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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.248727840994713,0,0,0,0,0,0,0,0,0,0,0,0,1.06025229517666,0.942229228655151,0.976836602907396,0,0,0,0,0,0.139179090293218,1.22367037375877,1.24726419402701,1.21515715012423,1.36798233971145,1.35416439735351,1.30758026990212,1.21932921978764,1.14673645762448,1.06121604160114,1.34415968979485,1.18155969116215,1.16369703800109,1.15938034114582,1.05842023940724,1.14432406156028,1.24901076646045,1.13015366299977,1.14293555507175,1.36080885211102,1.18821669116545,1.25928539158211,1.31025913338281,1.17156418039074,1.09186843533675,1.08494119123915,1.06174720106472,1.06261454667729,1.38562154980708,1.29493915079461,1.33393541105045,1.04761985013103,1.15505141826125,1.1674489046467,1.40291566959197,1.33859917120276,1.30987534129132,1.05162768592999,1.14607363624535,1.18596148583251,1.21194167583424,1.28207578245601,1.26788047003288,0.916575055300877,0.690428265375538,0.843997746667234,0,0.238731797192202,0.074105787380289,0.45596771769825,0.0192329816597939,0.149967188415809,0.283458384258396,0,0.100978382569579,0.152475118137746,0.204945575431157,0,0.785242073431206,0.164735009754065,0.0366474972054856,0.0079085117257726,0.164941055534382,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0063769831534802,0,0,0.322890042474855,0,0,0.355666420318302,0.172196593167638,0.527694066305552,0.237596080817648,0.32495565208795,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0731709495695972,0.410220460375151,0,0,0.108622809454255,0.182525697750157,0.388250512774096,0.472335240837601,0.57023707790068,0.322994277618242,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.08787575099926,1.32952827495809,0,0,0,0.0270016908376832,0,0.070839010769474,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0339828641605205,0,0,0,0,0,0,0,0.0141918373961481,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.274200894538017,0.676760175615988,0.426649117526349,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.4194291987984,1.21461606715306,1.37117982670489,0,0,0,0,0,0,0,0,0.092043539351297,0.288626950061093,0.143175990334464,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0206910107952029,1.15522827796208,1.32463890106678,1.27929297832981,0,0,0,0,0,0,0,0.451335742069982,0.0442626127348551,0.373118073837456,0,0,0,0.280462107394008,0,1.08837704376965,0.923173298305491,1.00247080672296,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.754618461004556,0.930128643656549,0.757127688958048,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.420276409876709,0,0,0,0,0,0,0,0,0,0,0,0.0177602205939906,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.042404359391321,0,0,0,0,0,0,0,0,0,0,0,0,0.317926967410818,0,0,0,0,0.846140175074807,0.655051218394962,0.907379333761318,0.807197045078307,0.736384424036253,0.906957416395616,0.80610459794518,0.759172502177101,0,0,0,0,0,0,0,0,0.069605543717038,0,0,0,0,0.0632131871850751,0,0,0.0323390519651663,0.0399160469324161,0.210820777883811,0.267362128877383,0,0.0960875985747307,0.0245030743117865,0.306825117910029,0,0,0,0,0,0,0.496120470253294,0,0,0,0,0.122131567484392,0,0.387590410836665,0.395455849234659,0,0,0,0.175943047488103,0.312192507520898,0.0347120504226252,0,0,0,0,0,0.153013477156965,0.219281259137526,0.761435998150065,0,0.404734288338377,0.467430133063252,0.238280904943946,0,0,0.296775433892522,0,0,0,0,0,0,0.275482132507796,0.455936477178152,0,0.196002000727301,0.254092386647658,0.292843712140281,0,0,0.144721755951626,0,0,0,0,0.151077815610547,0.0568543650084656,0.141370439456765,0,0,0,0,0,0,0,0,0,0,0,0,0.197281509986737,0.238465026927549,0.39086504245025,0,0,0,0.438625387898071,0.127946990667188,0.391574149461403,0,0,0,0,0.118294567417379,0.29005727509709,0.746677687726768,0,0,0,0,0,0,0,0,0,0,0,0.402727139569952,0,0,0,0,0.151770953725702,0,0.223183271817872,0,0,0.297555455378466,0,0,0.484745007280442,0,0,0,0,0,0,0,0,0,0,0,0.347098570925588,0.455887370817147,0.178725939705534,0,0,0.269941146227734,0.266338902590327,0.132272653643919,0.0962949168021401,0.163495432270445,0.190284825644413,0.175070887562828,0,0,0,0,0,0,0,0.254120022070344,0.420816193234704,0,0,0,0,0,0.26977361522305,0,0.235070931112