Coexpression cluster:C726

Full id: C726_chronic_CD4_Hodgkin_CD8_thymus_CD19_blood

Phase1 CAGE Peaks

Hg19::chr10:6622629..6622638,+	p4@uc001ijl.2
Hg19::chr10:6622667..6622678,+	p5@uc001ijl.2
Hg19::chr11:118211212..118211232,-	p@chr11:118211212..118211232 -
Hg19::chr11:6423982..6423997,-	p9@APBB1
Hg19::chr15:22448832..22448885,-	p1@AJ004954
Hg19::chr1:117307142..117307156,+	p3@CD2
Hg19::chr1:117307157..117307178,+	p2@CD2
Hg19::chr1:117311220..117311234,+	p@chr1:117311220..117311234 +
Hg19::chr2:99388276..99388311,-	p3@ENST00000448595
Hg19::chr2:99388349..99388378,-	p1@ENST00000448595
Hg19::chr9:35649814..35649823,-	p@chr9:35649814..35649823 -

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:0030887	positive regulation of myeloid dendritic cell activation	0.00239899918896269
GO:0050760	negative regulation of thymidylate synthase biosynthetic process	0.00239899918896269
GO:0050758	regulation of thymidylate synthase biosynthetic process	0.00239899918896269
GO:0050757	thymidylate synthase biosynthetic process	0.00239899918896269
GO:0051665	lipid raft localization	0.00239899918896269
GO:0031580	lipid raft distribution	0.00239899918896269
GO:0001766	lipid raft polarization	0.00239899918896269
GO:0030885	regulation of myeloid dendritic cell activation	0.00239899918896269
GO:0001773	myeloid dendritic cell activation	0.00383828571022355
GO:0031579	lipid raft organization and biogenesis	0.00383828571022355
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.00610609398962248
GO:0045580	regulation of T cell differentiation	0.0073369270873641
GO:0001540	beta-amyloid binding	0.0073369270873641
GO:0007090	regulation of S phase of mitotic cell cycle	0.0073369270873641
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0073369270873641
GO:0007009	plasma membrane organization and biogenesis	0.0073369270873641
GO:0051668	localization within membrane	0.0073369270873641
GO:0033261	regulation of progression through S phase	0.00784942111105822
GO:0045619	regulation of lymphocyte differentiation	0.00784942111105822
GO:0000084	S phase of mitotic cell cycle	0.00784942111105822
GO:0030101	natural killer cell activation	0.00784942111105822
GO:0030426	growth cone	0.00784942111105822
GO:0030427	site of polarized growth	0.00792514425191407
GO:0051320	S phase	0.00839414904394305
GO:0048468	cell development	0.00870786176931244
GO:0002274	myeloid leukocyte activation	0.0099614067426714
GO:0007346	regulation of progression through mitotic cell cycle	0.0113680113202635
GO:0048731	system development	0.0126841943224681
GO:0030027	lamellipodium	0.0126841943224681
GO:0030217	T cell differentiation	0.0126841943224681
GO:0017148	negative regulation of translation	0.0126841943224681
GO:0031327	negative regulation of cellular biosynthetic process	0.0134858298228399
GO:0048869	cellular developmental process	0.0136017999257637
GO:0030154	cell differentiation	0.0136017999257637
GO:0009890	negative regulation of biosynthetic process	0.0139726535835333
GO:0030308	negative regulation of cell growth	0.0139942492563816
GO:0045792	negative regulation of cell size	0.0139942492563816
GO:0050863	regulation of T cell activation	0.0145514290056884
GO:0048856	anatomical structure development	0.0145514290056884
GO:0045926	negative regulation of growth	0.0146211869705408
GO:0030098	lymphocyte differentiation	0.0149654475969592
GO:0031252	leading edge	0.0164333313353733
GO:0051249	regulation of lymphocyte activation	0.01694189346195
GO:0007275	multicellular organismal development	0.0169587749440453
GO:0050865	regulation of cell activation	0.017039964487941
GO:0051329	interphase of mitotic cell cycle	0.0177100711960359
GO:0002521	leukocyte differentiation	0.0179691892931388
GO:0051325	interphase	0.0179691892931388
GO:0042110	T cell activation	0.0191648754036795
GO:0007050	cell cycle arrest	0.0193556682424319
GO:0051248	negative regulation of protein metabolic process	0.019538929159613
GO:0007409	axonogenesis	0.0210026976150678
GO:0048667	neuron morphogenesis during differentiation	0.0212874009302865
GO:0048812	neurite morphogenesis	0.0212874009302865
GO:0000904	cellular morphogenesis during differentiation	0.0219434337308529
GO:0031175	neurite development	0.0230879213432029
GO:0048666	neuron development	0.0254244349158173
GO:0046649	lymphocyte activation	0.0254244349158173
GO:0016043	cellular component organization and biogenesis	0.0254244349158173
GO:0030097	hemopoiesis	0.0254244349158173
GO:0001558	regulation of cell growth	0.0254244349158173
GO:0032502	developmental process	0.0255122121187149
GO:0048534	hemopoietic or lymphoid organ development	0.0262752118608913
GO:0045321	leukocyte activation	0.0262752118608913
GO:0002520	immune system development	0.0262752118608913
GO:0006417	regulation of translation	0.0262752118608913
GO:0031326	regulation of cellular biosynthetic process	0.0262752118608913
GO:0016049	cell growth	0.0262752118608913
GO:0040008	regulation of growth	0.0262752118608913
GO:0032990	cell part morphogenesis	0.0262752118608913
GO:0048858	cell projection morphogenesis	0.0262752118608913
GO:0030030	cell projection organization and biogenesis	0.0262752118608913
GO:0008361	regulation of cell size	0.0262752118608913
GO:0001775	cell activation	0.0262752118608913
GO:0030182	neuron differentiation	0.0262752118608913
GO:0006917	induction of apoptosis	0.0262752118608913
GO:0012502	induction of programmed cell death	0.0262752118608913
GO:0032501	multicellular organismal process	0.0262752118608913
GO:0009889	regulation of biosynthetic process	0.0262752118608913
GO:0045786	negative regulation of progression through cell cycle	0.0269001568217935
GO:0048699	generation of neurons	0.0285682467560399
GO:0043065	positive regulation of apoptosis	0.0297161269138546
GO:0043068	positive regulation of programmed cell death	0.0297161269138546
GO:0022008	neurogenesis	0.0298158318010825
GO:0051239	regulation of multicellular organismal process	0.0311450839206244
GO:0016044	membrane organization and biogenesis	0.0315575748587551
GO:0042995	cell projection	0.0343654970695894
GO:0000278	mitotic cell cycle	0.0353792794685426
GO:0016337	cell-cell adhesion	0.0372236214630119
GO:0000074	regulation of progression through cell cycle	0.0374431864112437
GO:0051726	regulation of cell cycle	0.0376578140057725
GO:0022403	cell cycle phase	0.0382803873763502
GO:0031324	negative regulation of cellular metabolic process	0.0390933314854237
GO:0007165	signal transduction	0.0397200677172096
GO:0051246	regulation of protein metabolic process	0.0423629181842233
GO:0008134	transcription factor binding	0.0428569954657122
GO:0009892	negative regulation of metabolic process	0.0428569954657122
GO:0007154	cell communication	0.0445454702098529
GO:0000902	cell morphogenesis	0.0454903912728169
GO:0032989	cellular structure morphogenesis	0.0454903912728169
GO:0050794	regulation of cellular process	0.0454903912728169

