Coexpression cluster:C817

Full id: C817_cord_CD14_mycosis_xeroderma_migratory_B_hairy

Phase1 CAGE Peaks

Hg19::chr12:24858680..24858711,-	p@chr12:24858680..24858711 -
Hg19::chr12:39300630..39300641,-	p@chr12:39300630..39300641 -
Hg19::chr12:47787958..47787968,-	p@chr12:47787958..47787968 -
Hg19::chr17:40440359..40440386,+	p4@STAT5A
Hg19::chr2:223288634..223288698,+	p2@SGPP2
Hg19::chr3:47032286..47032317,+	p@chr3:47032286..47032317 +
Hg19::chr6:138192164..138192180,+	p4@TNFAIP3
Hg19::chr6:138192205..138192214,+	p15@TNFAIP3
Hg19::chr6:138192259..138192268,+	p18@TNFAIP3
Hg19::chr8:145086442..145086455,+	p2@SPATC1

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:0006916	anti-apoptosis	0.0098087440622032
GO:0046544	development of secondary male sexual characteristics	0.0098087440622032
GO:0001779	natural killer cell differentiation	0.0098087440622032
GO:0001553	luteinization	0.0098087440622032
GO:0046543	development of secondary female sexual characteristics	0.0098087440622032
GO:0043066	negative regulation of apoptosis	0.0098087440622032
GO:0043069	negative regulation of programmed cell death	0.0098087440622032
GO:0045136	development of secondary sexual characteristics	0.010829102476073
GO:0045647	negative regulation of erythrocyte differentiation	0.010829102476073
GO:0045579	positive regulation of B cell differentiation	0.010829102476073
GO:0045931	positive regulation of progression through mitotic cell cycle	0.010829102476073
GO:0043029	T cell homeostasis	0.010829102476073
GO:0042104	positive regulation of activated T cell proliferation	0.010829102476073
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.010829102476073
GO:0007243	protein kinase cascade	0.010829102476073
GO:0045621	positive regulation of lymphocyte differentiation	0.010829102476073
GO:0046006	regulation of activated T cell proliferation	0.010829102476073
GO:0030856	regulation of epithelial cell differentiation	0.010829102476073
GO:0050798	activated T cell proliferation	0.010829102476073
GO:0019915	sequestering of lipid	0.010829102476073
GO:0045885	positive regulation of survival gene product activity	0.010829102476073
GO:0045577	regulation of B cell differentiation	0.010829102476073
GO:0019218	regulation of steroid metabolic process	0.0116977484600152
GO:0002260	lymphocyte homeostasis	0.0116977484600152
GO:0050729	positive regulation of inflammatory response	0.0116977484600152
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.0116977484600152
GO:0031349	positive regulation of defense response	0.0116977484600152
GO:0045646	regulation of erythrocyte differentiation	0.0116977484600152
GO:0040018	positive regulation of multicellular organism growth	0.0123205953733832
GO:0030879	mammary gland development	0.0125345319247793
GO:0001776	leukocyte homeostasis	0.0125345319247793
GO:0042981	regulation of apoptosis	0.0125345319247793
GO:0043067	regulation of programmed cell death	0.0125345319247793
GO:0048872	homeostasis of number of cells	0.0125345319247793
GO:0045076	regulation of interleukin-2 biosynthetic process	0.0125345319247793
GO:0045884	regulation of survival gene product activity	0.0125345319247793
GO:0042094	interleukin-2 biosynthetic process	0.0125345319247793
GO:0045619	regulation of lymphocyte differentiation	0.0125345319247793
GO:0030101	natural killer cell activation	0.0130683881921848
GO:0050871	positive regulation of B cell activation	0.0130683881921848
GO:0045638	negative regulation of myeloid cell differentiation	0.0130683881921848
GO:0005737	cytoplasm	0.0137767055420435
GO:0032623	interleukin-2 production	0.0137767055420435
GO:0007595	lactation	0.0137767055420435
GO:0040014	regulation of multicellular organism growth	0.0137767055420435
GO:0045927	positive regulation of growth	0.0137767055420435
GO:0035264	multicellular organism growth	0.0137767055420435
GO:0045787	positive regulation of progression through cell cycle	0.0137767055420435
GO:0022601	menstrual cycle phase	0.0137767055420435
GO:0031347	regulation of defense response	0.0137767055420435
GO:0050727	regulation of inflammatory response	0.0137767055420435
GO:0042102	positive regulation of T cell proliferation	0.0137767055420435
GO:0022602	menstrual cycle process	0.0137767055420435
GO:0050864	regulation of B cell activation	0.0137767055420435
GO:0008585	female gonad development	0.0145156931210802
GO:0019216	regulation of lipid metabolic process	0.0145156931210802
GO:0030183	B cell differentiation	0.0145156931210802
GO:0046545	development of primary female sexual characteristics	0.0145156931210802
GO:0046660	female sex differentiation	0.0145156931210802
GO:0032946	positive regulation of mononuclear cell proliferation	0.0145156931210802
GO:0050671	positive regulation of lymphocyte proliferation	0.0145156931210802
GO:0006915	apoptosis	0.0145156931210802
GO:0012501	programmed cell death	0.0145156931210802
