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{{Coexpression_clusters
{
|full_id=C143_Monocytederived_CD14_Macrophage_Dendritic_Basophils_CD14CD16_Osteoblast
|

Latest revision as of 10:41, 17 September 2013


Full id: C143_Monocytederived_CD14_Macrophage_Dendritic_Basophils_CD14CD16_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:73576710..73576740,+p1@CU678651
Hg19::chr10:73577061..73577104,-p@chr10:73577061..73577104
-
Hg19::chr10:73579309..73579331,-p5@PSAP
Hg19::chr10:73579559..73579597,+p@chr10:73579559..73579597
+
Hg19::chr10:73581627..73581654,+p@chr10:73581627..73581654
+
Hg19::chr10:73581681..73581767,-p4@PSAP
Hg19::chr10:73581705..73581729,+p@chr10:73581705..73581729
+
Hg19::chr10:73587798..73587813,-p6@PSAP
Hg19::chr10:73587830..73587856,+p@chr10:73587830..73587856
+
Hg19::chr10:73588656..73588715,-p@chr10:73588656..73588715
-
Hg19::chr10:73588784..73588799,-p@chr10:73588784..73588799
-
Hg19::chr10:73588807..73588828,-p@chr10:73588807..73588828
-
Hg19::chr10:73590916..73590954,-p@chr10:73590916..73590954
-
Hg19::chr10:73591593..73591618,+p@chr10:73591593..73591618
+
Hg19::chr10:73591637..73591683,-p@chr10:73591637..73591683
-
Hg19::chr10:73594155..73594181,-p@chr10:73594155..73594181
-
Hg19::chr10:73610996..73611015,-p1@PSAP
Hg19::chr11:117712954..117712981,-p@chr11:117712954..117712981
-
Hg19::chr11:118571152..118571171,+p@chr11:118571152..118571171
+
Hg19::chr11:124933168..124933179,+p4@SLC37A2
Hg19::chr11:124933191..124933208,+p1@SLC37A2
Hg19::chr11:1785100..1785113,-p2@CTSD
Hg19::chr11:58977278..58977289,-p@chr11:58977278..58977289
-
Hg19::chr11:58977419..58977436,-p@chr11:58977419..58977436
-
Hg19::chr11:58977483..58977488,-p@chr11:58977483..58977488
-
Hg19::chr11:58977583..58977594,-p@chr11:58977583..58977594
-
Hg19::chr11:58977674..58977688,-p1@AK024358
Hg19::chr11:58977802..58977807,-p4@AK024358
Hg19::chr11:58977815..58977826,-p3@AK024358
Hg19::chr11:58978340..58978355,-p2@AK024358
Hg19::chr11:58979630..58979649,-p6@MPEG1
Hg19::chr11:58979924..58979941,-p4@MPEG1
Hg19::chr11:61732595..61732605,-p7@FTH1
Hg19::chr11:71709940..71710001,+p1@IL18BP
Hg19::chr14:21249146..21249155,+p4@RNASE6
Hg19::chr15:63414832..63414860,+p6@LACTB
Hg19::chr15:72668733..72668748,-p5@HEXA
Hg19::chr15:72668750..72668798,-p3@HEXA
Hg19::chr16:31393381..31393393,+p@chr16:31393381..31393393
+
Hg19::chr17:21195625..21195644,+p@chr17:21195625..21195644
+
Hg19::chr17:42422662..42422678,+p1@GRN
Hg19::chr17:42427043..42427062,+p@chr17:42427043..42427062
+
Hg19::chr17:42427826..42427839,+p5@GRN
Hg19::chr17:42428048..42428067,+p@chr17:42428048..42428067
+
Hg19::chr17:4638750..4638769,-p@chr17:4638750..4638769
-
Hg19::chr17:7482899..7482979,+p1@CD68
Hg19::chr17:7483236..7483258,-p@chr17:7483236..7483258
-
Hg19::chr17:7483266..7483402,-p@chr17:7483266..7483402
-
Hg19::chr17:7483418..7483445,-p@chr17:7483418..7483445
-
Hg19::chr17:7483451..7483494,-p@chr17:7483451..7483494
-
Hg19::chr17:7483531..7483548,-p@chr17:7483531..7483548
-
Hg19::chr17:7483761..7483825,+p@chr17:7483761..7483825
+
Hg19::chr17:7483828..7483845,-p@chr17:7483828..7483845
-
Hg19::chr18:2890629..2890633,+p@chr18:2890629..2890633
+
Hg19::chr19:10222364..10222370,+p1@P2RY11
Hg19::chr19:12992212..12992237,-p3@DNASE2
Hg19::chr19:18284716..18284723,+p2@IFI30
Hg19::chr19:18285845..18285861,+p@chr19:18285845..18285861
