Coexpression cluster:C973

Full id: C973_acute_granulocyte_CD34_CD133_myelodysplastic_biphenotypic_liver

Phase1 CAGE Peaks

Hg19::chr10:129717770..129717798,+	p@chr10:129717770..129717798 +
Hg19::chr14:21387508..21387523,+	p1@ENST00000555624
Hg19::chr14:21423643..21423665,+	p1@RNASE2
Hg19::chr19:827823..827845,+	p1@AZU1
Hg19::chr19:829566..829598,+	p@chr19:829566..829598 +
Hg19::chr1:200821566..200821577,+	p@chr1:200821566..200821577 +
Hg19::chr1:92952473..92952489,-	p3@GFI1
Hg19::chr9:137037139..137037152,-	p@chr9:137037139..137037152 -

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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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

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GO ID	GO name	FDR corrected p-value
GO:0007610	behavior	0.000170668921953427
GO:0009605	response to external stimulus	0.000856400268727817
GO:0042330	taxis	0.00156594942771625
GO:0006935	chemotaxis	0.00156594942771625
GO:0007626	locomotory behavior	0.00156594942771625
GO:0042660	positive regulation of cell fate specification	0.00156594942771625
GO:0042659	regulation of cell fate specification	0.00156594942771625
GO:0010453	regulation of cell fate commitment	0.00156594942771625
GO:0009996	negative regulation of cell fate specification	0.00156594942771625
GO:0010454	negative regulation of cell fate commitment	0.00156594942771625
GO:0005764	lysosome	0.00156594942771625
GO:0000323	lytic vacuole	0.00156594942771625
GO:0005773	vacuole	0.00156594942771625
GO:0042222	interleukin-1 biosynthetic process	0.00156594942771625
GO:0050720	interleukin-1 beta biosynthetic process	0.00156594942771625
GO:0050725	positive regulation of interleukin-1 beta biosynthetic process	0.00156594942771625
GO:0032603	fractalkine production	0.00156594942771625
GO:0050752	regulation of fractalkine biosynthetic process	0.00156594942771625
GO:0045360	regulation of interleukin-1 biosynthetic process	0.00156594942771625
GO:0050829	defense response to Gram-negative bacterium	0.00156594942771625
GO:0001774	microglial cell activation	0.00156594942771625
GO:0050756	fractalkine metabolic process	0.00156594942771625
GO:0042582	azurophil granule	0.00156594942771625
GO:0050722	regulation of interleukin-1 beta biosynthetic process	0.00156594942771625
GO:0050751	fractalkine biosynthetic process	0.00156594942771625
GO:0042117	monocyte activation	0.00156594942771625
GO:0045362	positive regulation of interleukin-1 biosynthetic process	0.00156594942771625
GO:0000083	G1/S-specific transcription in mitotic cell cycle	0.00156594942771625
GO:0005766	primary lysosome	0.00156594942771625
GO:0050754	positive regulation of fractalkine biosynthetic process	0.00156594942771625
GO:0043114	regulation of vascular permeability	0.00227308547991789
GO:0015643	toxin binding	0.00276327747248584
GO:0048246	macrophage chemotaxis	0.00276327747248584
GO:0045123	cellular extravasation	0.00276327747248584
GO:0008347	glial cell migration	0.00309041672193129
GO:0045348	positive regulation of MHC class II biosynthetic process	0.00309041672193129
GO:0032611	interleukin-1 beta production	0.00309041672193129
GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	0.00309041672193129
GO:0045342	MHC class II biosynthetic process	0.00327718265173903
GO:0045346	regulation of MHC class II biosynthetic process	0.00327718265173903
GO:0007638	mechanosensory behavior	0.00327718265173903
GO:0045080	positive regulation of chemokine biosynthetic process	0.00327718265173903
GO:0032612	interleukin-1 production	0.00327718265173903
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.0040843639790859
GO:0042533	tumor necrosis factor biosynthetic process	0.0040843639790859
GO:0050930	induction of positive chemotaxis	0.0040843639790859
GO:0050766	positive regulation of phagocytosis	0.00415297302491087
GO:0042116	macrophage activation	0.00415297302491087
GO:0045073	regulation of chemokine biosynthetic process	0.00415297302491087
GO:0050926	regulation of positive chemotaxis	0.00415297302491087
GO:0032602	chemokine production	0.00415297302491087
GO:0050764	regulation of phagocytosis	0.00415297302491087
GO:0050755	chemokine metabolic process	0.00415297302491087
GO:0050927	positive regulation of positive chemotaxis	0.00415297302491087
GO:0050918	positive chemotaxis	0.00415297302491087
GO:0042033	chemokine biosynthetic process	0.00415297302491087
GO:0042221	response to chemical stimulus	0.00415297302491087
GO:0050921	positive regulation of chemotaxis	0.00445367597835105
GO:0050920	regulation of chemotaxis	0.00469646549209633
GO:0042491	auditory receptor cell differentiation	0.00469646549209633
GO:0032640	tumor necrosis factor production	0.00500428311171623
GO:0042490	mechanoreceptor differentiation	0.00541852004735126
GO:0001708	cell fate specification	0.00541852004735126
GO:0060113	inner ear receptor cell differentiation	0.00541852004735126
GO:0045785	positive regulation of cell adhesion	0.00541852004735126
GO:0009612	response to mechanical stimulus	0.00604758798271926
GO:0045807	positive regulation of endocytosis	0.00630757067606722
GO:0004522	pancreatic ribonuclease activity	0.00782490789235098
GO:0030595	leukocyte chemotaxis	0.00782490789235098
GO:0048522	positive regulation of cellular process	0.00880198465200129
GO:0002274	myeloid leukocyte activation	0.00880198465200129
GO:0042472	inner ear morphogenesis	0.00880198465200129
GO:0016892	endoribonuclease activity, producing 3'-phosphomonoesters	0.00900267811959809
GO:0016894	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	0.00951481855163653
GO:0042471	ear morphogenesis	0.00957296098955781
GO:0050900	leukocyte migration	0.00957296098955781
GO:0048518	positive regulation of biological process	0.00990815612220235
