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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.776952972030492,0.518905469136572,0.72712233114462,0,0,0,0,0,0.111800154394222,0.815574699308565,0.735276999989378,0.6726899818394,1.35210309338665,1.21871653647988,1.33457528453892,0.967908160688305,0.892192975194883,0.930444992668081,0.834725772851795,0.742162993860838,0.761401209865638,0.770172115772911,0.749031964901489,0.854217228737854,0.857659436487552,0.659186452081371,0.80733606370589,0.834771083467235,0.72969100428824,0.862861999649598,0.852582324259177,0.739810103370759,0.82956325105582,0.880616434307977,0.791413783873003,0.81563895409467,0.694265001065248,0.535990962209249,0.578755589589983,0.779955127021461,0.713647041291335,0.836583526449418,0.665805773168088,0.637863970433687,0.619575784459513,1.12917609936319,1.1233586254668,1.07562905231337,0.99940419511744,1.01329941191205,1.07661641284753,1.14068315436931,1.16215602703472,1.12183872407324,0,0,0,0.267983322146663,0,0,0.220381364985783,0,0,0.0135324669484714,0,0,0.193266156112807,0.148252655902006,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.120101680109954,0,0,0.243751094557381,0.141123485815535,0.352048786074314,0.30370957478378,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267491812392555,0,0,0.768505714093136,0.714255445029934,0.972033880367631,0.16937498165142,0.331222719243351,0.13718235424895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.560577092055277,0.19786780858233,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.201612826790636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.20464183676031,1.01738914588136,0.976440600452727,0,0,0,0,0,0,0,0,0.0443803983898163,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.11933436092095,1.2059540588537,1.07316363586263,0,0,0,0,0,0,0,0.144281939746476,0,0.099226801963929,0,0,0,0.0672629396841865,0,0.601628533058228,0.601148601595643,0.591165774058572,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.67410983851669,0.72931253298207,0.538414592711266,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.369129203568351,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11721277736131,0,0,0,0,0,0,0,0,0,0,0,0,0.347109281048989,0,0,0,0,0.65821496763222,0.608370775349503,0.697885547997245,0.708293165212344,0.694519700703913,0.627608190431052,0.662401050257142,0.620396418749604,0,0,0,0,0,0,0,0,0.194437309258732,0.0833856393724342,0,0,0.163301352154438,0,0,0,0,0.147243178344539,0.357465767743922,0.128239398490303,0.116355582210209,0.127816056190673,0.125057592200758,0.200348167154155,0,0,0,0,0,0,0.504827216846555,0,0,0,0,0,0,0,0.327431548746431,0,0,0,0.254546132326747,0.36259776015009,0,0,0,0,0,0,0.179428944922886,0.201904988352547,0.582628905519565,0,0,0.166841122776361,0,0,0,0.239000368732729,0,0,0,0,0,0,0,0.236431101238142,0,0.0455495587624001,0,0.0861409897892114,0,0,0.187140351923826,0,0,0,0,0.0677777952777681,0,0.185552006688486,0,0.0633259478784096,0.0667773874189013,0,0,0,0,0,0,0,0,0,0,0.232401536920605,0.207103666835013,0,0,0,0.31773292160509,0.255893981334376,0.166882495138135,0,0,0,0.0377343413032156,0.294527884877003,0,0.539612561015965,0,0,0,0,0,0,0,0,0,0,0,0.346956396082,0,0,0,0,0.142375719277435,0,0.161955095312168,0,0,0.119438670232611,0,0,0.214938901586878,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0.387476440244109,0,0,0,0.192