+
Hg19::chr19:18285866..18285913,+p@chr19:18285866..18285913
+
Hg19::chr19:18285955..18285972,+p@chr19:18285955..18285972
+
Hg19::chr19:18285973..18285996,+p@chr19:18285973..18285996
+
Hg19::chr19:18286116..18286156,+p@chr19:18286116..18286156
+
Hg19::chr19:18286406..18286470,+p@chr19:18286406..18286470
+
Hg19::chr19:18287936..18287989,+p@chr19:18287936..18287989
+
Hg19::chr19:18288001..18288020,-p@chr19:18288001..18288020
-
Hg19::chr19:18288651..18288682,+p5@IFI30
Hg19::chr19:18288727..18288790,-p1@CU676849
p1@CU689079
Hg19::chr19:18288828..18288861,+p7@IFI30
Hg19::chr19:18288839..18288881,-p2@CU676849
p2@CU689079
Hg19::chr19:36395335..36395392,+p@chr19:36395335..36395392
+
Hg19::chr19:36395378..36395433,-p@chr19:36395378..36395433
-
Hg19::chr19:36395478..36395489,-p@chr19:36395478..36395489
-
Hg19::chr19:36395505..36395529,-p@chr19:36395505..36395529
-
Hg19::chr19:36398154..36398173,-p@chr19:36398154..36398173
-
Hg19::chr19:36398391..36398405,-p@chr19:36398391..36398405
-
Hg19::chr19:36398412..36398445,-p@chr19:36398412..36398445
-
Hg19::chr19:48828539..48828550,+p4@EMP3
Hg19::chr19:49469949..49469978,+p@chr19:49469949..49469978
+
Hg19::chr19:50015936..50015981,+p3@FCGRT
Hg19::chr19:54872562..54872573,-p12@LAIR1
Hg19::chr19:55174400..55174461,+p1@LILRB4
Hg19::chr19:55177293..55177307,+p2@LILRB4
Hg19::chr1:111434009..111434022,+p1@AB529033
Hg19::chr1:161187774..161187799,+p@chr1:161187774..161187799
+
Hg19::chr1:161187824..161187847,+p@chr1:161187824..161187847
+
Hg19::chr1:161188022..161188042,+p@chr1:161188022..161188042
+
Hg19::chr1:161188686..161188721,+p@chr1:161188686..161188721
+
Hg19::chr1:161188746..161188758,+p@chr1:161188746..161188758
+
Hg19::chr1:161188763..161188824,+p@chr1:161188763..161188824
+
Hg19::chr1:161188826..161188842,+p@chr1:161188826..161188842
+
Hg19::chr1:161188869..161188889,+p@chr1:161188869..161188889
+
Hg19::chr1:31211779..31211826,+p@chr1:31211779..31211826
+
Hg19::chr1:31215379..31215390,-p@chr1:31215379..31215390
-
Hg19::chr1:36767139..36767159,+p@chr1:36767139..36767159
+
Hg19::chr20:39317067..39317115,-p1@AB464740
Hg19::chr21:34804479..34804505,+p7@IFNGR2
Hg19::chr21:46323305..46323316,-p@chr21:46323305..46323316
-
Hg19::chr21:46323370..46323382,-p@chr21:46323370..46323382
-
Hg19::chr2:219646666..219646681,+p5@CYP27A1
Hg19::chr2:71295766..71295788,+p1@NAGK
Hg19::chr3:112269078..112269100,-p@chr3:112269078..112269100
-
Hg19::chr3:126675882..126675901,+p2@CHCHD6
Hg19::chr3:136651075..136651077,+p@chr3:136651075..136651077
+
Hg19::chr3:46243584..46243605,-p@chr3:46243584..46243605
-
Hg19::chr3:46243618..46243632,-p@chr3:46243618..46243632
-
Hg19::chr3:46244481..46244493,-p@chr3:46244481..46244493
-
Hg19::chr3:46244558..46244569,-p@chr3:46244558..46244569
-
Hg19::chr5:119593640..119593641,+p@chr5:119593640..119593641
+
Hg19::chr5:139976080..139976122,+p@chr5:139976080..139976122
+
Hg19::chr5:140011978..140011999,-p@chr5:140011978..140011999
-
Hg19::chr5:140012086..140012110,-p6@CD14
Hg19::chr5:65017887..65017901,-p2@SGTB
Hg19::chr6:30710968..30710978,-p22@FLOT1
Hg19::chr6:31322987..31323005,-p13@HLA-B
Hg19::chr6:31584212..31584228,+p6@AIF1
Hg19::chr8:11721825..11721827,-p@chr8:11721825..11721827
-
Hg19::chr8:11723522..11723526,-p@chr8:11723522..11723526
-
Hg19::chr8:15997253..15997257,-p@chr8:15997253..15997257
-
