Coexpression cluster:C439

Full id: C439_acute_CD14_Macrophage_biphenotypic_neuroblastoma_Monocytederived_myelodysplastic

Phase1 CAGE Peaks

Hg19::chr10:112206899..112206910,-	p@chr10:112206899..112206910 -
Hg19::chr10:112206925..112206940,-	p@chr10:112206925..112206940 -
Hg19::chr11:4475700..4475705,+	p@chr11:4475700..4475705 +
Hg19::chr12:12869857..12869890,+	p5@CDKN1B
Hg19::chr13:32388796..32388841,-	p@chr13:32388796..32388841 -
Hg19::chr13:88463369..88463374,-	p3@BC040238
Hg19::chr13:90031645..90031658,-	p@chr13:90031645..90031658 -
Hg19::chr13:90031665..90031668,-	p@chr13:90031665..90031668 -
Hg19::chr13:90436412..90436420,+	p@chr13:90436412..90436420 +
Hg19::chr13:90436562..90436573,+	p@chr13:90436562..90436573 +
Hg19::chr13:90494305..90494309,+	p@chr13:90494305..90494309 +
Hg19::chr13:90526930..90526934,+	p@chr13:90526930..90526934 +
Hg19::chr13:90531106..90531112,+	p@chr13:90531106..90531112 +
Hg19::chr16:85935894..85935904,+	p9@IRF8
Hg19::chr18:20407272..20407304,-	p@chr18:20407272..20407304 -
Hg19::chr1:38969182..38969229,-	p@chr1:38969182..38969229 -
Hg19::chr2:119710557..119710561,-	p1@ENST00000556770
Hg19::chr2:60754889..60754902,-	p2@uc002sag.2
Hg19::chr3:21584319..21584331,+	p4@ZNF385D-AS1
Hg19::chr7:27205043..27205050,-	p5@HOXA9
Hg19::chr7:27205066..27205067,-	p7@HOXA9
Hg19::chr9:30349695..30349701,-	p@chr9:30349695..30349701 -