GO:0030100	regulation of endocytosis	0.0100997738254567
GO:0000082	G1/S transition of mitotic cell cycle	0.0100997738254567
GO:0042063	gliogenesis	0.0104899480711891
GO:0030141	secretory granule	0.0104899480711891
GO:0048523	negative regulation of cellular process	0.0104899480711891
GO:0007205	protein kinase C activation	0.0104899480711891
GO:0051050	positive regulation of transport	0.0104899480711891
GO:0048839	inner ear development	0.0104899480711891
GO:0048519	negative regulation of biological process	0.0109312917185369
GO:0042108	positive regulation of cytokine biosynthetic process	0.0109312917185369
GO:0006909	phagocytosis	0.0109312917185369
GO:0043583	ear development	0.0110717633364782
GO:0003018	vascular process in circulatory system	0.0112090980154521
GO:0006401	RNA catabolic process	0.0118583097527806
GO:0045597	positive regulation of cell differentiation	0.0119840494268425
GO:0045727	positive regulation of translation	0.0133662548911064
GO:0042035	regulation of cytokine biosynthetic process	0.0148099953883953
GO:0031328	positive regulation of cellular biosynthetic process	0.0148099953883953
GO:0045596	negative regulation of cell differentiation	0.0158746968744691
GO:0030155	regulation of cell adhesion	0.0159416713843611
GO:0042089	cytokine biosynthetic process	0.0159416713843611
GO:0042107	cytokine metabolic process	0.0159416713843611
GO:0051094	positive regulation of developmental process	0.0159416713843611
GO:0009891	positive regulation of biosynthetic process	0.0160878208787198
GO:0032147	activation of protein kinase activity	0.0160878208787198
GO:0045165	cell fate commitment	0.0161587471360076
GO:0004521	endoribonuclease activity	0.0162282961567073
GO:0048731	system development	0.0164203155052355
GO:0008201	heparin binding	0.0168046828430292
GO:0051093	negative regulation of developmental process	0.0168661806243705
GO:0051329	interphase of mitotic cell cycle	0.0182725799938739
GO:0051247	positive regulation of protein metabolic process	0.0182725799938739
GO:0007423	sensory organ development	0.0183189431602503
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0185749969893607
GO:0051325	interphase	0.0188264291644334
GO:0048598	embryonic morphogenesis	0.0189890375418583
GO:0048869	cellular developmental process	0.0189890375418583
GO:0030154	cell differentiation	0.0189890375418583
GO:0042742	defense response to bacterium	0.0191842623325334
GO:0004540	ribonuclease activity	0.020018412964898
GO:0009617	response to bacterium	0.0210359718380921
GO:0005539	glycosaminoglycan binding	0.0214634223031036
GO:0051049	regulation of transport	0.0214634223031036
GO:0001816	cytokine production	0.0218646338971738
GO:0048856	anatomical structure development	0.0218780868660204
GO:0030247	polysaccharide binding	0.0220781977342848
GO:0001871	pattern binding	0.0239691140554861
GO:0048015	phosphoinositide-mediated signaling	0.0241503841239292
GO:0045860	positive regulation of protein kinase activity	0.0261781708991172
GO:0033674	positive regulation of kinase activity	0.0263150892349328
GO:0045595	regulation of cell differentiation	0.0263150892349328
GO:0051347	positive regulation of transferase activity	0.0266527202851605
GO:0007275	multicellular organismal development	0.0268340692406326
GO:0004519	endonuclease activity	0.0269568012619041
GO:0008015	blood circulation	0.0281265077720594
GO:0003013	circulatory system process	0.0281265077720594
GO:0009628	response to abiotic stimulus	0.0287847587402314
GO:0006916	anti-apoptosis	0.0294330029785452
GO:0003823	antigen binding	0.0304133414117029
GO:0045321	leukocyte activation	0.0307003479160626
GO:0006417	regulation of translation	0.0311514931079144
GO:0010324	membrane invagination	0.0326221341500384
GO:0006897	endocytosis	0.0326221341500384
GO:0031326	regulation of cellular biosynthetic process	0.0326221341500384
GO:0043231	intracellular membrane-bound organelle	0.0326221341500384
GO:0043227	membrane-bound organelle	0.0326221341500384
GO:0051707	response to other organism	0.033401276685319
GO:0001775	cell activation	0.0336510168235666
GO:0009889	regulation of biosynthetic process	0.0346915974216573
GO:0043066	negative regulation of apoptosis	0.036032784237899
GO:0043069	negative regulation of programmed cell death	0.0362590966960609
GO:0016477	cell migration	0.0363718945290016
GO:0009790	embryonic development	0.0363718945290016
GO:0050793	regulation of developmental process	0.0363718945290016
GO:0045859	regulation of protein kinase activity	0.0363718945290016
GO:0043549	regulation of kinase activity	0.0368910510366623
GO:0004518	nuclease activity	0.0371619311005411
GO:0051338	regulation of transferase activity	0.0371619311005411
GO:0043085	positive regulation of catalytic activity	0.038258949687505
GO:0022008	neurogenesis	0.0388993562932272
GO:0019932	second-messenger-mediated signaling	0.0395313438068861
GO:0003702	RNA polymerase II transcription factor activity	0.0408817939762674
GO:0016044	membrane organization and biogenesis	0.0413482492717847
GO:0009607	response to biotic stimulus	0.0418086971382871
GO:0006954	inflammatory response	0.0418356961900068
GO:0032502	developmental process	0.0443893580854093
GO:0000278	mitotic cell cycle	0.0462481083833369
GO:0051704	multi-organism process	0.0466623480129664
GO:0004252	serine-type endopeptidase activity	0.0466623480129664
GO:0016023	cytoplasmic membrane-bound vesicle	0.0483129848461117
GO:0031988	membrane-bound vesicle	0.048710221809748
GO:0009887	organ morphogenesis	0.0493156047145424
GO:0043229	intracellular organelle	0.0493156047145424
GO:0043226	organelle	0.0493156047145424
GO:0031325	positive regulation of cellular metabolic process	0.0493156047145424
GO:0022403	cell cycle phase	0.0495620072767533