724864233909,0.163853084473343,0.121555690749196,0.0930171097487756,0.111490326439272,0.160271272478474,0.125779594255495,0,0,0,0,0,0,0,0,0.290796484255617,0,0,0,0.223994502679913,0.0800430695798856,0.134972693361015,0,0.210378881857923,0.101153272350709,0,0,0,0.385497356176373,0.220655051407841,0,0,0,0,0,0,0,0,0.238738706742733,0,0.190945407067727,0.253676102438086,0,0,0.465705987031086,0.211872352186983,0.63487132620824,0.541682826933118,0,0,0,0,0,0,0,0,0,0.0948387187168004,0.211108429329865,0.196841684047034,0.387759472510953,0.299625487216171,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.227817127229447,0,0,0,0,0,0,0,0.0850782273463656,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.161249551184946,0,0.291769023891927,0.0810289837637627,0,0.0818769814509043,0.171558826597626,0,0,0,0,0,0,0,0,0.224505340200385,0,0,0,0,0,0.10385512828298,0,0.209531203640986,0.119611842060913,0,0,0.214784093242143,0,0,0,0.223383639238987,0,0.162959805635483,0.298732586424532,0,0,0.213608164853801,0.101434673044707,0,0,0.270311689669048,0.118671766513265,0,0.181785787527008,0,0,0.268979913061351,0,0,0,0,0,0,0,0.155405081403798,0,0,0.153323010348428,0,0,0,0,0,0,0,0.081104385612865,0,0.171934336795599,0,0,0,0,0,0,0.210673317927481,0.202519250627827,0,0.173272723322218,0,0.297003355453999,0.528450187475503,0.15309981666883,0,0.571188487081195,0.504004128008427,0,0,0,0,0,0.163974701329705,0.367522214145108,0,0.169068829801421,0,0.184415109078388,0,0,0,0,0,0,0,0,0,0,0.225828130386425,0.05440766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|full_id=C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral
|full_id=C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral
|gostat_on_coexpression_clusters=GO:0006952!defense response!0.000349565744672719!4688;4048;1536;929;6280;10871$GO:0006954!inflammatory response!0.00448776427999258!4048;1536;929;6280$GO:0009611!response to wounding!0.0127504247667843!4048;1536;929;6280$GO:0009605!response to external stimulus!0.0246489756269869!4048;1536;929;6280$GO:0045113!regulation of integrin biosynthetic process!0.0246489756269869!6280$GO:0004218!cathepsin S activity!0.0246489756269869!1520$GO:0008747!N-acetylneuraminate lyase activity!0.0246489756269869!80896$GO:0045112!integrin biosynthetic process!0.0246489756269869!6280$GO:0006950!response to stress!0.026619015725701!23678;4048;1536;929;6280$GO:0006968!cellular defense response!0.0289096751976543!4688;10871$GO:0005011!macrophage colony stimulating factor receptor activity!0.0358425014391679!1436
|gostat_on_coexpression_clusters=GO:0006952!defense response!0.000349565744672719!4688;4048;1536;929;6280;10871$GO:0006954!inflammatory response!0.00448776427999258!4048;1536;929;6280$GO:0009611!response to wounding!0.0127504247667843!4048;1536;929;6280$GO:0009605!response to external stimulus!0.0246489756269869!4048;1536;929;6280$GO:0045113!regulation of integrin biosynthetic process!0.0246489756269869!6280$GO:0004218!cathepsin S activity!0.0246489756269869!1520$GO:0008747!N-acetylneuraminate lyase activity!0.0246489756269869!80896$GO:0045112!integrin biosynthetic process!0.0246489756269869!6280$GO:0006950!response to stress!0.026619015725701!23678;4048;1536;929;6280$GO:0006968!cellular defense response!0.0289096751976543!4688;10871$GO:0005011!macrophage colony stimulating factor receptor activity!0.0358425014391679!1436