409,0.390190345348797,0,0.030887658663257,0,0.394116535697646,0.331690461928726,0,0,0,0,0,0,0,0.081169921670872,0.372616129795822,0.448170512073699,0.272253485444549,0.320868789058773,0,0,0.506419149288721,0.218370041790589,0.575418819955984,0.782071792088998,0,0,0,0.201755094293259,0.0642980313197485,0.0590862349070791,0.109496760406267,0,0,0.199452405071302,0.397729128851654,0.196841684047034,0.404691763695498,0.453974363223077,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.347937100750116,0,0,0,0,0,0,0,0.258521977897285,0,0,0,0,0.140153322040224,0,0,0,0,0,0,0,0,0,0,0,0,0.054991283739851,0.398935648300557,0.175433220007505,0.280324279638997,0.0810289837637627,0.0976291981890722,0.308774396099199,0.310564687979339,0,0,0,0,0,0,0,0,0.197098745901308,0,0.109192591878289,0,0,0,0.396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|full_id=C803_Macrophage_CD14_Monocytederived_Eosinophils_Basophils_CD14CD16_Dendritic
|full_id=C803_Macrophage_CD14_Monocytederived_Eosinophils_Basophils_CD14CD16_Dendritic
|gostat_on_coexpression_clusters=GO:0009611!response to wounding!0.00259656563361436!1536;929;6916$GO:0009605!response to external stimulus!0.00432029297768241!1536;929;6916$GO:0004796!thromboxane-A synthase activity!0.0135397656327913!6916$GO:0006950!response to stress!0.0151692776269214!1536;929;6916$GO:0006954!inflammatory response!0.016921717954316!1536;929$GO:0016019!peptidoglycan receptor activity!0.016921717954316!929$GO:0042834!peptidoglycan binding!0.0203000847796423!929$GO:0046457!prostanoid biosynthetic process!0.0203000847796423!6916$GO:0002237!response to molecule of bacterial origin!0.0203000847796423!929$GO:0001516!prostaglandin biosynthetic process!0.0203000847796423!6916$GO:0008329!pattern recognition receptor activity!0.0221429395266416!929$GO:0005506!iron ion binding!0.0244276827821287!1536;6916$GO:0006693!prostaglandin metabolic process!0.0245847341859006!6916$GO:0006692!prostanoid metabolic process!0.0245847341859006!6916$GO:0044459!plasma membrane part!0.0245847341859006!1536;929;23312$GO:0006952!defense response!0.0245847341859006!1536;929$GO:0017137!Rab GTPase binding!0.0322090574849813!23312$GO:0006118!electron transport!0.0334093525836169!1536;6916$GO:0046456!icosanoid biosynthetic process!0.0352103301235468!6916$GO:0006909!phagocytosis!0.0415392895817162!929$GO:0045121!lipid raft!0.0421923624208418!929$GO:0016712!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen!0.0421923624208418!6916$GO:0006091!generation of precursor metabolites and energy!0.0421923624208418!1536;6916$GO:0006690!icosanoid metabolic process!0.0421923624208418!6916
|gostat_on_coexpression_clusters=GO:0009611!response to wounding!0.00259656563361436!1536;929;6916$GO:0009605!response to external stimulus!0.00432029297768241!1536;929;6916$GO:0004796!thromboxane-A synthase activity!0.0135397656327913!6916$GO:0006950!response to stress!0.0151692776269214!1536;929;6916$GO:0006954!inflammatory response!0.016921717954316!1536;929$GO:0016019!peptidoglycan receptor activity!0.016921717954316!929$GO:0042834!peptidoglycan binding!0.0203000847796423!929$GO:0046457!prostanoid biosynthetic process!0.0203000847796423!6916$GO:0002237!response to molecule of bacterial origin!0.0203000847796423!929$GO:0001516!prostaglandin biosynthetic process!0.0203000847796423!6916$GO:0008329!pattern recognition receptor activity!0.0221429395266416!929$GO:0005506!iron ion binding!0.0244276827821287!1536;6916$GO:0006693!prostaglandin metabolic process!0.0245847341859006!6916$GO:0006692!prostanoid metabolic process!0.0245847341859006!6916$GO:0044459!plasma membrane part!0.0245847341859006!1536;929;23312$GO:0006952!defense response!0.0245847341859006!1536;929$GO:0017137!Rab GTPase binding!0.0322090574849813!23312$GO:0006118!electron transport!0.0334093525836169!1536;6916$GO:0046456!icosanoid biosynthetic process!0.0352103301235468!6916$GO:0006909!phagocytosis!0.0415392895817162!929$GO:0045121!lipid raft!0.0421923624208418!929$GO:0016712!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen!0.0421923624208418!6916$GO:0006091!generation of precursor metabolites and energy!0.0421923624208418!1536;6916$GO:0006690!icosanoid metabolic process!0.0421923624208418!6916

