Coexpression cluster:C300

Full id: C300_CD4_CD8_NK_Natural_blood_mycosis_Basophils

Phase1 CAGE Peaks

Hg19::chr14:22362614..22362619,+	p1@TRAV8-4
Hg19::chr14:22446777..22446791,+	p2@uc010tml.1 p2@uc010tmm.1
Hg19::chr14:91708304..91708315,+	p@chr14:91708304..91708315 +
Hg19::chr14:91708318..91708330,+	p@chr14:91708318..91708330 +
Hg19::chr14:94442986..94442992,-	p15@ASB2
Hg19::chr18:67624010..67624041,-	p5@CD226
Hg19::chr19:17295496..17295508,+	p@chr19:17295496..17295508 +
Hg19::chr1:150082476..150082490,+	p@chr1:150082476..150082490 +
Hg19::chr22:39147814..39147833,-	p11@SUN2
Hg19::chr2:182249921..182249925,+	p@chr2:182249921..182249925 +
Hg19::chr2:191931233..191931243,-	p@chr2:191931233..191931243 -
Hg19::chr2:197041193..197041212,-	p5@STK17B
Hg19::chr2:39347524..39347552,-	p4@SOS1
Hg19::chr2:39347770..39347791,-	p5@SOS1
Hg19::chr2:39348137..39348212,-	p1@SOS1
Hg19::chr2:39348418..39348431,-	p17@SOS1
Hg19::chr2:39348469..39348498,-	p9@SOS1
Hg19::chr2:39351689..39351715,+	p@chr2:39351689..39351715 +
Hg19::chr2:7865859..7865862,+	p3@ENST00000417930
Hg19::chr2:7865873..7865921,+	p1@ENST00000417930
Hg19::chr2:7865923..7865941,+	p2@ENST00000417930
Hg19::chr3:45984947..45984966,+	p1@CXCR6
Hg19::chr3:46395344..46395359,+	p2@CCR2
Hg19::chr3:46395363..46395374,+	p7@CCR2
Hg19::chr3:4867715..4867729,-	p@chr3:4867715..4867729 -
Hg19::chr3:51715738..51715765,+	p2@TEX264
Hg19::chr4:6692260..6692274,-	p2@ENST00000499502
Hg19::chr4:6692355..6692360,-	p3@ENST00000499502
Hg19::chr5:54398463..54398480,+	p1@GZMA
Hg19::chr6:128201709..128201716,-	p@chr6:128201709..128201716 -
Hg19::chr6:149555824..149555843,-	p@chr6:149555824..149555843 -
Hg19::chrX:135721685..135721705,+	p1@LOC100128420
Hg19::chrX:135721762..135721773,+	p4@ENST00000429841
Hg19::chrX:135721794..135721808,+	p3@ENST00000429841
Hg19::chrX:135721811..135721833,+	p1@ENST00000429841
Hg19::chrX:135721840..135721857,+	p2@ENST00000429841
Hg19::chrX:135721874..135721887,+	p1@ENST00000427517 p1@uc004ezz.2
Hg19::chrX:135730297..135730350,+	p1@CD40LG
Hg19::chrX:135730373..135730399,+	p2@CD40LG
Hg19::chrX:135741632..135741643,+	p@chrX:135741632..135741643 +
Hg19::chrX:135742035..135742051,+	p@chrX:135742035..135742051 +
Hg19::chrX:135742088..135742115,+	p@chrX:135742088..135742115 +

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
0.000163562511943431	0.0258837675150479	3	265	Cytokine-cytokine receptor interaction (KEGG):04060
6.01405003919819e-05	0.0126896455827082	3	189	Chemokine signaling pathway (KEGG):04062
4.48189730095749e-05	0.0126896455827082	4	511	Signaling in Immune system (Reactome):REACT_6900
2.34678751347395e-05	0.0126896455827082	4	433	IL-2 up reg. targets (Netpath):NetPath_14

