Coexpression cluster:C244

Full id: C244_CD14_Monocytederived_Hepatocyte_heart_Neutrophils_acute_Macrophage

Phase1 CAGE Peaks

Hg19::chr10:81025241..81025245,+	p@chr10:81025241..81025245 +
Hg19::chr10:81111074..81111077,+	p@chr10:81111074..81111077 +
Hg19::chr11:104815548..104815551,-	p@chr11:104815548..104815551 -
Hg19::chr12:56046384..56046387,+	p@chr12:56046384..56046387 +
Hg19::chr12:89431933..89431936,-	p@chr12:89431933..89431936 -
Hg19::chr14:100828867..100828870,-	p@chr14:100828867..100828870 -
Hg19::chr14:55603238..55603250,+	p15@LGALS3
Hg19::chr16:21623958..21623973,+	p@chr16:21623958..21623973 +
Hg19::chr16:31360617..31360620,-	p@chr16:31360617..31360620 -
Hg19::chr16:31381019..31381027,+	p@chr16:31381019..31381027 +
Hg19::chr16:31926633..31926654,+	p@chr16:31926633..31926654 +
Hg19::chr16:50706590..50706610,-	p@chr16:50706590..50706610 -
Hg19::chr17:54976102..54976122,-	p@chr17:54976102..54976122 -
Hg19::chr17:75352671..75352704,+	p@chr17:75352671..75352704 +
Hg19::chr19:40972117..40972122,-	p4@BLVRB
Hg19::chr19:4569647..4569651,+	p@chr19:4569647..4569651 +
Hg19::chr19:6663476..6663487,-	p8@AK026704
Hg19::chr19:6663488..6663497,-	p5@AK026704
Hg19::chr19:6663518..6663558,-	p2@AK026704
Hg19::chr19:6663572..6663662,-	p1@AK026704
Hg19::chr19:6663833..6663841,-	p6@AK026704
Hg19::chr19:6663876..6663885,-	p7@AK026704
Hg19::chr1:145038845..145038849,-	p@chr1:145038845..145038849 -
Hg19::chr1:154435643..154435648,+	p@chr1:154435643..154435648 +
Hg19::chr1:159787777..159787780,-	p@chr1:159787777..159787780 -
Hg19::chr1:25362175..25362187,+	p@chr1:25362175..25362187 +
Hg19::chr1:25362249..25362302,+	p@chr1:25362249..25362302 +
Hg19::chr1:25362605..25362625,+	p@chr1:25362605..25362625 +
Hg19::chr20:39690091..39690102,+	p@chr20:39690091..39690102 +
Hg19::chr20:48809000..48809053,+	p12@CEBPB
Hg19::chr21:30613305..30613309,+	p@chr21:30613305..30613309 +
Hg19::chr22:36632299..36632310,-	p@chr22:36632299..36632310 -
Hg19::chr2:240202309..240202321,+	p@chr2:240202309..240202321 +
Hg19::chr2:240202391..240202405,+	p@chr2:240202391..240202405 +
Hg19::chr2:240202435..240202445,+	p@chr2:240202435..240202445 +
Hg19::chr2:240202757..240202766,+	p@chr2:240202757..240202766 +
Hg19::chr2:87781799..87781811,+	p@chr2:87781799..87781811 +
Hg19::chr2:87781831..87781841,+	p@chr2:87781831..87781841 +
Hg19::chr3:122399875..122399886,+	p7@PARP14
Hg19::chr3:122444648..122444658,+	p@chr3:122444648..122444658 +
Hg19::chr3:15483499..15483511,+	p@chr3:15483499..15483511 +
Hg19::chr3:196044455..196044479,-	p@chr3:196044455..196044479 -
Hg19::chr5:55160032..55160047,+	p@chr5:55160032..55160047 +
Hg19::chr5:55160483..55160494,+	p@chr5:55160483..55160494 +
Hg19::chr6:74410846..74410849,+	p@chr6:74410846..74410849 +
Hg19::chr6:74492716..74492719,+	p@chr6:74492716..74492719 +
Hg19::chr6:74512050..74512056,+	p@chr6:74512050..74512056 +
Hg19::chr7:130575788..130575792,-	p@chr7:130575788..130575792 -
Hg19::chr7:47513678..47513702,+	p@chr7:47513678..47513702 +
Hg19::chr7:47514268..47514279,+	p@chr7:47514268..47514279 +
Hg19::chr8:20094845..20094867,+	p@chr8:20094845..20094867 +
Hg19::chr8:24250424..24250429,+	p@chr8:24250424..24250429 +
Hg19::chr8:62606823..62606835,-	p@chr8:62606823..62606835 -
Hg19::chr9:90343853..90343856,+	p@chr9:90343853..90343856 +
Hg19::chrX:118129290..118129323,+	p@chrX:118129290..118129323 +

