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Coexpression cluster:C187: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0002504!antigen processing and presentation of peptide or polysaccharide antigen via MHC class II!3.33465469112867e-15!3117;3113;3127;3115;3122;3108;3119$GO:0042613!MHC class II protein complex!7.24859124767789e-15!3117;3113;3127;3115;3122;3108;3119$GO:0019882!antigen processing and presentation!2.10238166781827e-14!3117;3113;3127;3115;3122;3108;972;3119$GO:0042611!MHC protein complex!4.28799775432895e-12!3117;3113;3127;3115;3122;3108;3119$GO:0006955!immune response!5.98637520332393e-11!3117;3113;3127;3115;3122;3108;972;3119$GO:0002376!immune system process!1.70644799795459e-10!3117;3113;3127;3115;3122;3108;972;3119$GO:0044459!plasma membrane part!9.03430251421799e-07!3117;3113;3127;3115;3122;3108;3119$GO:0043234!protein complex!3.96528655498425e-06!3117;3113;3127;3115;3122;3108;3119$GO:0005886!plasma membrane!2.44804717330264e-05!3117;3113;3127;3115;3122;3108;3119$GO:0032991!macromolecular complex!2.48418984192689e-05!3117;3113;3127;3115;3122;3108;3119$GO:0016021!integral to membrane!2.68591686971208e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0031224!intrinsic to membrane!2.68591686971208e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0044425!membrane part!7.19850934887258e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0032395!MHC class II receptor activity!7.19850934887258e-05!3113;3122$GO:0016020!membrane!0.000415486121188224!3117;3113;3127;3115;3122;3108;972;3119$GO:0042289!MHC class II protein binding!0.00688692842383888!972$GO:0043030!regulation of macrophage activation!0.00688692842383888!972$GO:0005764!lysosome!0.00688692842383888!3122;3108$GO:0000323!lytic vacuole!0.00688692842383888!3122;3108$GO:0005773!vacuole!0.00867876218897856!3122;3108$GO:0045058!T cell selection!0.0130909043296571!972$GO:0042116!macrophage activation!0.0130909043296571!972$GO:0046457!prostanoid biosynthetic process!0.0133319549255772!972$GO:0001516!prostaglandin biosynthetic process!0.0133319549255772!972$GO:0006693!prostaglandin metabolic process!0.0209058329785795!972$GO:0006692!prostanoid metabolic process!0.0209058329785795!972$GO:0019883!antigen processing and presentation of endogenous antigen!0.0213135556485108!972$GO:0042287!MHC protein binding!0.0262478235200968!972$GO:0002274!myeloid leukocyte activation!0.0297379024138541!972$GO:0031902!late endosome membrane!0.0308696602270396!3108$GO:0046456!icosanoid biosynthetic process!0.033980396421052!972$GO:0030217!T cell differentiation!0.0408650733729104!972$GO:0006690!icosanoid metabolic process!0.0447742305917279!972$GO:0005765!lysosomal membrane!0.0447742305917279!3108$GO:0016064!immunoglobulin mediated immune response!0.0447742305917279!972$GO:0005770!late endosome!0.0447742305917279!3108$GO:0019724!B cell mediated immunity!0.0447742305917279!972