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
myeloid cell	1.05e-40	112
common myeloid progenitor	1.05e-40	112
hematopoietic stem cell	5.37e-38	172
angioblastic mesenchymal cell	5.37e-38	172
hematopoietic cell	5.31e-37	182
hematopoietic oligopotent progenitor cell	3.67e-35	165
hematopoietic multipotent progenitor cell	3.67e-35	165
myeloid leukocyte	9.25e-35	76
myeloid lineage restricted progenitor cell	3.25e-31	70
monopoietic cell	4.52e-29	63
monocyte	4.52e-29	63
monoblast	4.52e-29	63
promonocyte	4.52e-29	63
granulocyte monocyte progenitor cell	1.00e-28	71
leukocyte	5.26e-28	140
macrophage dendritic cell progenitor	3.20e-27	65
nongranular leukocyte	1.22e-23	119
hematopoietic lineage restricted progenitor cell	5.24e-23	124
CD14-positive, CD16-negative classical monocyte	5.57e-23	42
classical monocyte	3.41e-21	45

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.45e-34	102
blood island	7.45e-34	102
hemolymphoid system	1.65e-29	112
bone marrow	6.93e-24	80
bone element	1.05e-22	86
immune system	2.23e-19	115
adult organism	2.19e-16	115
skeletal element	3.70e-15	101
skeletal system	3.70e-15	101
blood	1.63e-09	15
haemolymphatic fluid	1.63e-09	15
organism substance	1.63e-09	15

Disease

Ontology term	p-value	n
myeloid leukemia	6.38e-09	31
leukemia	2.46e-08	39
hematologic cancer	4.93e-07	51
immune system cancer	4.93e-07	51

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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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

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This analysis result is provided for C0 - C305 clusters.