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:0042602	flavin reductase activity	0.0151883084852404
GO:0004074	biliverdin reductase activity	0.0151883084852404
GO:0001892	embryonic placenta development	0.0189828707762266
GO:0019863	IgE binding	0.0189828707762266
GO:0045408	regulation of interleukin-6 biosynthetic process	0.0220784317266505
GO:0042226	interleukin-6 biosynthetic process	0.0220784317266505
GO:0032635	interleukin-6 production	0.0220784317266505
GO:0001890	placenta development	0.0220784317266505
GO:0045444	fat cell differentiation	0.0220784317266505
GO:0016628	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor	0.0220784317266505
GO:0019865	immunoglobulin binding	0.0220784317266505
GO:0005737	cytoplasm	0.0252768643803778
GO:0006953	acute-phase response	0.0368338048269068
GO:0016646	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	0.0368338048269068
GO:0003950	NAD+ ADP-ribosyltransferase activity	0.0384159270903756
GO:0001701	in utero embryonic development	0.0463558843129863
GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	0.0463558843129863

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
classical monocyte	2.30e-135	42
CD14-positive, CD16-negative classical monocyte	2.30e-135	42
defensive cell	9.49e-118	48
phagocyte	9.49e-118	48
monopoietic cell	4.45e-93	59
monocyte	4.45e-93	59
monoblast	4.45e-93	59
promonocyte	4.45e-93	59
macrophage dendritic cell progenitor	6.81e-90	61
myeloid lineage restricted progenitor cell	9.19e-83	66
granulocyte monocyte progenitor cell	1.84e-81	67
myeloid leukocyte	1.71e-75	72
stuff accumulating cell	1.99e-62	87
nongranular leukocyte	5.98e-55	115
hematopoietic lineage restricted progenitor cell	2.76e-49	120
myeloid cell	1.15e-48	108
common myeloid progenitor	1.15e-48	108
leukocyte	1.25e-45	136
hematopoietic stem cell	7.17e-36	168
angioblastic mesenchymal cell	7.17e-36	168
hematopoietic oligopotent progenitor cell	2.54e-35	161
hematopoietic multipotent progenitor cell	2.54e-35	161
hematopoietic cell	9.33e-34	177
mesenchymal cell	6.99e-14	354
connective tissue cell	1.71e-13	361
motile cell	4.04e-12	386
multi fate stem cell	1.94e-10	427
somatic stem cell	3.31e-10	433
stem cell	6.61e-10	441

Uber Anatomy

Ontology term	p-value	n
bone marrow	2.81e-71	76
bone element	1.03e-65	82
skeletal element	1.97e-59	90
hematopoietic system	8.96e-58	98
blood island	8.96e-58	98
immune system	2.37e-57	93
skeletal system	5.61e-53	100
hemolymphoid system	6.09e-52	108
musculoskeletal system	1.61e-29	167
lateral plate mesoderm	5.33e-25	203
mesoderm	5.59e-14	315
mesoderm-derived structure	5.59e-14	315
presumptive mesoderm	5.59e-14	315
connective tissue	5.82e-13	371

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
FOSL1#8061	5	3.61032542876118	0.0123941264726273	0.0448722631356719
STAT2#6773	4	4.74645608628659	0.0100948890446183	0.03780479478381

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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