Revision as of 18:32, 12 September 2012


Full id: C803_Macrophage_CD14_Monocytederived_Eosinophils_Basophils_CD14CD16_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:58980342..58980431,-p1@MPEG1
Hg19::chr13:51289225..51289244,-p@chr13:51289225..51289244
-
Hg19::chr14:103587774..103587784,+p@chr14:103587774..103587784
+
Hg19::chr15:51914996..51915035,-p2@DMXL2
Hg19::chr20:1472164..1472175,-p3@SIRPB2
Hg19::chr5:140012540..140012567,-p8@CD14
Hg19::chr5:140012752..140012768,-p1@CD14
Hg19::chr5:140012773..140012794,-p2@CD14
Hg19::chr7:139529007..139529038,+p3@TBXAS1
Hg19::chrX:37639302..37639326,+p1@CYBB


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:0009611response to wounding0.00259656563361436
GO:0009605response to external stimulus0.00432029297768241
GO:0004796thromboxane-A synthase activity0.0135397656327913
GO:0006950response to stress0.0151692776269214
GO:0006954inflammatory response0.016921717954316
GO:0016019peptidoglycan receptor activity0.016921717954316
GO:0042834peptidoglycan binding0.0203000847796423
GO:0046457prostanoid biosynthetic process0.0203000847796423
GO:0002237response to molecule of bacterial origin0.0203000847796423
GO:0001516prostaglandin biosynthetic process0.0203000847796423
GO:0008329pattern recognition receptor activity0.0221429395266416
GO:0005506iron ion binding0.0244276827821287
GO:0006693prostaglandin metabolic process0.0245847341859006
GO:0006692prostanoid metabolic process0.0245847341859006
GO:0044459plasma membrane part0.0245847341859006
GO:0006952defense response0.0245847341859006
GO:0017137Rab GTPase binding0.0322090574849813
GO:0006118electron transport0.0334093525836169
GO:0046456icosanoid biosynthetic process0.0352103301235468
GO:0006909phagocytosis0.0415392895817162
GO:0045121lipid raft0.0421923624208418
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0421923624208418
GO:0006091generation of precursor metabolites and energy0.0421923624208418
GO:0006690icosanoid metabolic process0.0421923624208418



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
leukocyte1.18e-33140
myeloid leukocyte4.25e-3376
hematopoietic stem cell2.97e-31172
angioblastic mesenchymal cell2.97e-31172
nongranular leukocyte4.57e-29119
granulocyte monocyte progenitor cell6.08e-2971
hematopoietic oligopotent progenitor cell7.04e-29165
hematopoietic multipotent progenitor cell7.04e-29165
macrophage dendritic cell progenitor1.88e-2865
hematopoietic lineage restricted progenitor cell2.38e-28124
myeloid lineage restricted progenitor cell3.60e-2870
monopoietic cell3.76e-2863
monocyte3.76e-2863
monoblast3.76e-2863
promonocyte3.76e-2863
hematopoietic cell2.07e-27182
CD14-positive, CD16-negative classical monocyte3.01e-2742
myeloid cell4.18e-26112
common myeloid progenitor4.18e-26112
classical monocyte8.61e-2445
mesenchymal cell7.26e-08358
connective tissue cell2.02e-07365
Uber Anatomy
Ontology termp-valuen
adult organism1.39e-37115
hematopoietic system1.78e-31102
blood island1.78e-31102
hemolymphoid system2.77e-29112
bone marrow6.70e-2580
immune system6.23e-24115
bone element5.16e-2186
skeletal element2.41e-16101
skeletal system2.41e-16101
neural tube4.87e-1157
neural rod4.87e-1157
future spinal cord4.87e-1157
neural keel4.87e-1157
lateral plate mesoderm5.34e-10216
anterior neural tube1.45e-0942
regional part of brain2.71e-0959
regional part of forebrain3.16e-0941
forebrain3.16e-0941
future forebrain3.16e-0941
tissue1.24e-08787
gray matter8.68e-0834
brain grey matter8.68e-0834
brain9.33e-0869
future brain9.33e-0869
telencephalon9.86e-0834
regional part of telencephalon1.66e-0733
musculoskeletal system2.15e-07167
connective tissue3.19e-07375
cerebral hemisphere5.13e-0732


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


No analysis results for this cluster

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.