Coexpression cluster:C314

Full id: C314_Macrophage_Dendritic_Monocytederived_CD14_Esophageal_Mast_Keratinocyte

Phase1 CAGE Peaks

Hg19::chr10:49893321..49893329,+	p8@WDFY4
Hg19::chr11:72431299..72431322,-	p@chr11:72431299..72431322 -
Hg19::chr12:65153154..65153171,-	p2@GNS
Hg19::chr12:9102224..9102270,-	p1@M6PR
Hg19::chr14:61449197..61449207,+	p15@SLC38A6
Hg19::chr15:78351618..78351622,-	p@chr15:78351618..78351622 -
Hg19::chr17:46022728..46022773,+	p@chr17:46022728..46022773 +
Hg19::chr17:7483714..7483726,+	p@chr17:7483714..7483726 +
Hg19::chr17:7483994..7484032,+	p@chr17:7483994..7484032 +
Hg19::chr17:7484124..7484142,+	p@chr17:7484124..7484142 +
Hg19::chr17:78180739..78180750,+	p2@AK095416
Hg19::chr17:78180789..78180807,+	p1@AK095416
Hg19::chr17:78193607..78193642,+	p@chr17:78193607..78193642 +
Hg19::chr17:78194046..78194081,+	p2@SLC26A11
Hg19::chr18:9772139..9772150,+	p@chr18:9772139..9772150 +
Hg19::chr19:11689752..11689799,-	p2@ACP5
Hg19::chr19:11689803..11689815,-	p5@ACP5
Hg19::chr1:159796480..159796494,+	p5@SLAMF8
Hg19::chr1:46016762..46016777,+	p3@AKR1A1
Hg19::chr20:1875058..1875060,+	p21@SIRPA
Hg19::chr20:39518079..39518082,-	p@chr20:39518079..39518082 -
Hg19::chr20:57582296..57582325,-	p1@CTSZ
Hg19::chr3:69591495..69591521,-	p7@FRMD4B
Hg19::chr5:131280548..131280574,-	p1@ENST00000425320
Hg19::chr5:131280595..131280605,-	p2@ENST00000425320
Hg19::chr5:150632732..150632758,+	p1@GM2A
Hg19::chr6:134758827..134758863,+	p1@LOC154092
Hg19::chr6:160406578..160406590,+	p@chr6:160406578..160406590 +
Hg19::chr6:36097945..36097981,+	p3@MAPK13
Hg19::chr6:36097992..36098038,+	p4@MAPK13
Hg19::chr6:46703069..46703081,-	p2@PLA2G7
Hg19::chr6:46703092..46703156,-	p1@PLA2G7
Hg19::chr6:46703447..46703465,-	p3@PLA2G7
Hg19::chr6:6799417..6799457,-	p@chr6:6799417..6799457 -
Hg19::chr6:6801396..6801410,-	p@chr6:6801396..6801410 -
Hg19::chr8:132916703..132916721,+	p@chr8:132916703..132916721 +
Hg19::chr8:66891425..66891440,+	p@chr8:66891425..66891440 +
Hg19::chr9:127023704..127023756,+	p3@NEK6

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
5.2977040485515e-09	3.3534466627331e-06	5	121	Lysosome (KEGG):04142
4.72529853545926e-05	0.00997037990981903	3	128	Osteoclast differentiation (KEGG):04380
2.61528773412653e-05	0.00827738567851046	3	105	Membrane Trafficking (Reactome):REACT_11123
0.000300489277244246	0.047552428123902	2	46	Interactions of the immunoglobulin superfamily (IgSF) member proteins (Reactome):REACT_23853

