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Coexpression cluster:C597: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0000185!activation of MAPKKK activity!0.0119487317818538!4616$GO:0000186!activation of MAPKK activity!0.0119487317818538!4616$GO:0008440!inositol trisphosphate 3-kinase activity!0.0119487317818538!80271$GO:0051766!inositol trisphosphate kinase activity!0.0119487317818538!80271$GO:0006469!negative regulation of protein kinase activity!0.0265308474773421!4616$GO:0033673!negative regulation of kinase activity!0.0265308474773421!4616$GO:0051348!negative regulation of transferase activity!0.0265308474773421!4616$GO:0004428!inositol or phosphatidylinositol kinase activity!0.0265308474773421!80271$GO:0032147!activation of protein kinase activity!0.0265308474773421!4616$GO:0043086!negative regulation of catalytic activity!0.0296692149196469!4616$GO:0045860!positive regulation of protein kinase activity!0.0340708838298483!4616$GO:0005516!calmodulin binding!0.0340708838298483!80271$GO:0033674!positive regulation of kinase activity!0.0340708838298483!4616$GO:0051347!positive regulation of transferase activity!0.0340708838298483!4616$GO:0000165!MAPKKK cascade!0.0340708838298483!4616$GO:0045859!regulation of protein kinase activity!0.0458342550450001!4616$GO:0043549!regulation of kinase activity!0.0458342550450001!4616$GO:0051338!regulation of transferase activity!0.0458342550450001!4616$GO:0043085!positive regulation of catalytic activity!0.0458342550450001!4616
|gostat_on_coexpression_clusters=GO:0000185!activation of MAPKKK activity!0.0119487317818538!4616$GO:0000186!activation of MAPKK activity!0.0119487317818538!4616$GO:0008440!inositol trisphosphate 3-kinase activity!0.0119487317818538!80271$GO:0051766!inositol trisphosphate kinase activity!0.0119487317818538!80271$GO:0006469!negative regulation of protein kinase activity!0.0265308474773421!4616$GO:0033673!negative regulation of kinase activity!0.0265308474773421!4616$GO:0051348!negative regulation of transferase activity!0.0265308474773421!4616$GO:0004428!inositol or phosphatidylinositol kinase activity!0.0265308474773421!80271$GO:0032147!activation of protein kinase activity!0.0265308474773421!4616$GO:0043086!negative regulation of catalytic activity!0.0296692149196469!4616$GO:0045860!positive regulation of protein kinase activity!0.0340708838298483!4616$GO:0005516!calmodulin binding!0.0340708838298483!80271$GO:0033674!positive regulation of kinase activity!0.0340708838298483!4616$GO:0051347!positive regulation of transferase activity!0.0340708838298483!4616$GO:0000165!MAPKKK cascade!0.0340708838298483!4616$GO:0045859!regulation of protein kinase activity!0.0458342550450001!4616$GO:0043549!regulation of kinase activity!0.0458342550450001!4616$GO:0051338!regulation of transferase activity!0.0458342550450001!4616$GO:0043085!positive regulation of catalytic activity!0.0458342550450001!4616
|id=C597
|id=C597
|ontology_enrichment_celltype=CL:0002057!3.34e-20!42;CL:0000860!7.72e-17!45;CL:0000766!2.92e-13!76;CL:0000557!8.84e-11!71;CL:0002009!3.05e-10!65;CL:0002194!2.74e-09!63;CL:0000576!2.74e-09!63;CL:0000040!2.74e-09!63;CL:0000559!2.74e-09!63;CL:0000839!4.80e-09!70