|gostat_on_coexpression_clusters=GO:0002504!antigen processing and presentation of peptide or polysaccharide antigen via MHC class II!3.33465469112867e-15!3117;3113;3127;3115;3122;3108;3119$GO:0042613!MHC class II protein complex!7.24859124767789e-15!3117;3113;3127;3115;3122;3108;3119$GO:0019882!antigen processing and presentation!2.10238166781827e-14!3117;3113;3127;3115;3122;3108;972;3119$GO:0042611!MHC protein complex!4.28799775432895e-12!3117;3113;3127;3115;3122;3108;3119$GO:0006955!immune response!5.98637520332393e-11!3117;3113;3127;3115;3122;3108;972;3119$GO:0002376!immune system process!1.70644799795459e-10!3117;3113;3127;3115;3122;3108;972;3119$GO:0044459!plasma membrane part!9.03430251421799e-07!3117;3113;3127;3115;3122;3108;3119$GO:0043234!protein complex!3.96528655498425e-06!3117;3113;3127;3115;3122;3108;3119$GO:0005886!plasma membrane!2.44804717330264e-05!3117;3113;3127;3115;3122;3108;3119$GO:0032991!macromolecular complex!2.48418984192689e-05!3117;3113;3127;3115;3122;3108;3119$GO:0016021!integral to membrane!2.68591686971208e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0031224!intrinsic to membrane!2.68591686971208e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0044425!membrane part!7.19850934887258e-05!3117;3113;3127;3115;3122;3108;972;3119$GO:0032395!MHC class II receptor activity!7.19850934887258e-05!3113;3122$GO:0016020!membrane!0.000415486121188224!3117;3113;3127;3115;3122;3108;972;3119$GO:0042289!MHC class II protein binding!0.00688692842383888!972$GO:0043030!regulation of macrophage activation!0.00688692842383888!972$GO:0005764!lysosome!0.00688692842383888!3122;3108$GO:0000323!lytic vacuole!0.00688692842383888!3122;3108$GO:0005773!vacuole!0.00867876218897856!3122;3108$GO:0045058!T cell selection!0.0130909043296571!972$GO:0042116!macrophage activation!0.0130909043296571!972$GO:0046457!prostanoid biosynthetic process!0.0133319549255772!972$GO:0001516!prostaglandin biosynthetic process!0.0133319549255772!972$GO:0006693!prostaglandin metabolic process!0.0209058329785795!972$GO:0006692!prostanoid metabolic process!0.0209058329785795!972$GO:0019883!antigen processing and presentation of endogenous antigen!0.0213135556485108!972$GO:0042287!MHC protein binding!0.0262478235200968!972$GO:0002274!myeloid leukocyte activation!0.0297379024138541!972$GO:0031902!late endosome membrane!0.0308696602270396!3108$GO:0046456!icosanoid biosynthetic process!0.033980396421052!972$GO:0030217!T cell differentiation!0.0408650733729104!972$GO:0006690!icosanoid metabolic process!0.0447742305917279!972$GO:0005765!lysosomal membrane!0.0447742305917279!3108$GO:0016064!immunoglobulin mediated immune response!0.0447742305917279!972$GO:0005770!late endosome!0.0447742305917279!3108$GO:0019724!B cell mediated immunity!0.0447742305917279!972
|id=C187
|id=C187
|ontology_enrichment_celltype=CL:0000738!9.41e-51!140;CL:0000037!2.03e-45!172;CL:0000566!2.03e-45!172;CL:0002087!1.47e-44!119;CL:0000988!3.90e-43!182;CL:0002031!6.98e-43!124;CL:0002032!9.99e-43!165;CL:0000837!9.99e-43!165;CL:0002009!7.52e-29!65;CL:0000766!9.86e-29!76;CL:0000557!3.63e-28!71;CL:0002194!1.81e-27!63;CL:0000576!1.81e-27!63;CL:0000040!1.81e-27!63;CL:0000559!1.81e-27!63;CL:0000839!4.60e-26!70;CL:0000763!7.18e-26!112;CL:0000049!7.18e-26!112;CL:0002057!1.56e-25!42;CL:0000860!1.01e-21!45;CL:0000542!4.16e-15!53;CL:0000051!4.16e-