Coexpression cluster:C2173

Full id: C2173_CD14_Hepatocyte_liver_Monocytederived_Macrophage_myeloma_lung

Phase1 CAGE Peaks

Hg19::chr11:914812..914866,-	p3@CHID1
Hg19::chr6:31895467..31895479,+	p4@C2 p6@CFB
Hg19::chr6:31895480..31895530,+	p1@C2
Hg19::chr7:150488653..150488682,-	p@chr7:150488653..150488682 -

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:0003813	classical-complement-pathway C3/C5 convertase activity	0.00523960908983869
GO:0006032	chitin catabolic process	0.0112254201983592
GO:0006046	N-acetylglucosamine catabolic process	0.0112254201983592
GO:0006043	glucosamine catabolic process	0.0112254201983592
GO:0006030	chitin metabolic process	0.0112254201983592
GO:0004568	chitinase activity	0.0112254201983592
GO:0046348	amino sugar catabolic process	0.0112254201983592
GO:0044247	cellular polysaccharide catabolic process	0.0122221556631645
GO:0000272	polysaccharide catabolic process	0.0122221556631645
GO:0006958	complement activation, classical pathway	0.0134185936103104
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0134185936103104
GO:0006044	N-acetylglucosamine metabolic process	0.0134185936103104
GO:0006041	glucosamine metabolic process	0.0134185936103104
GO:0006956	complement activation	0.0134185936103104
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0134185936103104
GO:0006040	amino sugar metabolic process	0.0134185936103104
GO:0016064	immunoglobulin mediated immune response	0.0151252863041258
GO:0019724	B cell mediated immunity	0.0151252863041258
GO:0002253	activation of immune response	0.0155187118245836
GO:0002449	lymphocyte mediated immunity	0.0155187118245836
GO:0006959	humoral immune response	0.0155187118245836
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0155187118245836
GO:0002250	adaptive immune response	0.0155187118245836
GO:0002443	leukocyte mediated immunity	0.0155187118245836
GO:0002526	acute inflammatory response	0.0155187118245836
GO:0044264	cellular polysaccharide metabolic process	0.0155187118245836
GO:0050778	positive regulation of immune response	0.0155187118245836
GO:0005976	polysaccharide metabolic process	0.0155187118245836
GO:0002684	positive regulation of immune system process	0.0155187118245836
GO:0050776	regulation of immune response	0.0168773365271673
GO:0002682	regulation of immune system process	0.0168773365271673
GO:0051240	positive regulation of multicellular organismal process	0.0171661505175509
GO:0002252	immune effector process	0.017437343782983
GO:0045087	innate immune response	0.0175388820935643
GO:0044275	cellular carbohydrate catabolic process	0.0270582014484685
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0270582014484685
GO:0016052	carbohydrate catabolic process	0.0270582014484685
GO:0005764	lysosome	0.0270582014484685
GO:0000323	lytic vacuole	0.0270582014484685
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0287249603360411
GO:0016787	hydrolase activity	0.0289680995531216
GO:0005773	vacuole	0.0289680995531216
GO:0051239	regulation of multicellular organismal process	0.0336157169153266
GO:0006954	inflammatory response	0.0345049587537292
GO:0004252	serine-type endopeptidase activity	0.0385836416675041
GO:0008236	serine-type peptidase activity	0.0417957633034446
GO:0017171	serine hydrolase activity	0.0417957633034446
GO:0009611	response to wounding	0.0458872597308855
GO:0043285	biopolymer catabolic process	0.0482229001898716
GO:0044260	cellular macromolecule metabolic process	0.0493324365086639

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
defensive cell	2.97e-26	48
phagocyte	2.97e-26	48
monopoietic cell	2.99e-26	59
monocyte	2.99e-26	59
monoblast	2.99e-26	59
promonocyte	2.99e-26	59
myeloid lineage restricted progenitor cell	7.13e-25	66
macrophage dendritic cell progenitor	1.03e-24	61
granulocyte monocyte progenitor cell	3.50e-24	67
myeloid leukocyte	6.09e-22	72
classical monocyte	3.74e-21	42
CD14-positive, CD16-negative classical monocyte	3.74e-21	42
stuff accumulating cell	5.79e-14	87
myeloid cell	2.44e-12	108
common myeloid progenitor	2.44e-12	108
nongranular leukocyte	4.33e-07	115
macrophage	7.62e-07	6

Uber Anatomy

Ontology term	p-value	n
adult organism	6.81e-28	114
bone marrow	2.39e-23	76
immune system	6.79e-23	93
bone element	5.11e-20	82
hematopoietic system	1.77e-19	98
blood island	1.77e-19	98
hemolymphoid system	9.90e-19	108
skeletal element	1.12e-17	90
skeletal system	4.44e-17	100
organ	4.56e-14	503
germ layer	5.07e-09	560
germ layer / neural crest	5.07e-09	560
embryonic tissue	5.07e-09	560
presumptive structure	5.07e-09	560
germ layer / neural crest derived structure	5.07e-09	560
epiblast (generic)	5.07e-09	560
musculoskeletal system	7.09e-09	167
embryonic structure	7.89e-09	564
anatomical system	1.21e-08	624
anatomical group	1.56e-08	625
multi-cellular organism	3.49e-08	656
developing anatomical structure	8.20e-08	581
embryo	1.22e-07	592
neural tube	1.63e-07	56
neural rod	1.63e-07	56
future spinal cord	1.63e-07	56
neural keel	1.63e-07	56

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
BHLHE40#8553	2	22.4359067734887	0.00289146449685312	0.0156369956807603
FOXA2#3170	2	12.3152318763326	0.00936191628546724	0.0353347972584263
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992187977192428
HNF4A#3172	2	11.5661451814768	0.0105758568176249	0.0390611419236811
HNF4G#3174	2	14.3767112632234	0.00692416998043918	0.0293000035892828
RXRA#6256	3	15.05596285435	0.000475830799730358	0.00433641299241177
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464858870704779
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898160279798865
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482781012554489

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.