|ontology_enrichment_celltype=CL:0000860!1.69e-65!42;CL:0002057!1.69e-65!42;CL:0000473!2.17e-56!48;CL:0000234!2.17e-56!48;CL:0000557!4.08e-54!67;CL:0000766!2.31e-49!72;CL:0002009!4.75e-49!61;CL:0000839!8.44e-48!66;CL:0002194!1.21e-43!59;CL:0000576!1.21e-43!59;CL:0000040!1.21e-43!59;CL:0000559!1.21e-43!59;CL:0000763!6.64e-35!108;CL:0000049!6.64e-35!108;CL:0000738!2.79e-33!136;CL:0000325!2.02e-32!87;CL:0002031!1.67e-30!120;CL:0002087!8.02e-26!115;CL:0000037!3.32e-25!168;CL:0000566!3.32e-25!168;CL:0000988!5.93e-25!177;CL:0002032!1.47e-23!161;CL:0000837!1.47e-23!161;CL:0000134!2.21e-12!354;CL:0002320!6.08e-12!361;CL:0000219!2.12e-10!386;CL:0001014!3.44e-09!2;CL:0001016!3.44e-09!2;CL:0000034!1.31e-08!441;CL:0000048!1.61e-08!427;CL:0000723!2.92e-08!433;CL:0002274!2.51e-07!5;CL:0000457!2.51e-07!5;CL:0002191!2.51e-07!5;CL:0000097!2.51e-07!5;CL:0000831!2.51e-07!5;CL:0002028!2.51e-07!5;CL:0002393!6.48e-07!9;CL:0002397!6.48e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002405!2.59e-10!115;UBERON:0000062!7.89e-10!511;UBERON:0002371!4.72e-09!80;UBERON:0000468!4.66e-08!659;UBERON:0001474!5.59e-08!86;UBERON:0000467!1.20e-07!625;UBERON:0000480!1.95e-07!626;UBERON:0002193!2.44e-07!112;UBERON:0003081!8.44e-07!216
|ontology_enrichment_uberon=UBERON:0002371!8.30e-47!76;UBERON:0002390!3.01e-44!98;UBERON:0003061!3.01e-44!98;UBERON:0001474!8.13e-43!82;UBERON:0002193!2.35e-39!108;UBERON:0002405!3.23e-39!93;UBERON:0004765!2.58e-38!90;UBERON:0001434!1.08e-33!100;UBERON:0003081!8.20e-22!203;UBERON:0002204!5.75e-17!167;UBERON:0000926!1.69e-11!315;UBERON:0004120!1.69e-11!315;UBERON:0006603!1.69e-11!315;UBERON:0002384!2.41e-11!371
|tf_chipseq_enrich=ETS1#2113;5:3.24292030740078:0.0142357715348991:0.0499334926392386!NFKB1#4790;7:2.56109626462379:0.0108752592113249:0.0401031423194533!REST#5978;6:3.86001148645121:0.00270193564832292:0.014863705934959!STAT3#6774;5:3.50648833238475:0.0103118355458907:0.0383013654092497
|tf_chipseq_enrich=ETS1#2113;5:3.24292030740078:0.0142357715348991:0.0499334926392386!NFKB1#4790;7:2.56109626462379:0.0108752592113249:0.0401031423194533!REST#5978;6:3.86001148645121:0.00270193564832292:0.014863705934959!STAT3#6774;5:3.50648833238475:0.0103118355458907:0.0383013654092497
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0.617635,0.901088,0.154781,0.63166,0.710461,0.182373,0.264717,0.75446,0.479652,0.0208423,0.441658,0.78025,0.135062,0.563666,0.541932,0.179723,0.367181,0.24648,0.540592,0.768481,0.12566,0.651424,0.156698,0.457455,0.000510449,0.504044,0.326917,0.611971,0.34762,0.635326,0.604786,0.550255,0.533561,0.599568,0.531273,0.372391,0.843129,0.504309,0.215174,0.392525,0.341267,0.509791,0.331688,0.439061,0.151667,0.505726,0.363739,0.347855,0.233675,0.407539,0.226368,0.273208,0.0595726,0.388388,0.540612,0.158915,0.319809,0.482262,0.663478,0.440924,0.706195,0.818693,0.133458,0.289571,0.624641,0.90611,0.256564,0.216359,0.45514,0.269486,0.618557,0.533476,0.30924,0.718381,0.513033,0.165697,0.488864,0.250422,0.238269,0.156558,0.685327,0.348451,0.436169,0.294337,0.437654,0.223799,0.395767,0.31984,0.324936,0.208357,0.44227,0.305343,0.722525,0.565276,0.174777,0.509038,0.205654,0.24203,0.454777,0.0865317,0.611817,0.425563,0.714314,0.254974,0.385459,0.326406,0.503769,0.200788,0.661828,0.708068,0.414762,0.588704,0.613121,0.875652,0.560447,0.276477,0.654185,0.552561,0.681342,0.57128,0.311354,0.382458,0.267022,0.541227,0.557937,0.400873,0.56927,0.606796,0.659114,0.521917,0.726044,0.424688,0.242528,0.469353,0.354726,0.866443,0.451391,0.44986,0.644026,0.617298,0.392405,0.784148,0.761188,0.531029,0.408774,0.438594,0.421442