15!53;CL:0000838!1.05e-14!52;CL:0000945!6.87e-13!24;CL:0000826!6.87e-13!24;CL:0000236!5.97e-09!14;CL:0000451!2.12e-08!10;CL:0000990!1.57e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.39e-35!102;UBERON:0003061!1.39e-35!102;UBERON:0002193!4.65e-32!112;UBERON:0007023!1.10e-28!115;UBERON:0002371!1.92e-26!80;UBERON:0002405!3.04e-23!115;UBERON:0001474!9.18e-21!86;UBERON:0004765!5.56e-15!101;UBERON:0001434!5.56e-15!101;UBERON:0001049!1.34e-08!57;UBERON:0005068!1.34e-08!57;UBERON:0006241!1.34e-08!57;UBERON:0007135!1.34e-08!57;UBERON:0000178!2.42e-07!15;UBERON:0000179!2.42e-07!15;UBERON:0000463!2.42e-07!15
}}
}}

Revision as of 14:17, 21 May 2012


Full id: C187_migratory_immature_Dendritic_CD19_CD14_Monocytederived_Macrophage



Phase1 CAGE Peaks

Hg19::chr10:64638741..64638750,-p@chr10:64638741..64638750
-
Hg19::chr19:36233332..36233360,-p1@IGFLR1
Hg19::chr3:115292801..115292805,+p@chr3:115292801..115292805
+
Hg19::chr5:149781290..149781299,+p@chr5:149781290..149781299
+
Hg19::chr5:149781314..149781325,+p@chr5:149781314..149781325
+
Hg19::chr5:149781351..149781369,-p@chr5:149781351..149781369
-
Hg19::chr5:149781430..149781445,+p@chr5:149781430..149781445
+
Hg19::chr5:149781437..149781469,-p@chr5:149781437..149781469
-
Hg19::chr5:149781469..149781549,+p@chr5:149781469..149781549
+
Hg19::chr5:149781540..149781551,-p@chr5:149781540..149781551
-
Hg19::chr5:149781552..149781565,-p@chr5:149781552..149781565
-
Hg19::chr5:149781568..149781579,+p@chr5:149781568..149781579
+
Hg19::chr5:149781573..149781585,-p@chr5:149781573..149781585
-
Hg19::chr5:149781608..149781658,+p3@CU676295
Hg19::chr5:149781661..149781703,+p2@CU676295
Hg19::chr5:149781710..149781737,-p@chr5:149781710..149781737
-
Hg19::chr5:149781713..149781789,+p1@CU676295
Hg19::chr5:149781783..149781794,-p@chr5:149781783..149781794
-
Hg19::chr5:149781813..149781820,-p@chr5:149781813..149781820
-
Hg19::chr5:149782124..149782163,+p4@CU676295
Hg19::chr5:149782153..149782196,-p@chr5:149782153..149782196
-
Hg19::chr5:149782716..149782733,-p6@CD74
Hg19::chr5:149782735..149782776,-p4@CD74
Hg19::chr5:149782779..149782826,-p3@CD74
Hg19::chr5:149782838..149782866,-p5@CD74
Hg19::chr5:149784249..149784283,+p@chr5:149784249..149784283
+
Hg19::chr5:149784263..149784302,-p@chr5:149784263..149784302
-
Hg19::chr5:149784286..149784311,+p@chr5:149784286..149784311
+
Hg19::chr5:149784308..149784339,-p@chr5:149784308..149784339
-
Hg19::chr5:149784637..149784692,+p@chr5:149784637..149784692
+
Hg19::chr5:149784680..149784743,-p@chr5:149784680..149784743
-
Hg19::chr5:149784695..149784700,+p@chr5:149784695..149784700
+
Hg19::chr5:149784705..149784710,+p@chr5:149784705..149784710
+
Hg19::chr5:149785822..149785851,+p@chr5:149785822..149785851
+
Hg19::chr5:149785846..149785897,-p2@CD74
Hg19::chr5:149786466..149786530,-p@chr5:149786466..149786530
-
Hg19::chr5:149786708..149786792,+p@chr5:149786708..149786792
+
Hg19::chr5:149786736..149786745,-p@chr5:149786736..149786745
-
Hg19::chr5:149786751..149786792,-p@chr5:149786751..149786792
-
Hg19::chr5:149786795..149786900,-p@chr5:149786795..149786900
-
Hg19::chr5:149786798..149786817,+p@chr5:149786798..149786817