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:0048102	autophagic cell death	0.0132419139814746
GO:0007275	multicellular organismal development	0.0132419139814746
GO:0031324	negative regulation of cellular metabolic process	0.0132419139814746
GO:0005072	transforming growth factor beta receptor, cytoplasmic mediator activity	0.0132419139814746
GO:0009892	negative regulation of metabolic process	0.0132419139814746
GO:0005071	transmembrane receptor protein serine/threonine kinase signaling protein activity	0.0132419139814746
GO:0031116	positive regulation of microtubule polymerization	0.0132419139814746
GO:0031112	positive regulation of microtubule polymerization or depolymerization	0.0132419139814746
GO:0031113	regulation of microtubule polymerization	0.0132419139814746
GO:0045736	negative regulation of cyclin-dependent protein kinase activity	0.0132419139814746
GO:0046785	microtubule polymerization	0.0132419139814746
GO:0032502	developmental process	0.0132419139814746
GO:0050680	negative regulation of epithelial cell proliferation	0.0132419139814746
GO:0042326	negative regulation of phosphorylation	0.0132419139814746
GO:0045936	negative regulation of phosphate metabolic process	0.0133886521848548
GO:0051130	positive regulation of cellular component organization and biogenesis	0.0135169912685775
GO:0004861	cyclin-dependent protein kinase inhibitor activity	0.013630178137687
GO:0032501	multicellular organismal process	0.0138347601184434
GO:0031323	regulation of cellular metabolic process	0.0142823592713417
GO:0019222	regulation of metabolic process	0.0159409183996984
GO:0051271	negative regulation of cell motility	0.0168473917503124
GO:0040013	negative regulation of locomotion	0.0168473917503124
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0181276571780347
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0185223108448601
GO:0050678	regulation of epithelial cell proliferation	0.0185223108448601
GO:0031109	microtubule polymerization or depolymerization	0.0185223108448601
GO:0050673	epithelial cell proliferation	0.0185223108448601
GO:0000082	G1/S transition of mitotic cell cycle	0.0185223108448601
GO:0048523	negative regulation of cellular process	0.0185223108448601
GO:0048513	organ development	0.0185223108448601
GO:0048839	inner ear development	0.0185223108448601
GO:0004860	protein kinase inhibitor activity	0.0185223108448601
GO:0048519	negative regulation of biological process	0.0185223108448601
GO:0019210	kinase inhibitor activity	0.0185223108448601
GO:0043583	ear development	0.0185223108448601
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.0210047719963499
GO:0030308	negative regulation of cell growth	0.0212837253173523
GO:0050794	regulation of cellular process	0.0212837253173523
GO:0045792	negative regulation of cell size	0.0212837253173523
GO:0006469	negative regulation of protein kinase activity	0.0212837253173523
GO:0033673	negative regulation of kinase activity	0.0212837253173523
GO:0051348	negative regulation of transferase activity	0.0212837253173523
GO:0045926	negative regulation of growth	0.0212837253173523
GO:0042325	regulation of phosphorylation	0.0212837253173523
GO:0003700	transcription factor activity	0.0212837253173523
GO:0005634	nucleus	0.0212837253173523
GO:0050789	regulation of biological process	0.0212837253173523
GO:0051174	regulation of phosphorus metabolic process	0.0212837253173523
GO:0019220	regulation of phosphate metabolic process	0.0212837253173523
GO:0051270	regulation of cell motility	0.0212837253173523
GO:0040012	regulation of locomotion	0.0214018511426233
GO:0040011	locomotion	0.0214018511426233
GO:0048731	system development	0.0214018511426233
GO:0030099	myeloid cell differentiation	0.0219868582700736
GO:0051329	interphase of mitotic cell cycle	0.0234601208300242
GO:0007423	sensory organ development	0.0234601208300242
GO:0043086	negative regulation of catalytic activity	0.0234601208300242
GO:0065007	biological regulation	0.0234601208300242
GO:0051325	interphase	0.0235120435595065
GO:0048869	cellular developmental process	0.0235519771064894
GO:0030154	cell differentiation	0.0235519771064894
GO:0051258	protein polymerization	0.024109619292839
GO:0051128	regulation of cellular component organization and biogenesis	0.0241787107162548
GO:0007050	cell cycle arrest	0.0241787107162548
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0241787107162548
GO:0019887	protein kinase regulator activity	0.0245105635014252
GO:0048856	anatomical structure development	0.0262090200083905
GO:0019207	kinase regulator activity	0.027627480156269
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0283387694782635
GO:0050954	sensory perception of mechanical stimulus	0.0286205475494717
GO:0007605	sensory perception of sound	0.0286205475494717
GO:0030097	hemopoiesis	0.0341326831092626
GO:0001558	regulation of cell growth	0.0341326831092626
GO:0048534	hemopoietic or lymphoid organ development	0.0359461017745621
GO:0005057	receptor signaling protein activity	0.0362825827367684
GO:0002520	immune system development	0.036811198128807
GO:0043231	intracellular membrane-bound organelle	0.0385003076234806
GO:0043227	membrane-bound organelle	0.0385003076234806
GO:0016049	cell growth	0.0385003076234806
GO:0040008	regulation of growth	0.0385003076234806
GO:0045892	negative regulation of transcription, DNA-dependent	0.0385003076234806
GO:0008361	regulation of cell size	0.0385894082372106
GO:0006917	induction of apoptosis	0.0389426403976106
GO:0012502	induction of programmed cell death	0.0389426403976106
GO:0045786	negative regulation of progression through cell cycle	0.0401657058010235
GO:0008285	negative regulation of cell proliferation	0.0401657058010235
GO:0008284	positive regulation of cell proliferation	0.0411060267430774
GO:0045859	regulation of protein kinase activity	0.0413316983284109
GO:0043549	regulation of kinase activity	0.041723320584043
GO:0051338	regulation of transferase activity	0.0421059891855547
GO:0006813	potassium ion transport	0.0425485939208282
GO:0043065	positive regulation of apoptosis	0.0425485939208282
GO:0043068	positive regulation of programmed cell death	0.0425485939208282
GO:0003702	RNA polymerase II transcription factor activity	0.0454941576303647
GO:0016481	negative regulation of transcription	0.0469347838142736
GO:0016563	transcription activator activity	0.0492155317148664
GO:0006355	regulation of transcription, DNA-dependent	0.0492155317148664
GO:0007017	microtubule-based process	0.0492155317148664
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0493123270482924
GO:0000278	mitotic cell cycle	0.0493123270482924
GO:0006351	transcription, DNA-dependent	0.0493123270482924
GO:0032774	RNA biosynthetic process	0.0493123270482924

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	9.09e-25	112
common myeloid progenitor	9.09e-25	112
monopoietic cell	4.15e-23	63
monocyte	4.15e-23	63
monoblast	4.15e-23	63
promonocyte	4.15e-23	63
granulocyte monocyte progenitor cell	3.20e-22	71
macrophage dendritic cell progenitor	4.80e-22	65
myeloid lineage restricted progenitor cell	7.56e-22	70
myeloid leukocyte	2.05e-21	76
hematopoietic cell	1.11e-20	182
hematopoietic stem cell	1.34e-20	172
angioblastic mesenchymal cell	1.34e-20	172
hematopoietic oligopotent progenitor cell	2.65e-20	165
hematopoietic multipotent progenitor cell	2.65e-20	165
nongranular leukocyte	3.36e-17	119
classical monocyte	5.57e-17	45
CD14-positive, CD16-negative classical monocyte	7.20e-17	42
hematopoietic lineage restricted progenitor cell	1.90e-15	124
leukocyte	2.63e-14	140
motile cell	7.83e-09	390
connective tissue cell	1.98e-08	365
mesenchymal cell	4.98e-08	358

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.85e-24	102
blood island	1.85e-24	102
hemolymphoid system	2.72e-22	112
bone marrow	1.84e-21	80
bone element	5.31e-21	86
skeletal element	1.86e-17	101
skeletal system	1.86e-17	101
immune system	3.32e-13	115
connective tissue	9.75e-09	375
lateral plate mesoderm	2.09e-08	216

Disease

Ontology term	p-value	n
myeloid leukemia	4.08e-09	31
leukemia	1.69e-07	39
hematologic cancer	2.31e-07	51
immune system cancer	2.31e-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.