,0.451155,0.121414,0.601112,0.378227,0.81527,0.598846,0.648409,0.345883,0.0203998,0.572397,0.845679,0.481755,0.262554,0.758432,0.625604,0.707991,0.378057,0.267305,0.711296,0.167866,0.130721,0.156707,0.199217,0.511852,0.752729,0.201546,0.79791,0.735674,0.731856,0.553695,0.329295,0.406785,0.30307,0.949119,0.667134,0.718633,0.893837,0.482709,0.691303,0.807948,0.412242,0.314405,0.45823,0.449625,0.847152,0.457213,0.172724,0.169938,0.169185,0.572888,0.368938,0.706894,0.707245,0.700761,0.49887,0.865535,0.569287,0.635452,0.0940746,0.592132,0.816118,0.242131,0.926557,0.228727,0.607212,0.61163,0.775416,0.948076,0.406264,0.868723,0.916212,0.224991,0.824822,0.585751,0.394582,0.965065,0.856105,0.411201,0.903536,0.778451,0.961002,0.643191,0.911252,0.459468,0.314543,0.307848,0.68359,0.533276,0.436246,0.524639,0.883252,0.910792,0.571999,0.533166,0.275934,0.396764,0.562711,0.643204,0.59123,0.730341,0.472945,0.498026,0.396994,0.292911,0.264569,0.231844,0.485682,0.951895,0.737356,0.49191,0.308335,0.28859,0.343123,0.507612,0.702119,0.88353,0.0688138,0.739698,0.132738,0.93243,0.504357,0.0949911,0.790681,0.929859,0.317742,0.950773,0.526477,0.487547,0.598696,0.667852,0.352955,0.850775,0.635709,0.61828,0.867904,0.903526,0.884507,0.488706,0.195487,0.531781,0.916148,0.392377,0.389389,0.314694,0.797474,0.418837,0.794546,0.367114,0.800175,0.141094,0.112855,0.74833,0.0311416,0.546374,0.836336,0.260425,0.230351,0.473482,0.17744,0.434641,0.953177,0.865486,0.353138,0.150039,0.666079,0.654574,0.817491,0.18263,0.840552,0.953968,0.496319,0.238056,0.82908,0.722917,0.79731,0.402657,0.0241557,0.91173,0.228339,0.891979,0.61405,0.6678,0.193337,0.442655,0.86776,0.724132,0.531956,0.389408,0.683257,0.621028,0.333365,0.802264,0.683028,0.15758,0.650589,0.776375,0.647568,0.311463,0.785326,0.588141,0.653553,0.589343,0.710222,0.688406,0.376218,0.394146,0.596813,0.76613,0.686514,0.771295,0.687453,0.344626,0.627929,0.292131,0.712952,0.71675,0.617892,0.554835,0.70758,0.669472,0.276715,0.482161,0.671228,0.15268,0.38724,0.484299,0.62901,0.368399,0.804782,0.360598,0.504775,0.325888,0.758854,0.133175,0.294279,0.689303,0.458747,0.451227,0.544961,0.37428,0.587101,0.373192,0.603116,0.178215,0.2896,0.235131,0.207933,0.7909,0.104822,0.365841,0.569042,0.472855,0.405145,0.436753,0.264384,0.703671,0.577987,0.711872,0.66241,0.48478,0.443192,0.549057,0.630628,0.581499,0.187965,0.558205,0.345967,0.48391,0.638918,0.641165,0.31298,0.775835,0.780702,0.31537,0.699663,0.687511,0.534658,0.657796,0.419307,0.460081,0.719638,0.75647,0.613225,0.673203,0.528985,0.666362,0.747244,0.572915,0.504664,0.437157,0.13384,0.611134,0.621945,0.399385,0.311607,0.844055,0.807772,0.348379,0.348894,0.676528,0.431288,0.240791,0.241466,0.559235,0.333781,0.187694,0.241313,0.574081,0.780673,0.694879,0.64641,0.149951,0.282953,0.345521,0.403299,0.282135,0.477978,0.281079,0.424456,0.29046,0.327384,0.497947,0.438989,0.201933,0.292836,0.374626,0.170712,0.515655,0.681219,0.826788,0.815334,0.881301,0.534283,0.782795,0.0629455,0.306962,0.724882,0.528704,0.768195,0.623948,0.496729,0.784638,0.506604,0.583424,0.6849,0.670761,0.815591,0.390427,0.860028,0.127016,0.127047,0.718304,0.457962,0.661914,0.653454,0.808817,0.810793,0.42125,0.593207,0.719076,0.388139,0.862574,0.365832,0.687969,0.395855,0.361878,0.297716,0.610074,0.57891,0.469331,0.308457,0.467832,0.412853,0.715967,0.619978,0.574957,0.342733,0.42771,0.684335,0.388701
}}
}}