+
Hg19::chr5:149786845..149786858,+p@chr5:149786845..149786858
+
Hg19::chr5:149792306..149792326,-p1@CD74
Hg19::chr6:32407643..32407695,+p1@HLA-DRA
Hg19::chr6:32410239..32410261,+p3@HLA-DRA
Hg19::chr6:32410269..32410308,+p5@HLA-DRA
Hg19::chr6:32410343..32410407,+p2@HLA-DRA
Hg19::chr6:32410411..32410447,+p6@HLA-DRA
Hg19::chr6:32410996..32411064,+p4@HLA-DQA1
Hg19::chr6:32411003..32411021,-p@chr6:32411003..32411021
-
Hg19::chr6:32411062..32411086,-p@chr6:32411062..32411086
-
Hg19::chr6:32411123..32411172,+p3@HLA-DQA1
Hg19::chr6:32411178..32411194,+p6@HLA-DQA1
Hg19::chr6:32411190..32411212,-p@chr6:32411190..32411212
-
Hg19::chr6:32411208..32411220,+p10@HLA-DQA1
Hg19::chr6:32411527..32411547,+p4@HLA-DRA
Hg19::chr6:32411668..32411693,-p1@CU687129
Hg19::chr6:32412417..32412458,+p@chr6:32412417..32412458
+
Hg19::chr6:32412534..32412660,+p@chr6:32412534..32412660
+
Hg19::chr6:32498046..32498073,-p1@HLA-DRB5
Hg19::chr6:32557564..32557604,-p1@HLA-DRB1
p2@HLA-DRB5
Hg19::chr6:32557610..32557630,-p2@HLA-DRB1
Hg19::chr6:32610723..32610733,+p11@HLA-DQA1
Hg19::chr6:32628018..32628030,-p@chr6:32628018..32628030
-
Hg19::chr6:32629150..32629194,-p@chr6:32629150..32629194
-
Hg19::chr6:32632683..32632724,-p2@HLA-DQB1
Hg19::chr6:32634425..32634479,-p1@HLA-DQB1
Hg19::chr6:32920794..32920890,-p1@HLA-DMA
Hg19::chr6:33033006..33033048,-p@chr6:33033006..33033048
-
Hg19::chr6:33033060..33033133,-p@chr6:33033060..33033133
-
Hg19::chr6:33036431..33036464,-p@chr6:33036431..33036464
-
Hg19::chr6:33036485..33036527,-p@chr6:33036485..33036527
-
Hg19::chr6:33036570..33036581,-p@chr6:33036570..33036581
-
Hg19::chr6:33036819..33036830,-p@chr6:33036819..33036830
-
Hg19::chr6:33036843..33036862,-p@chr6:33036843..33036862
-
Hg19::chr6:33036862..33036892,+p@chr6:33036862..33036892
+
Hg19::chr6:33036875..33036943,-p@chr6:33036875..33036943
-
Hg19::chr6:33036897..33036925,+p@chr6:33036897..33036925
+
Hg19::chr6:33036947..33036959,-p@chr6:33036947..33036959
-
Hg19::chr6:33036979..33037004,-p@chr6:33036979..33037004
-
Hg19::chr6:33037019..33037047,-p5@HLA-DPA1
Hg19::chr6:33037413..33037424,+p@chr6:33037413..33037424
+
Hg19::chr6:33037447..33037514,-p3@HLA-DPA1
Hg19::chr6:33037520..33037535,-p8@HLA-DPA1
Hg19::chr6:33037580..33037614,-p@chr6:33037580..33037614
-
Hg19::chr6:33037634..33037668,-p@chr6:33037634..33037668
-
Hg19::chr6:33041386..33041439,-p1@HLA-DPA1
Hg19::chr6:33043729..33043782,+p1@HLA-DPB1
Hg19::chr6:33052940..33052953,+p@chr6:33052940..33052953
+
Hg19::chr6:33053612..33053625,+p3@S66883
Hg19::chr6:33053627..33053641,+p1@S66883


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:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II3.33465469112867e-15
GO:0042613MHC class II protein complex7.24859124767789e-15
GO:0019882antigen processing and presentation2.10238166781827e-14
GO:0042611MHC protein complex4.28799775432895e-12
GO:0006955immune response5.98637520332393e-11
GO:0002376immune system process1.70644799795459e-10
GO:0044459plasma membrane part9.03430251421799e-07
GO:0043234protein complex3.96528655498425e-06
GO:0005886plasma membrane2.44804717330264e-05