Hg19::chr8:20067907..20067920,+p2@ATP6V1B2
Hg19::chrX:37664265..37664282,+p@chrX:37664265..37664282
+
Hg19::chrX:37664331..37664352,+p@chrX:37664331..37664352
+


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
1.14448180130357e-077.24456980225158e-055121Lysosome (KEGG):04142
0.0001260282790224710.0398879503106125511Signaling in Immune system (Reactome):REACT_6900



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:0005764lysosome1.02017609261701e-06
GO:0000323lytic vacuole1.02017609261701e-06
GO:0005773vacuole1.59528494725119e-06
GO:0048770pigment granule0.00221597962737036
GO:0042470melanosome0.00221597962737036
GO:0006687glycosphingolipid metabolic process0.00520441115129939
GO:0007040lysosome organization and biogenesis0.00520441115129939
GO:0007033vacuole organization and biogenesis0.00553175778217785
GO:0044444cytoplasmic part0.00555041723408132
GO:0006955immune response0.00573924456023113
GO:0006664glycolipid metabolic process0.00692069824548751
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.00692069824548751
GO:0042127regulation of cell proliferation0.00940463468647706
GO:0002376immune system process0.00940463468647706
GO:0045121lipid raft0.0105707968653924
GO:0008285negative regulation of cell proliferation0.0105707968653924
GO:0006952defense response0.0105707968653924
GO:0017001antibiotic catabolic process0.0105707968653924
GO:0042007interleukin-18 binding0.0105707968653924
GO:0006051N-acetylmannosamine metabolic process0.0105707968653924
GO:0008800beta-lactamase activity0.0105707968653924
GO:0030655beta-lactam antibiotic catabolic process0.0105707968653924
GO:0006050mannosamine metabolic process0.0105707968653924
GO:0047749cholestanetriol 26-monooxygenase activity0.0105707968653924
GO:0004192cathepsin D activity0.0105707968653924
GO:0030653beta-lactam antibiotic metabolic process0.0105707968653924
GO:0045127N-acetylglucosamine kinase activity0.0105707968653924
GO:0006665sphingolipid metabolic process0.0152799311272439
GO:0009384N-acylmannosamine kinase activity0.015422426849066
GO:0004098cerebroside-sulfatase activity0.015422426849066
GO:0016889endodeoxyribonuclease activity, producing 3'-phosphomonoesters0.015422426849066
GO:0006880intracellular sequestering of iron ion0.015422426849066
GO:0004557alpha-galactosidase activity0.015422426849066
GO:0004531deoxyribonuclease II activity0.015422426849066
GO:0019964interferon-gamma binding0.015422426849066
GO:0004906interferon-gamma receptor activity0.015422426849066
GO:0008043ferritin complex0.015422426849066
GO:0051704multi-organism process0.0172391392478423
GO:0008283cell proliferation0.0178054596596289
GO:0016023cytoplasmic membrane-bound vesicle0.0184179678797753
GO:0031988membrane-bound vesicle0.0187157340953274
GO:0004322ferroxidase activity0.0194467036203606
GO:0004336galactosylceramidase activity0.0194467036203606
GO:0016724oxidoreductase activity, oxidizing metal ions, oxygen as acceptor0.0194467036203606
GO:0019955cytokine binding0.0199777085932645
GO:0050884neuromuscular process controlling posture0.0232752477158334
GO:0004563beta-N-acetylhexosaminidase activity0.0232752477158334
GO:0016999antibiotic metabolic process0.0232752477158334
GO:0006689ganglioside catabolic process0.0232752477158334
GO:0031410cytoplasmic vesicle0.0254486866919106
GO:0031982vesicle0.0254486866919106
