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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:52, 17 September 2013


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)
MA0003.14.0701e-06
MA0004.11.20795
MA0006.10.00647075
MA0007.10.0510684
MA0009.10.367285
MA0014.14.62099e-06
MA0017.11.89508
MA0019.10.0769485
MA0024.10.0705712
MA0025.10.185862
MA0027.11.48276
MA0028.10.00023646
MA0029.13.23897
MA0030.10.0734746
MA0031.10.0515676
MA0038.10.297678
MA0040.10.577793
MA0041.10.00415987
MA0042.10.00267279
MA0043.10.367676
MA0046.12.34902
MA0048.10.0106866
MA0050.10.0167305
MA0051.10.142598
MA0052.10.0816217
MA0055.10.644432
MA0056.10
MA0057.10.0725836
MA0058.13.38263
MA0059.10.484527
MA0060.10.289338
MA0061.10.123709
MA0063.10
MA0066.10.147373
MA0067.10.307426
MA0068.10.0835745
MA0069.10.107693
MA0070.10.102625
MA0071.10.407721
MA0072.10.100624
MA0073.10.0110214
MA0074.14.42185
MA0076.10.00652466
MA0077.10.321359
MA0078.10.0254452
MA0081.10.485145
MA0083.10.118136
MA0084.10.451809
MA0087.11.11445
MA0088.10.490568
MA0089.10
MA0090.10.840609
MA0091.10.270958
MA0092.11.30225
MA0093.12.89695
MA0095.10
MA0098.10
MA0100.10.0605826
MA0101.10.183686
MA0103.10.0170189
MA0105.10.000882638
MA0106.10.0747848
MA0107.10.0647912
MA0108.20.0506377
MA0109.10
MA0111.12.23563
MA0113.10.0841685
MA0114.12.12495
MA0115.12.01591
MA0116.10.0687893
MA0117.10.133014
MA0119.10.0911122
MA0122.10.146496
MA0124.10.226763
MA0125.10.175391
MA0130.10
MA0131.11.22571
MA0132.10
MA0133.10
MA0135.10.129356
MA0136.13.40951
MA0139.10.0166697
MA0140.11.22622
MA0141.10.671851
MA0142.10.0424045
MA0143.10.995709
MA0144.10.937338
MA0145.10.00742747
MA0146.10.008046
MA0147.10.204141
MA0148.10.00451826
MA0149.13.85392
MA0062.20.57715
MA0035.21.58773
MA0039.22.59892e-06
MA0138.20.493766
MA0002.20.0634921
MA0137.20.219533
MA0104.20.198297
MA0047.20.178725
MA0112.20.22742
MA0065.22.43295
MA0150.11.06853
MA0151.10
MA0152.12.04913
MA0153.10.165772
MA0154.11.79724
MA0155.10.00178624
MA0156.12.43796
MA0157.10.141167
MA0158.10
MA0159.13.37337
MA0160.10.55778
MA0161.10
MA0162.12.08907e-12
MA0163.10.00506747
MA0164.11.43623
MA0080.22.52158
MA0018.20.075551
MA0099.20.00760093
MA0079.22.14563e-14
MA0102.20.48239
MA0258.10.11894
MA0259.10.00201626
MA0442.10



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C187&oldid=3067305"