Revision as of 16:28, 19 October 2012


Full id: C597_CD14_mature_immature_Eosinophils_Mast_embryonic_chorionic



Phase1 CAGE Peaks

Hg19::chr13:28615672..28615689,-p@chr13:28615672..28615689
-
Hg19::chr17:19091325..19091326,+p1@SNORD3A
Hg19::chr17:76320827..76320838,+p@chr17:76320827..76320838
+
Hg19::chr19:2476116..2476132,+p1@GADD45B
Hg19::chr19:41222998..41223057,+p1@ITPKC
Hg19::chr19:45350840..45350859,-p@chr19:45350840..45350859
-
Hg19::chr19:45947096..45947113,+p@chr19:45947096..45947113
+
Hg19::chr1:39324762..39324790,+p@chr1:39324762..39324790
+
Hg19::chr1:85461941..85461949,+p@chr1:85461941..85461949
+
Hg19::chr21:38740608..38740619,-p@chr21:38740608..38740619
-
Hg19::chr2:102759127..102759136,-p@chr2:102759127..102759136
-
Hg19::chr5:395563..395569,+p@chr5:395563..395569
+
Hg19::chr6:14109177..14109181,+p@chr6:14109177..14109181
+
Hg19::chr7:151033644..151033667,+p@chr7:151033644..151033667
+
Hg19::chrX:20284429..20284435,+p@chrX:20284429..20284435
+


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:0000185activation of MAPKKK activity0.0119487317818538
GO:0000186activation of MAPKK activity0.0119487317818538
GO:0008440inositol trisphosphate 3-kinase activity0.0119487317818538
GO:0051766inositol trisphosphate kinase activity0.0119487317818538
GO:0006469negative regulation of protein kinase activity0.0265308474773421
GO:0033673negative regulation of kinase activity0.0265308474773421
GO:0051348negative regulation of transferase activity0.0265308474773421
GO:0004428inositol or phosphatidylinositol kinase activity0.0265308474773421
GO:0032147activation of protein kinase activity0.0265308474773421
GO:0043086negative regulation of catalytic activity0.0296692149196469
GO:0045860positive regulation of protein kinase activity0.0340708838298483
GO:0005516calmodulin binding0.0340708838298483
GO:0033674positive regulation of kinase activity0.0340708838298483
GO:0051347positive regulation of transferase activity0.0340708838298483
GO:0000165MAPKKK cascade0.0340708838298483
GO:0045859regulation of protein kinase activity0.0458342550450001
GO:0043549regulation of kinase activity0.0458342550450001
GO:0051338regulation of transferase activity0.0458342550450001
GO:0043085positive regulation of catalytic activity0.0458342550450001



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 monocyte1.69e-6542
CD14-positive, CD16-negative classical monocyte1.69e-6542
defensive cell2.17e-5648
phagocyte2.17e-5648
granulocyte monocyte progenitor cell4.08e-5467
myeloid leukocyte2.31e-4972
macrophage dendritic cell progenitor4.75e-4961
myeloid lineage restricted progenitor cell8.44e-4866
monopoietic cell1.21e-4359
monocyte1.21e-4359
monoblast1.21e-4359
promonocyte1.21e-4359
myeloid cell6.64e-35108
common myeloid progenitor6.64e-35108
leukocyte2.79e-33136
stuff accumulating cell2.02e-3287
hematopoietic lineage restricted progenitor cell1.67e-30120
nongranular leukocyte8.02e-26115
hematopoietic stem cell3.32e-25168
angioblastic mesenchymal cell3.32e-25168
hematopoietic cell5.93e-25177
hematopoietic oligopotent progenitor cell1.47e-23161
hematopoietic multipotent progenitor cell1.47e-23161
mesenchymal cell2.21e-12354
connective tissue cell6.08e-12361
motile cell2.12e-10386
CD1a-positive Langerhans cell3.44e-092
immature CD1a-positive Langerhans cell3.44e-092
stem cell1.31e-08441
multi fate stem cell1.61e-08427
somatic stem cell2.92e-08433
histamine secreting cell2.51e-075
biogenic amine secreting cell2.51e-075
granulocytopoietic cell2.51e-075
mast cell2.51e-075
mast cell progenitor2.51e-075
basophil mast progenitor cell2.51e-075
intermediate monocyte6.48e-079
CD14-positive, CD16-positive monocyte6.48e-079
Uber Anatomy
Ontology termp-valuen
bone marrow8.30e-4776
hematopoietic system3.01e-4498
blood island3.01e-4498
bone element8.13e-4382
hemolymphoid system2.35e-39108
immune system3.23e-3993
skeletal element2.58e-3890
skeletal system1.08e-33100
lateral plate mesoderm8.20e-22203
musculoskeletal system5.75e-17167
mesoderm1.69e-11315
mesoderm-derived structure1.69e-11315
presumptive mesoderm1.69e-11315
connective tissue2.41e-11371


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)

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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
ETS1#211353.242920307400780.01423577153489910.0499334926392386
NFKB1#479072.561096264623790.01087525921132490.0401031423194533
REST#597863.860011486451210.002701935648322920.014863705934959
STAT3#677453.506488332384750.01031183554589070.0383013654092497



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.