GO:0016019peptidoglycan receptor activity0.0254486866919106
GO:0046479glycosphingolipid catabolic process0.0254486866919106
GO:0019961interferon binding0.0254486866919106
GO:0004904interferon receptor activity0.0254486866919106
GO:0004348glucosylceramidase activity0.0254486866919106
GO:0017144drug metabolic process0.0299925093723461
GO:0016722oxidoreductase activity, oxidizing metal ions0.0337936779888668
GO:0019377glycolipid catabolic process0.0337936779888668
GO:0004519endonuclease activity0.0342058332122311
GO:0019915sequestering of lipid0.0350444381671572
GO:0001573ganglioside metabolic process0.0350444381671572
GO:0007628adult walking behavior0.0350444381671572
GO:0019864IgG binding0.0350444381671572
GO:0016600flotillin complex0.0350444381671572
GO:0042834peptidoglycan binding0.0371269217025048
GO:0004767sphingomyelin phosphodiesterase activity0.0371269217025048
GO:0030547receptor inhibitor activity0.0371269217025048
GO:0048019receptor antagonist activity0.0371269217025048
GO:0015988energy coupled proton transport, against electrochemical gradient0.0395199232746048
GO:0046677response to antibiotic0.0395199232746048
GO:0002237response to molecule of bacterial origin0.0395199232746048
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0417189232038694
GO:0030545receptor regulator activity0.0417189232038694
GO:0004565beta-galactosidase activity0.0417189232038694
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0421027854628203
GO:0042088T-helper 1 type immune response0.0426526501935049
GO:0008329pattern recognition receptor activity0.0426526501935049
GO:0017040ceramidase activity0.0426526501935049
GO:0015925galactosidase activity0.0426526501935049
GO:0016812hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides0.0450267385812422
GO:0051238sequestering of metal ion0.0450267385812422
GO:0051707response to other organism0.0450267385812422
GO:0008344adult locomotory behavior0.0468836779009948
GO:0009308amine metabolic process0.0468836779009948
GO:0005737cytoplasm0.0478754189442239
GO:0016798hydrolase activity, acting on glycosyl bonds0.0478757263869966
GO:0008395steroid hydroxylase activity0.0478757263869966
GO:0030149sphingolipid catabolic process0.0478757263869966



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
myeloid leukocyte9.69e-9572
monopoietic cell4.13e-8859
monocyte4.13e-8859
monoblast4.13e-8859
promonocyte4.13e-8859
macrophage dendritic cell progenitor8.98e-8861
granulocyte monocyte progenitor cell1.19e-8667
defensive cell8.44e-8648
phagocyte8.44e-8648
myeloid lineage restricted progenitor cell3.14e-8566
classical monocyte2.92e-7442
CD14-positive, CD16-negative classical monocyte2.92e-7442
myeloid cell1.32e-58108
common myeloid progenitor1.32e-58108
leukocyte2.13e-47136
nongranular leukocyte1.06e-41115
hematopoietic lineage restricted progenitor cell2.73e-40120
stuff accumulating cell5.63e-4087
hematopoietic stem cell1.73e-34168
angioblastic mesenchymal cell1.73e-34168
hematopoietic oligopotent progenitor cell8.03e-33161
hematopoietic multipotent progenitor cell8.03e-33161
hematopoietic cell1.03e-31177
intermediate monocyte2.48e-159
CD14-positive, CD16-positive monocyte2.48e-159
macrophage1.89e-126
mesenchymal cell1.59e-08354
connective tissue cell4.99e-08361
granulocyte2.01e-078
immature conventional dendritic cell3.02e-075
common dendritic progenitor3.02e-075
