0.170461,0.499347,0.0530156,0.0736126,0.557732,0.490527,0.356232,0.44799,0.236683,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.048795,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.0463258,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.0671246,0.501812,0.128553,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.0133669,0.174153,0.0972854,0.333309,0.249919,0.339517,0.0516568,0.198326,0.394084,0.458518,0.282501,0.252005,0.0889203,0.238377,0.334983,0.197875,0.287909,0.046623,0.117618,0.392533,0.396962,0.316002,0.330317,0.0582923,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.0526496,0.367733,0.246925,0.208775,0.390438,0.343014,0.0402908,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.00427288,0.396935,0.326779,0.292869,0.00113333,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.11881,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.107309,0.380826,0.259046,0.345068,0.151046,0.483953,0.0687784,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.0986342,0.115686,0.0981568,0.162633,0.342661,0.27567,0.248127,0.33299,0.0858973,0.319112,0.526476
}}
}}

Revision as of 11:26, 19 October 2012


Full id: C1561_Mast_Eosinophils_Neutrophils_CD14_immature_Whole_Hep2



Phase1 CAGE Peaks

Hg19::chr10:106113292..106113306,-p3@ENST00000435434
Hg19::chr14:35452304..35452319,+p4@SRP54
Hg19::chr1:203273760..203273784,-p1@ENST00000425698
Hg19::chr6:31702698..31702709,+p@chr6:31702698..31702709
+
Hg19::chr8:22553096..22553123,+p@chr8:22553096..22553123
+


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


GO IDGO nameFDR corrected p-value
GO:0005786signal recognition particle, endoplasmic reticulum targeting0.00671140939597315
GO:0048500signal recognition particle0.00671140939597315
GO:0045047protein targeting to ER0.00671140939597315
GO:0006614SRP-dependent cotranslational protein targeting to membrane0.00671140939597315
GO:00083127S RNA binding0.00671140939597315
GO:0006613cotranslational protein targeting to membrane0.00735900153067232
GO:0006612protein targeting to membrane0.00908311046071554
GO:0016607nuclear speck0.0183239138113741
GO:0016604nuclear body0.0211939244083363
GO:0006605protein targeting0.0385022960084776
GO:0045045secretory pathway0.0385344080151568
GO:0032940secretion by cell0.0437124690921936



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
myeloid leukocyte4.67e-7772
classical monocyte8.86e-7442
CD14-positive, CD16-negative classical monocyte8.86e-7442
granulocyte monocyte progenitor cell6.95e-6767
defensive cell4.49e-6648
phagocyte4.49e-6648
myeloid lineage restricted progenitor cell2.85e-6266
macrophage dendritic cell progenitor5.03e-5961
myeloid cell5.53e-56108
common myeloid progenitor5.53e-56108
monopoietic cell1.19e-5559
monocyte1.19e-5559
monoblast1.19e-5559
promonocyte1.19e-5559
leukocyte1.88e-53136
hematopoietic stem cell4.20e-44168
angioblastic mesenchymal cell4.20e-44168
hematopoietic lineage restricted progenitor cell7.59e-44120
hematopoietic oligopotent progenitor cell1.69e-43161
hematopoietic multipotent progenitor cell1.69e-43161
hematopoietic cell2.23e-42177
nongranular leukocyte3.96e-37115
stuff accumulating cell2.50e-3287
mesenchymal cell1.82e-16354
connective tissue cell9.18e-16361
intermediate monocyte2.20e-139
CD14-positive, CD16-positive monocyte2.20e-139
motile cell2.66e-13386
granulocyte2.75e-138
multi fate stem cell5.31e-12427
blood cell7.17e-1211
stem cell1.24e-11441
somatic stem cell1.47e-11433
histamine secreting cell8.26e-115
biogenic amine secreting cell8.26e-115
granulocytopoietic cell8.26e-115
mast cell8.26e-115
mast cell progenitor8.26e-115
basophil mast progenitor cell8.26e-115
basophil7.76e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.36e-7098
blood island9.36e-7098
hemolymphoid system1.19e-61108
bone marrow1.34e-5976
bone element3.80e-5482
immune system7.59e-5093
skeletal element5.30e-4890
skeletal system1.52e-43100
lateral plate mesoderm8.19e-28203
musculoskeletal system3.74e-23167
mesoderm5.68e-15315
mesoderm-derived structure5.68e-15315
presumptive mesoderm5.68e-15315
connective tissue8.30e-15371
blood7.13e-1215
haemolymphatic fluid7.13e-1215
organism substance7.13e-1215


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
EBF1#187935.34388010794140.01187615563868110.0432232303717668
ELF1#199743.406478367046030.01235066105299550.0447195496364511
ELK4#200539.741408995080820.00212558656574340.0122852316181337
POU2F2#545247.284899246194020.0006631223288743860.00542247360674225



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.