Coexpression cluster:C143

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

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p.value	FDR	nGenes	nPathway	Name
1.14448180130357e-07	7.24456980225158e-05	5	121	Lysosome (KEGG):04142
0.000126028279022471	0.039887950310612	5	511	Signaling 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

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GO ID	GO name	FDR corrected p-value
GO:0005764	lysosome	1.02017609261701e-06
GO:0000323	lytic vacuole	1.02017609261701e-06
GO:0005773	vacuole	1.59528494725119e-06
GO:0048770	pigment granule	0.00221597962737036
GO:0042470	melanosome	0.00221597962737036
GO:0006687	glycosphingolipid metabolic process	0.00520441115129939
GO:0007040	lysosome organization and biogenesis	0.00520441115129939
GO:0007033	vacuole organization and biogenesis	0.00553175778217785
GO:0044444	cytoplasmic part	0.00555041723408132
GO:0006955	immune response	0.00573924456023113
GO:0006664	glycolipid metabolic process	0.00692069824548751
GO:0016894	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	0.00692069824548751
GO:0042127	regulation of cell proliferation	0.00940463468647706
GO:0002376	immune system process	0.00940463468647706
GO:0045121	lipid raft	0.0105707968653924
GO:0008285	negative regulation of cell proliferation	0.0105707968653924
GO:0006952	defense response	0.0105707968653924
GO:0017001	antibiotic catabolic process	0.0105707968653924
GO:0042007	interleukin-18 binding	0.0105707968653924
GO:0006051	N-acetylmannosamine metabolic process	0.0105707968653924
GO:0008800	beta-lactamase activity	0.0105707968653924
GO:0030655	beta-lactam antibiotic catabolic process	0.0105707968653924
GO:0006050	mannosamine metabolic process	0.0105707968653924
GO:0047749	cholestanetriol 26-monooxygenase activity	0.0105707968653924
GO:0004192	cathepsin D activity	0.0105707968653924
GO:0030653	beta-lactam antibiotic metabolic process	0.0105707968653924
GO:0045127	N-acetylglucosamine kinase activity	0.0105707968653924
GO:0006665	sphingolipid metabolic process	0.0152799311272439
GO:0009384	N-acylmannosamine kinase activity	0.015422426849066
GO:0004098	cerebroside-sulfatase activity	0.015422426849066
GO:0016889	endodeoxyribonuclease activity, producing 3'-phosphomonoesters	0.015422426849066
GO:0006880	intracellular sequestering of iron ion	0.015422426849066
GO:0004557	alpha-galactosidase activity	0.015422426849066
GO:0004531	deoxyribonuclease II activity	0.015422426849066
GO:0019964	interferon-gamma binding	0.015422426849066
GO:0004906	interferon-gamma receptor activity	0.015422426849066
GO:0008043	ferritin complex	0.015422426849066
GO:0051704	multi-organism process	0.0172391392478423
GO:0008283	cell proliferation	0.0178054596596289
GO:0016023	cytoplasmic membrane-bound vesicle	0.0184179678797753
GO:0031988	membrane-bound vesicle	0.0187157340953274
GO:0004322	ferroxidase activity	0.0194467036203606
GO:0004336	galactosylceramidase activity	0.0194467036203606
GO:0016724	oxidoreductase activity, oxidizing metal ions, oxygen as acceptor	0.0194467036203606
GO:0019955	cytokine binding	0.0199777085932645
GO:0050884	neuromuscular process controlling posture	0.0232752477158334
GO:0004563	beta-N-acetylhexosaminidase activity	0.0232752477158334
GO:0016999	antibiotic metabolic process	0.0232752477158334
GO:0006689	ganglioside catabolic process	0.0232752477158334
GO:0031410	cytoplasmic vesicle	0.0254486866919106
GO:0031982	vesicle	0.0254486866919106
GO:0016019	peptidoglycan receptor activity	0.0254486866919106
GO:0046479	glycosphingolipid catabolic process	0.0254486866919106
GO:0019961	interferon binding	0.0254486866919106
GO:0004904	interferon receptor activity	0.0254486866919106
GO:0004348	glucosylceramidase activity	0.0254486866919106
GO:0017144	drug metabolic process	0.0299925093723461
GO:0016722	oxidoreductase activity, oxidizing metal ions	0.0337936779888668
GO:0019377	glycolipid catabolic process	0.0337936779888668
GO:0004519	endonuclease activity	0.0342058332122311
GO:0019915	sequestering of lipid	0.0350444381671572
GO:0001573	ganglioside metabolic process	0.0350444381671572
GO:0007628	adult walking behavior	0.0350444381671572
GO:0019864	IgG binding	0.0350444381671572
GO:0016600	flotillin complex	0.0350444381671572
GO:0042834	peptidoglycan binding	0.0371269217025048
GO:0004767	sphingomyelin phosphodiesterase activity	0.0371269217025048
GO:0030547	receptor inhibitor activity	0.0371269217025048
GO:0048019	receptor antagonist activity	0.0371269217025048
GO:0015988	energy coupled proton transport, against electrochemical gradient	0.0395199232746048
GO:0046677	response to antibiotic	0.0395199232746048
GO:0002237	response to molecule of bacterial origin	0.0395199232746048
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0417189232038694
GO:0030545	receptor regulator activity	0.0417189232038694
GO:0004565	beta-galactosidase activity	0.0417189232038694
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0421027854628203
GO:0042088	T-helper 1 type immune response	0.0426526501935049
GO:0008329	pattern recognition receptor activity	0.0426526501935049
GO:0017040	ceramidase activity	0.0426526501935049
GO:0015925	galactosidase activity	0.0426526501935049
GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	0.0450267385812422
GO:0051238	sequestering of metal ion	0.0450267385812422
GO:0051707	response to other organism	0.0450267385812422
GO:0008344	adult locomotory behavior	0.0468836779009948
GO:0009308	amine metabolic process	0.0468836779009948
GO:0005737	cytoplasm	0.0478754189442239
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0478757263869966
GO:0008395	steroid hydroxylase activity	0.0478757263869966
GO:0030149	sphingolipid catabolic process	0.0478757263869966