Revision as of 15:45, 12 September 2012


Full id: C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:117059709..117059733,+p11@SIDT2
Hg19::chr11:59950486..59950515,-p2@MS4A6A
Hg19::chr11:59950519..59950605,-p1@MS4A6A
Hg19::chr11:72433267..72433292,-p4@ARAP1
Hg19::chr11:72433293..72433345,-p3@ARAP1
Hg19::chr12:111127201..111127221,-p3@HVCN1
Hg19::chr12:96429349..96429381,-p1@LTA4H
Hg19::chr14:103587794..103587823,+p@chr14:103587794..103587823
+
Hg19::chr16:50308028..50308093,+p2@ADCY7
Hg19::chr17:29248896..29248906,+p5@ADAP2
Hg19::chr17:29248918..29248949,+p2@ADAP2
Hg19::chr17:29248955..29248978,+p1@ADAP2
Hg19::chr17:72542265..72542277,-p4@CD300C
Hg19::chr17:7462261..7462266,+p13@TNFSF13
Hg19::chr17:7462268..7462279,+p7@TNFSF13
Hg19::chr17:7462297..7462342,+p1@TNFSF13
Hg19::chr1:150738211..150738260,-p1@CTSS
Hg19::chr1:153330728..153330829,+p2@S100A9
Hg19::chr1:182758900..182758918,+p1@NPL
Hg19::chr1:182767386..182767390,+p@chr1:182767386..182767390
+
Hg19::chr1:183559693..183559704,-p5@NCF2
Hg19::chr20:1517945..1517963,-p@chr20:1517945..1517963
-
Hg19::chr22:17700260..17700331,-p1@CECR1
Hg19::chr2:68962023..68962095,+p5@ARHGAP25
Hg19::chr2:68962229..68962279,+p6@ARHGAP25
Hg19::chr2:74782818..74782845,-p3@LOXL3
Hg19::chr5:140012392..140012432,-p5@CD14
Hg19::chr5:140013191..140013202,-p10@CD14
Hg19::chr5:140013224..140013235,-p12@CD14
Hg19::chr5:140013241..140013270,-p3@CD14
Hg19::chr5:140013275..140013296,-p4@CD14
Hg19::chr5:149466042..149466143,-p1@CSF1R
Hg19::chr5:180230830..180230903,-p2@MGAT1
Hg19::chr5:39274617..39274636,-p7@FYB
Hg19::chr5:39274655..39274666,-p12@FYB
Hg19::chr6:25452404..25452424,-p@chr6:25452404..25452424
-
Hg19::chr7:157647472..157647497,+p1@ENST00000443338
Hg19::chr8:67624963..67625045,+p3@SGK3
Hg19::chr9:115983523..115983565,-p1@FKBP15
Hg19::chrX:37639279..37639290,+p2@CYBB
Hg19::chrX:80457922..80457946,+p4@SH3BGRL
Hg19::chrX:80457962..80457977,+p6@SH3BGRL
Hg19::chrX:80458001..80458016,+p8@SH3BGRL


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


p.valueFDRnGenesnPathwayName
8.37369675774424e-060.00530055004765214156Phagosome (KEGG):04145



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:0006952defense response0.000349565744672719
GO:0006954inflammatory response0.00448776427999258
GO:0009611response to wounding0.0127504247667843
GO:0009605response to external stimulus0.0246489756269869
GO:0045113regulation of integrin biosynthetic process0.0246489756269869
GO:0004218cathepsin S activity0.0246489756269869
GO:0008747N-acetylneuraminate lyase activity0.0246489756269869
GO:0045112integrin biosynthetic process0.0246489756269869
GO:0006950response to stress0.026619015725701
GO:0006968cellular defense response0.0289096751976543
GO:0005011macrophage colony stimulating factor receptor activity0.0358425014391679



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
hematopoietic stem cell4.12e-47172
angioblastic mesenchymal cell4.12e-47172
leukocyte1.19e-44140
hematopoietic oligopotent progenitor cell7.08e-44165
hematopoietic multipotent progenitor cell7.08e-44165
hematopoietic cell1.10e-41182
nongranular leukocyte5.14e-37119
hematopoietic lineage restricted progenitor cell1.12e-36124
myeloid cell8.42e-35112
common myeloid progenitor8.42e-35112
myeloid leukocyte2.87e-3376
granulocyte monocyte progenitor cell3.66e-3071
macrophage dendritic cell progenitor1.20e-2965
monopoietic cell8.86e-2963
monocyte8.86e-2963
monoblast8.86e-2963
promonocyte8.86e-2963
myeloid lineage restricted progenitor cell9.34e-2970
CD14-positive, CD16-negative classical monocyte5.80e-2742
classical monocyte1.31e-2245
lymphocyte1.44e-0853
common lymphoid progenitor1.44e-0853
lymphoid lineage restricted progenitor cell1.86e-0852
intermediate monocyte3.48e-079
CD14-positive, CD16-positive monocyte3.48e-079
Uber Anatomy
Ontology termp-valuen
adult organism4.00e-34115
hematopoietic system3.23e-32102
blood island3.23e-32102
hemolymphoid system3.02e-31112
bone marrow4.05e-2580
bone element6.53e-2186
immune system7.81e-20115
skeletal element2.58e-15101
skeletal system2.58e-15101
lateral plate mesoderm2.70e-09216
neural tube1.48e-0857
neural rod1.48e-0857
future spinal cord1.48e-0857
neural keel1.48e-0857
anterior neural tube1.26e-0742
regional part of forebrain2.72e-0741
forebrain2.72e-0741
future forebrain2.72e-0741


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
SPI1#6688193.625166201440271.80912235243461e-079.89748189449547e-06



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