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	4.52582062239315e-06
GO:0000323	lytic vacuole	4.52582062239315e-06
GO:0005773	vacuole	6.15010206948201e-06
GO:0030290	sphingolipid activator protein activity	0.012127634522548
GO:0032428	beta-N-acetylgalactosaminidase activity	0.012127634522548
GO:0047939	L-glucuronate reductase activity	0.012127634522548
GO:0046185	aldehyde catabolic process	0.012127634522548
GO:0042839	D-glucuronate metabolic process	0.012127634522548
GO:0042840	D-glucuronate catabolic process	0.012127634522548
GO:0008449	N-acetylglucosamine-6-sulfatase activity	0.012127634522548
GO:0019853	L-ascorbic acid biosynthetic process	0.012127634522548
GO:0006064	glucuronate catabolic process	0.012127634522548
GO:0007243	protein kinase cascade	0.0132272258457848
GO:0045177	apical part of cell	0.0132272258457848
GO:0009056	catabolic process	0.0132272258457848
GO:0005889	hydrogen:potassium-exchanging ATPase complex	0.0132272258457848
GO:0015761	mannose transport	0.0132272258457848
GO:0008106	alcohol dehydrogenase (NADP+) activity	0.0132272258457848
GO:0015578	mannose transmembrane transporter activity	0.0132272258457848
GO:0016004	phospholipase activator activity	0.0132272258457848
GO:0045179	apical cortex	0.0132272258457848
GO:0009313	oligosaccharide catabolic process	0.0132272258457848
GO:0008339	MP kinase activity	0.0161630403516077
GO:0004032	aldehyde reductase activity	0.0161630403516077
GO:0006063	uronic acid metabolic process	0.0161630403516077
GO:0019852	L-ascorbic acid metabolic process	0.0161630403516077
GO:0019585	glucuronate metabolic process	0.0161630403516077
GO:0004563	beta-N-acetylhexosaminidase activity	0.0191472672715482
GO:0008247	2-acetyl-1-alkylglycerophosphocholine esterase complex	0.0191472672715482
GO:0006689	ganglioside catabolic process	0.0191472672715482
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0191472672715482
GO:0016042	lipid catabolic process	0.0204320329707988
GO:0046479	glycosphingolipid catabolic process	0.021805657903249
GO:0008333	endosome to lysosome transport	0.021805657903249
GO:0006026	aminoglycan catabolic process	0.021805657903249
GO:0016909	SAP kinase activity	0.021805657903249
GO:0050700	CARD domain binding	0.021805657903249
GO:0003847	1-alkyl-2-acetylglycerophosphocholine esterase activity	0.021805657903249
GO:0006027	glycosaminoglycan catabolic process	0.021805657903249
GO:0009898	internal side of plasma membrane	0.021805657903249
GO:0005737	cytoplasm	0.0226485989309556
GO:0019377	glycolipid catabolic process	0.0242231611391587
GO:0019915	sequestering of lipid	0.0260623078098239
GO:0001573	ganglioside metabolic process	0.0260623078098239
GO:0044425	membrane part	0.0260623078098239
GO:0016054	organic acid catabolic process	0.0309027153522172
GO:0046395	carboxylic acid catabolic process	0.0309027153522172
GO:0016020	membrane	0.0322521867971921
GO:0030071	regulation of mitotic metaphase/anaphase transition	0.0325983230004245
GO:0004033	aldo-keto reductase activity	0.0328706422062493
GO:0005537	mannose binding	0.0328706422062493
GO:0007091	mitotic metaphase/anaphase transition	0.0328706422062493
GO:0007250	activation of NF-kappaB-inducing kinase	0.0328706422062493
GO:0005975	carbohydrate metabolic process	0.0331554372984391
GO:0044248	cellular catabolic process	0.033577971469853
GO:0043085	positive regulation of catalytic activity	0.0349332211990327
GO:0007041	lysosomal transport	0.0356421855368791
GO:0030149	sphingolipid catabolic process	0.0375213613292531
GO:0048029	monosaccharide binding	0.0410886012693866
GO:0015929	hexosaminidase activity	0.0410886012693866
GO:0050885	neuromuscular process controlling balance	0.0427829322362058
GO:0006687	glycosphingolipid metabolic process	0.0444215781542066

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	4.89e-35	76
granulocyte monocyte progenitor cell	1.13e-32	71
macrophage dendritic cell progenitor	1.85e-30	65
myeloid lineage restricted progenitor cell	6.45e-30	70
monopoietic cell	2.31e-29	63
monocyte	2.31e-29	63
monoblast	2.31e-29	63
promonocyte	2.31e-29	63
CD14-positive, CD16-negative classical monocyte	1.44e-26	42
classical monocyte	1.57e-22	45
myeloid cell	1.49e-19	112
common myeloid progenitor	1.49e-19	112
leukocyte	1.39e-18	140
hematopoietic lineage restricted progenitor cell	3.64e-13	124
nongranular leukocyte	2.20e-12	119
hematopoietic cell	2.13e-10	182
hematopoietic stem cell	2.20e-10	172
angioblastic mesenchymal cell	2.20e-10	172
hematopoietic oligopotent progenitor cell	1.37e-09	165
hematopoietic multipotent progenitor cell	1.37e-09	165
dendritic cell	9.57e-07	10

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.01e-35	112
hematopoietic system	6.45e-34	102
blood island	6.45e-34	102
bone marrow	7.00e-30	80
lateral plate mesoderm	1.39e-27	216
immune system	5.13e-27	115
bone element	6.24e-24	86
skeletal element	1.09e-20	101
skeletal system	1.09e-20	101
mesoderm	8.14e-12	448
mesoderm-derived structure	8.14e-12	448
presumptive mesoderm	8.14e-12	448
musculoskeletal system	1.27e-11	167
anatomical group	3.32e-10	626
anatomical system	4.48e-10	625
embryonic structure	1.34e-07	605
developing anatomical structure	1.34e-07	605
organ	1.43e-07	511
germ layer	1.67e-07	604
embryonic tissue	1.67e-07	604
presumptive structure	1.67e-07	604
epiblast (generic)	1.67e-07	604
multi-cellular organism	2.15e-07	659
embryo	4.64e-07	612

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.