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Coexpression cluster:C187

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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

p.valueFDRnGenesnPathwayName
5.94382887969353e-182.35152730052875e-168156Phagosome (KEGG):04145
1.93098502014593e-188.7308108410884e-178136Cell adhesion molecules (CAMs) (KEGG):04514
5.26434142643762e-242.05539956434154e-21978Antigen processing and presentation (KEGG):04612
2.34619914904252e-067.07211457782818e-05388Hematopoietic cell lineage (KEGG):04640
3.71045711134679e-223.91453225247086e-20849Intestinal immune network for IgA production (KEGG):04672
1.77370191667564e-222.24550662651136e-20845Type I diabetes mellitus (KEGG):04940
1.10513356590572e-206.99549547218323e-19873Leishmaniasis (KEGG):05140
1.60777920556184e-187.82864797785112e-178133Toxoplasmosis (KEGG):05145
1.16846740185803e-219.24549831720164e-20856Staphylococcus aureus infection (KEGG):05150
1.42563757096418e-208.20389620382114e-199182Tuberculosis (KEGG):05152
1.59233395404391e-175.9291023112341e-168176Influenza A (KEGG):05164
6.4941534418374e-242.05539956434154e-21831Asthma (KEGG):05310
8.5591783060609e-227.73994266819507e-20854Autoimmune thyroid disease (KEGG):05320
2.17679901415651e-189.18609183974046e-178138Systemic lupus erythematosus (KEGG):05322
7.6480321605904e-204.03433696471143e-18892Rheumatoid arthritis (KEGG):05323
5.06349289326769e-231.06839700047948e-20839Allograft rejection (KEGG):05330
1.19329207042133e-221.88838470144176e-20843Graft-versus-host disease (KEGG):05332
9.84053750225105e-216.9211780432499e-19872Viral myocarditis (KEGG):05416
2.22785252343004e-050.000641013930605097223Cytokines and Inflammatory Response (Wikipathways):WP530
1.97379666323609e-116.94118493238026e-107511Signaling in Immune system (Reactome):REACT_6900
7.87387450514271e-092.49208128087767e-07314{CD4,14} (Static Module):NA
6.46443797065419e-102.15367854496006e-086406{GRB2,414} (Static Module):NA



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
leukocyte1.88e-63136
nongranular leukocyte2.09e-63115
hematopoietic lineage restricted progenitor cell1.44e-56120
hematopoietic stem cell5.68e-54168
angioblastic mesenchymal cell5.68e-54168
hematopoietic cell2.95e-52177
hematopoietic oligopotent progenitor cell3.97e-50161
hematopoietic multipotent progenitor cell3.97e-50161
macrophage dendritic cell progenitor1.23e-4761
monopoietic cell1.99e-4559
monocyte1.99e-4559
monoblast1.99e-4559
promonocyte1.99e-4559
defensive cell4.56e-4548
phagocyte4.56e-4548
granulocyte monocyte progenitor cell3.92e-4167
classical monocyte3.04e-3942
CD14-positive, CD16-negative classical monocyte3.04e-3942
myeloid lineage restricted progenitor cell4.50e-3866
myeloid leukocyte2.94e-3772
myeloid cell3.11e-31108
common myeloid progenitor3.11e-31108
lymphocyte of B lineage7.09e-1924
pro-B cell7.09e-1924
lymphocyte1.46e-1653
common lymphoid progenitor1.46e-1653
lymphoid lineage restricted progenitor cell4.98e-1652
stuff accumulating cell9.05e-1687
nucleate cell1.86e-1555
B cell4.70e-1314
dendritic cell3.55e-1210
conventional dendritic cell8.25e-118
intermediate monocyte5.68e-099
CD14-positive, CD16-positive monocyte5.68e-099
mesenchymal cell2.13e-08354
immature conventional dendritic cell1.15e-075
common dendritic progenitor1.15e-075
connective tissue cell1.19e-07361
macrophage4.23e-076
Langerhans cell7.15e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.94e-5198
blood island4.94e-5198
hemolymphoid system3.00e-46108
bone marrow4.30e-3876
immune system2.80e-3693
bone element1.89e-3382
skeletal element2.81e-2890
adult organism1.16e-27114
skeletal system7.94e-24100
lateral plate mesoderm4.90e-16203
blood1.17e-1015
haemolymphatic fluid1.17e-1015
organism substance1.17e-1015
musculoskeletal system4.51e-08167
connective tissue5.64e-07371


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
BCL3#6022710.25023929341694.40179319354071e-201.12400703995159e-17
BCLAF1#9774266.18647074574913.91017816704815e-146.42099210044563e-12
IRF4#3662163.853101131735233.46807194950918e-060.000115534917491161
POLR2A#5430831.95866608411341.7046165343123e-194.13059039969936e-17
POU2F2#5452484.803230272215841.16950827676636e-223.35555700321983e-20
ZBTB33#10009165.567424181095592.6407718518275e-081.82286564066763e-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

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