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:0019957	C-C chemokine binding	0.00203275243585207
GO:0016493	C-C chemokine receptor activity	0.00203275243585207
GO:0004950	chemokine receptor activity	0.00203275243585207
GO:0001637	G-protein chemoattractant receptor activity	0.00203275243585207
GO:0019956	chemokine binding	0.00203275243585207
GO:0007165	signal transduction	0.00203275243585207
GO:0007242	intracellular signaling cascade	0.00236279697749897
GO:0007154	cell communication	0.00257076988205919
GO:0044459	plasma membrane part	0.00378351305242138
GO:0005887	integral to plasma membrane	0.00438007771105616
GO:0031226	intrinsic to plasma membrane	0.00438007771105616
GO:0031727	CCR2 chemokine receptor binding	0.00438007771105616
GO:0048020	CCR chemokine receptor binding	0.00438007771105616
GO:0004277	granzyme A activity	0.00438007771105616
GO:0005174	CD40 receptor binding	0.00438007771105616
GO:0019955	cytokine binding	0.00462889244648079
GO:0001816	cytokine production	0.00567214870023238
GO:0032735	positive regulation of interleukin-12 production	0.0072992699464958
GO:0001653	peptide receptor activity	0.00824820650737661
GO:0008528	peptide receptor activity, G-protein coupled	0.00824820650737661
GO:0006922	cleavage of lamin	0.00856769927397956
GO:0006923	cleavage of cytoskeletal proteins during apoptosis	0.00856769927397956
GO:0032655	regulation of interleukin-12 production	0.00856769927397956
GO:0006915	apoptosis	0.0120987350741618
GO:0012501	programmed cell death	0.0120987350741618
GO:0042277	peptide binding	0.0124533973568257
GO:0008219	cell death	0.0125502845118458
GO:0016265	death	0.0125502845118458
GO:0005886	plasma membrane	0.0130053297491197
GO:0032615	interleukin-12 production	0.0131324991110303
GO:0005625	soluble fraction	0.013179067182002
GO:0005515	protein binding	0.0151343927086091
GO:0006954	inflammatory response	0.0185092915895833
GO:0007159	leukocyte adhesion	0.0185092915895833
GO:0016494	C-X-C chemokine receptor activity	0.0185092915895833
GO:0002208	somatic diversification of immunoglobulins during immune response	0.0185092915895833
GO:0002381	immunoglobulin production during immune response	0.0185092915895833
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.0185092915895833
GO:0045190	isotype switching	0.0185092915895833
GO:0006955	immune response	0.0190092271228569
GO:0019958	C-X-C chemokine binding	0.0192047199434155
GO:0016447	somatic recombination of immunoglobulin gene segments	0.0197993162207085
GO:0048468	cell development	0.0197993162207085
GO:0031280	negative regulation of cyclase activity	0.0197993162207085
GO:0016444	somatic cell DNA recombination	0.0197993162207085
GO:0007194	negative regulation of adenylate cyclase activity	0.0197993162207085
GO:0051350	negative regulation of lyase activity	0.0197993162207085
GO:0016445	somatic diversification of immunoglobulins	0.0197993162207085
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.0197993162207085
GO:0007243	protein kinase cascade	0.0197993162207085
GO:0015026	coreceptor activity	0.0197993162207085
GO:0002200	somatic diversification of immune receptors	0.0197993162207085
GO:0019835	cytolysis	0.0197993162207085
GO:0001772	immunological synapse	0.0206447731653015
GO:0002376	immune system process	0.020706251242198
GO:0002377	immunoglobulin production	0.020706251242198
GO:0042100	B cell proliferation	0.020706251242198
GO:0009611	response to wounding	0.0224701169761612
GO:0006921	cell structure disassembly during apoptosis	0.0233301615954918
GO:0001819	positive regulation of cytokine production	0.0251202993534965
GO:0005100	Rho GTPase activator activity	0.0257797388481279
GO:0030168	platelet activation	0.026417657728311
GO:0002440	production of molecular mediator of immune response	0.0280715875138972
GO:0019079	viral genome replication	0.0296728701447912
GO:0042981	regulation of apoptosis	0.0356996152922203
GO:0043067	regulation of programmed cell death	0.0357711508412229
GO:0006952	defense response	0.0357711508412229
GO:0048869	cellular developmental process	0.0357711508412229
GO:0030154	cell differentiation	0.0357711508412229
GO:0005164	tumor necrosis factor receptor binding	0.0359283039721178
GO:0007259	JAK-STAT cascade	0.0359283039721178
GO:0001817	regulation of cytokine production	0.0361337348780551
GO:0045761	regulation of adenylate cyclase activity	0.0361337348780551
GO:0032813	tumor necrosis factor receptor superfamily binding	0.0361337348780551
GO:0031279	regulation of cyclase activity	0.0361337348780551
GO:0051339	regulation of lyase activity	0.0361337348780551
GO:0019221	cytokine and chemokine mediated signaling pathway	0.0363786717589302
GO:0009605	response to external stimulus	0.0363786717589302
GO:0022411	cellular component disassembly	0.0405217762126783
GO:0019058	viral infectious cycle	0.0408270885386266
GO:0016064	immunoglobulin mediated immune response	0.0411246731931978
GO:0019724	B cell mediated immunity	0.0412013747883468
GO:0032943	mononuclear cell proliferation	0.0412013747883468
GO:0046651	lymphocyte proliferation	0.0412013747883468
GO:0022415	viral reproductive process	0.0437690085605704
GO:0042113	B cell activation	0.0462740844094532