GO:0046661	male sex differentiation	0.0145156931210802
GO:0007346	regulation of progression through mitotic cell cycle	0.0145156931210802
GO:0030218	erythrocyte differentiation	0.0145156931210802
GO:0042698	menstrual cycle	0.0145156931210802
GO:0042129	regulation of T cell proliferation	0.0145156931210802
GO:0045637	regulation of myeloid cell differentiation	0.0145156931210802
GO:0048583	regulation of response to stimulus	0.0145156931210802
GO:0008219	cell death	0.0145156931210802
GO:0016265	death	0.0145156931210802
GO:0030855	epithelial cell differentiation	0.0146678950118608
GO:0042098	T cell proliferation	0.0154644313545556
GO:0007259	JAK-STAT cascade	0.0154644313545556
GO:0042108	positive regulation of cytokine biosynthetic process	0.0158086676443632
GO:0050870	positive regulation of T cell activation	0.0158086676443632
GO:0050670	regulation of lymphocyte proliferation	0.0158086676443632
GO:0032944	regulation of mononuclear cell proliferation	0.0158086676443632
GO:0019221	cytokine and chemokine mediated signaling pathway	0.0159820453218798
GO:0048732	gland development	0.0168837595886084
GO:0051251	positive regulation of lymphocyte activation	0.0181058406720078
GO:0008406	gonad development	0.0181058406720078
GO:0048608	reproductive structure development	0.0181058406720078
GO:0032943	mononuclear cell proliferation	0.0181058406720078
GO:0045727	positive regulation of translation	0.0181058406720078
GO:0046651	lymphocyte proliferation	0.0181058406720078
GO:0048523	negative regulation of cellular process	0.0184569630324013
GO:0048519	negative regulation of biological process	0.0188784886440321
GO:0050863	regulation of T cell activation	0.0188784886440321
GO:0045137	development of primary sexual characteristics	0.0188784886440321
GO:0042035	regulation of cytokine biosynthetic process	0.0188784886440321
GO:0031328	positive regulation of cellular biosynthetic process	0.0188784886440321
GO:0048609	reproductive process in a multicellular organism	0.0188784886440321
GO:0032504	multicellular organism reproduction	0.0188784886440321
GO:0042113	B cell activation	0.0188784886440321
GO:0002009	morphogenesis of an epithelium	0.0192947462408728
GO:0030098	lymphocyte differentiation	0.0193083537645488
GO:0048468	cell development	0.0193083537645488
GO:0045596	negative regulation of cell differentiation	0.0193083537645488
GO:0030155	regulation of cell adhesion	0.019410435056621
GO:0042089	cytokine biosynthetic process	0.0195104890621031
GO:0042107	cytokine metabolic process	0.0196085748296782
GO:0009891	positive regulation of biosynthetic process	0.019989442238841
GO:0051249	regulation of lymphocyte activation	0.0213652824192219
GO:0030099	myeloid cell differentiation	0.0213652824192219
GO:0051093	negative regulation of developmental process	0.0213652824192219
GO:0050865	regulation of cell activation	0.0218583455770107
GO:0007565	female pregnancy	0.0218583455770107
GO:0007548	sex differentiation	0.0218583455770107
GO:0051247	positive regulation of protein metabolic process	0.0225908458224773
GO:0043229	intracellular organelle	0.0225908458224773
GO:0043226	organelle	0.0225908458224773
GO:0003006	reproductive developmental process	0.022647707531505
GO:0002521	leukocyte differentiation	0.0232218577750432
GO:0042110	T cell activation	0.0250591822261653
GO:0009968	negative regulation of signal transduction	0.0263591358542017
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0271361788289405
GO:0001816	cytokine production	0.028147672630088
GO:0005813	centrosome	0.0318428891726392
GO:0048869	cellular developmental process	0.0328468075171884
GO:0030154	cell differentiation	0.0328468075171884
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0331898449785698
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0331898449785698
GO:0045595	regulation of cell differentiation	0.0341011196355686
GO:0005815	microtubule organizing center	0.0345306996525982
GO:0046649	lymphocyte activation	0.0361104615281305
GO:0007242	intracellular signaling cascade	0.0366690693465053
GO:0030097	hemopoiesis	0.0369169725815447
GO:0048534	hemopoietic or lymphoid organ development	0.0393425365237529
GO:0045321	leukocyte activation	0.0404395778703146
GO:0044424	intracellular part	0.0404395778703146
GO:0002520	immune system development	0.0404395778703146
GO:0006417	regulation of translation	0.0405752779607144
GO:0031326	regulation of cellular biosynthetic process	0.0435291181174172
GO:0040008	regulation of growth	0.0436394550898104
GO:0001775	cell activation	0.0450292094685027
GO:0009889	regulation of biosynthetic process	0.0463976173369759
GO:0045893	positive regulation of transcription, DNA-dependent	0.0469868872906378
GO:0008202	steroid metabolic process	0.0469868872906378
GO:0008284	positive regulation of cell proliferation	0.0487241955275788
GO:0050793	regulation of developmental process	0.0489975011728461