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>

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Cell Type

Ontology term	p-value	n
myeloid leukocyte	7.70e-37	76
macrophage dendritic cell progenitor	3.28e-32	65
granulocyte monocyte progenitor cell	3.32e-32	71
monopoietic cell	3.00e-31	63
monocyte	3.00e-31	63
monoblast	3.00e-31	63
promonocyte	3.00e-31	63
myeloid lineage restricted progenitor cell	7.61e-30	70
CD14-positive, CD16-negative classical monocyte	2.33e-27	42
myeloid cell	3.48e-24	112
common myeloid progenitor	3.48e-24	112
classical monocyte	1.11e-23	45
leukocyte	1.70e-11	140
hematopoietic stem cell	2.43e-07	172
angioblastic mesenchymal cell	2.43e-07	172
connective tissue cell	5.22e-07	365

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	3.74e-32	112
hematopoietic system	4.49e-31	102
blood island	4.49e-31	102
bone marrow	9.17e-29	80
immune system	7.54e-27	115
bone element	7.79e-24	86
lateral plate mesoderm	2.52e-21	216
skeletal element	2.13e-19	101
skeletal system	2.13e-19	101
musculoskeletal system	1.98e-13	167
adult organism	5.99e-12	115
mesoderm	5.53e-11	448
mesoderm-derived structure	5.53e-11	448
presumptive mesoderm	5.53e-11	448
anatomical system	1.15e-08	625
anatomical group	1.34e-08	626
organ	1.27e-07	511
multi-cellular organism	1.56e-07	659

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	10	2.34458306641381	0.0107510858275236	0.0396788696282684

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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