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
mature alpha-beta T cell	3.66e-54	18
alpha-beta T cell	3.66e-54	18
immature T cell	3.66e-54	18
mature T cell	3.66e-54	18
immature alpha-beta T cell	3.66e-54	18
T cell	7.29e-42	25
pro-T cell	7.29e-42	25
CD8-positive, alpha-beta T cell	4.99e-34	11
lymphoid lineage restricted progenitor cell	4.75e-24	52
lymphocyte	1.75e-23	53
common lymphoid progenitor	1.75e-23	53
nucleate cell	2.06e-22	55
CD4-positive, alpha-beta T cell	1.05e-18	6
nongranular leukocyte	4.29e-15	115
leukocyte	9.71e-13	136
hematopoietic lineage restricted progenitor cell	8.88e-11	120
naive T cell	3.49e-10	3
natural killer cell	6.10e-10	3
pro-NK cell	6.10e-10	3
single nucleate cell	8.05e-10	3
mononuclear cell	8.05e-10	3
hematopoietic stem cell	5.88e-09	168
angioblastic mesenchymal cell	5.88e-09	168
hematopoietic cell	3.75e-08	177
thymocyte	1.13e-07	2
double negative thymocyte	1.13e-07	2
double-positive, alpha-beta thymocyte	1.13e-07	2
DN4 thymocyte	1.13e-07	2
DN1 thymic pro-T cell	1.13e-07	2
DN2 thymocyte	1.13e-07	2
DN3 thymocyte	1.13e-07	2
immature single positive thymocyte	1.13e-07	2
early T lineage precursor	1.13e-07	2
hematopoietic oligopotent progenitor cell	3.04e-07	161
hematopoietic multipotent progenitor cell	3.04e-07	161
regulatory T cell	4.02e-07	2
CD4-positive, CD25-positive, alpha-beta regulatory T cell	4.02e-07	2
naive regulatory T cell	4.02e-07	2

Uber Anatomy

Ontology term	p-value	n
blood	2.82e-23	15
haemolymphatic fluid	2.82e-23	15
organism substance	2.82e-23	15
hemopoietic organ	6.95e-15	7
immune organ	6.95e-15	7
thymus	1.44e-12	4
hemolymphoid system gland	1.44e-12	4
thymic region	1.44e-12	4
pharyngeal gland	1.44e-12	4
thymus primordium	1.44e-12	4
pharyngeal epithelium	2.16e-08	6
hematopoietic system	2.95e-08	98
blood island	2.95e-08	98
hemolymphoid system	6.07e-08	108
chordate pharynx	1.94e-07	10
pharyngeal region of foregut	1.94e-07	10
neck	2.61e-07	10
pharynx	9.88e-07	11

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
RXRA#6256	7	3.34576952318888	0.00440402534344863	0.0208670720825892

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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