adult endothelial progenitor cell8.20e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.34e-9198
blood island8.34e-9198
hemolymphoid system4.42e-85108
bone marrow3.07e-7476
immune system3.12e-7093
bone element1.82e-6782
skeletal element7.75e-6090
skeletal system6.00e-54100
lateral plate mesoderm1.78e-38203
musculoskeletal system5.57e-26167
mesoderm1.61e-20315
mesoderm-derived structure1.61e-20315
presumptive mesoderm1.61e-20315
blood3.71e-1415
haemolymphatic fluid3.71e-1415
organism substance3.71e-1415
adult organism3.83e-11114
germ layer5.16e-09560
germ layer / neural crest5.16e-09560
embryonic tissue5.16e-09560
presumptive structure5.16e-09560
germ layer / neural crest derived structure5.16e-09560
epiblast (generic)5.16e-09560
embryonic structure8.94e-09564
developing anatomical structure3.03e-08581
organ5.26e-08503
connective tissue8.34e-08371
anatomical system8.68e-08624
anatomical group9.83e-08625
embryo1.24e-07592
multi-cellular organism4.73e-07656


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)
MA0003.11.03761e-05
MA0004.10.676232
MA0006.10.0848479
MA0007.11.0459
MA0009.10.237708
MA0014.14.30404e-07
MA0017.10.832217
MA0019.10.56671
MA0024.10.14428
MA0025.10.12256
MA0027.11.36139
MA0028.10.0302684
MA0029.10.159705
MA0030.10.347412
MA0031.10.477633
MA0038.10.43443
MA0040.10.16454
MA0041.10.00646524
MA0042.10.287406
MA0043.10.238025
MA0046.10.0633926
MA0048.10.0203157
MA0050.10.437758
MA0051.10.257183
MA0052.10.167779
MA0055.10.354433
MA0056.10
MA0057.10.0590709
MA0058.10.121645
MA0059.10.119672
MA0060.15.3053e-05
MA0061.10.000709978
MA0063.10
MA0066.10.265947
MA0067.10.64134
MA0068.10.146451
MA0069.10.0621016
MA0070.10.0584404
MA0071.10.197001
MA0072.10.456989
MA0073.10.511602
MA0074.10.420844
MA0076.10.0400475
MA0077.10.200968
MA0078.10.276689
MA0081.10.0650822
MA0083.10.24529
MA0084.10.356643
MA0087.10.0562341
MA0088.10.0351192
MA0089.10
MA0090.10.410004
MA0091.10.920198
MA0092.10.363937
MA0093.10.77613
MA0095.10
MA0098.10
MA0100.10.473378
MA0101.10.0516249
MA0103.10.284346
MA0105.10.00819223
MA0106.10.0299832
MA0107.10.0105869
MA0108.20.101925
MA0109.10
MA0111.11.08154
MA0113.10.0351152
MA0114.10.441909
MA0115.10.179567
MA0116.10.789801
MA0117.10.276777
MA0119.10.023351
MA0122.10.305253
MA0124.10.156374
MA0125.10.114106
MA0130.10
MA0131.10.152822
MA0132.10
MA0133.10
MA0135.10.0781646
MA0136.10.278704
MA0139.10.0385381
MA0140.10.0403472
MA0141.10.77412
MA0142.10.0844859
MA0143.10.606732
MA0144.10.0495517
MA0145.10.192415
MA0146.10.00256447
MA0147.10.286979
MA0148.10.246639
MA0149.10.0103388
MA0062.20.028084
MA0035.20.326087
MA0039.20.00594331
MA0138.20.00983517
MA0002.20.245079
MA0137.20.118836
MA0104.20.0398473
MA0047.20.17786
MA0112.21.07127
MA0065.22.14235
MA0150.10.388966
MA0151.10
MA0152.11.0131
MA0153.10.106423
MA0154.10.0681356
MA0155.10.155689
MA0156.10.564858
MA0157.10.357401
MA0158.10
MA0159.11.42972
MA0160.11.78446
MA0161.10
MA0162.16.69887e-05
MA0163.10.0160493
MA0164.10.112493
MA0080.20.455117
MA0018.20.196276
MA0099.20.344606
MA0079.26.26316e-05
MA0102.20.385033
MA0258.11.86006
MA0259.10.155653
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
BCL11A#53335102.344583066413810.01075108582752360.0396788696282684



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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