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
leukocyte	3.84e-31	140
hematopoietic stem cell	1.30e-25	172
angioblastic mesenchymal cell	1.30e-25	172
hematopoietic oligopotent progenitor cell	1.96e-25	165
hematopoietic multipotent progenitor cell	1.96e-25	165
nongranular leukocyte	7.01e-25	119
hematopoietic cell	1.79e-24	182
hematopoietic lineage restricted progenitor cell	2.05e-23	124
myeloid leukocyte	8.07e-22	76
granulocyte monocyte progenitor cell	8.95e-19	71
macrophage dendritic cell progenitor	9.33e-19	65
myeloid cell	2.58e-18	112
common myeloid progenitor	2.58e-18	112
monopoietic cell	8.70e-18	63
monocyte	8.70e-18	63
monoblast	8.70e-18	63
promonocyte	8.70e-18	63
CD14-positive, CD16-negative classical monocyte	4.21e-17	42
myeloid lineage restricted progenitor cell	8.38e-17	70
classical monocyte	3.98e-16	45
lymphocyte	5.43e-07	53
common lymphoid progenitor	5.43e-07	53

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	7.22e-19	112
hematopoietic system	1.13e-17	102
blood island	1.13e-17	102
bone marrow	6.89e-15	80
immune system	6.25e-14	115
bone element	5.97e-12	86
lateral plate mesoderm	4.87e-11	216
skeletal element	2.11e-08	101
skeletal system	2.11e-08	101

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
EBF1#1879	6	5.3438801079414	0.000280926593131646	0.00298988000204585
IRF4#3662	5	10.9572563433721	4.10495409675721e-05	0.000745854733666017
NFKB1#4790	9	4.93925708177445	1.84959706943667e-06	6.85973254030173e-05
TCF12#6938	4	4.25378596087457	0.0103111806051884	0.0383002948829986

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.