GO:0032991macromolecular complex2.48418984192689e-05
GO:0016021integral to membrane2.68591686971208e-05
GO:0031224intrinsic to membrane2.68591686971208e-05
GO:0044425membrane part7.19850934887258e-05
GO:0032395MHC class II receptor activity7.19850934887258e-05
GO:0016020membrane0.000415486121188224
GO:0042289MHC class II protein binding0.00688692842383888
GO:0043030regulation of macrophage activation0.00688692842383888
GO:0005764lysosome0.00688692842383888
GO:0000323lytic vacuole0.00688692842383888
GO:0005773vacuole0.00867876218897856
GO:0045058T cell selection0.0130909043296571
GO:0042116macrophage activation0.0130909043296571
GO:0046457prostanoid biosynthetic process0.0133319549255772
GO:0001516prostaglandin biosynthetic process0.0133319549255772
GO:0006693prostaglandin metabolic process0.0209058329785795
GO:0006692prostanoid metabolic process0.0209058329785795
GO:0019883antigen processing and presentation of endogenous antigen0.0213135556485108
GO:0042287MHC protein binding0.0262478235200968
GO:0002274myeloid leukocyte activation0.0297379024138541
GO:0031902late endosome membrane0.0308696602270396
GO:0046456icosanoid biosynthetic process0.033980396421052
GO:0030217T cell differentiation0.0408650733729104
GO:0006690icosanoid metabolic process0.0447742305917279
GO:0005765lysosomal membrane0.0447742305917279
GO:0016064immunoglobulin mediated immune response0.0447742305917279
GO:0005770late endosome0.0447742305917279
GO:0019724B cell mediated immunity0.0447742305917279



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
leukocyte9.41e-51140
hematopoietic stem cell2.03e-45172
angioblastic mesenchymal cell2.03e-45172
nongranular leukocyte1.47e-44119
hematopoietic cell3.90e-43182
hematopoietic lineage restricted progenitor cell6.98e-43124
hematopoietic oligopotent progenitor cell9.99e-43165
hematopoietic multipotent progenitor cell9.99e-43165
macrophage dendritic cell progenitor7.52e-2965
myeloid leukocyte9.86e-2976
granulocyte monocyte progenitor cell3.63e-2871
monopoietic cell1.81e-2763
monocyte1.81e-2763
monoblast1.81e-2763
promonocyte1.81e-2763
myeloid lineage restricted progenitor cell4.60e-2670
myeloid cell7.18e-26112
common myeloid progenitor7.18e-26112
CD14-positive, CD16-negative classical monocyte1.56e-2542
classical monocyte1.01e-2145
lymphocyte4.16e-1553
common lymphoid progenitor4.16e-1553
lymphoid lineage restricted progenitor cell1.05e-1452
lymphocyte of B lineage6.87e-1324
pro-B cell6.87e-1324
B cell5.97e-0914
dendritic cell2.12e-0810
conventional dendritic cell1.57e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.39e-35102
blood island1.39e-35102
hemolymphoid system4.65e-32112
adult organism1.10e-28115
bone marrow1.92e-2680
immune system3.04e-23115
bone element9.18e-2186
skeletal element5.56e-15101
skeletal system5.56e-15101
neural tube1.34e-0857
neural rod1.34e-0857
future spinal cord1.34e-0857
neural keel1.34e-0857
blood2.42e-0715
haemolymphatic fluid2.42e-0715
organism substance2.42e-0715


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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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