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
T cell	2.34e-54	25
pro-T cell	2.34e-54	25
mature alpha-beta T cell	7.64e-52	18
alpha-beta T cell	7.64e-52	18
immature T cell	7.64e-52	18
mature T cell	7.64e-52	18
immature alpha-beta T cell	7.64e-52	18
lymphoid lineage restricted progenitor cell	1.83e-35	52
lymphocyte	1.18e-34	53
common lymphoid progenitor	1.18e-34	53
nucleate cell	4.00e-33	55
CD8-positive, alpha-beta T cell	1.72e-32	11
nongranular leukocyte	1.86e-19	115
CD4-positive, alpha-beta T cell	2.44e-18	6
leukocyte	1.79e-16	136
hematopoietic lineage restricted progenitor cell	1.79e-14	120
hematopoietic stem cell	9.39e-12	168
angioblastic mesenchymal cell	9.39e-12	168
hematopoietic cell	9.59e-11	177
naive T cell	3.51e-10	3
natural killer cell	2.15e-09	3
pro-NK cell	2.15e-09	3
single nucleate cell	2.72e-09	3
mononuclear cell	2.72e-09	3
hematopoietic oligopotent progenitor cell	5.81e-09	161
hematopoietic multipotent progenitor cell	5.81e-09	161
regulatory T cell	2.05e-07	2
CD4-positive, CD25-positive, alpha-beta regulatory T cell	2.05e-07	2
naive regulatory T cell	2.05e-07	2
thymocyte	5.85e-07	2
double negative thymocyte	5.85e-07	2
double-positive, alpha-beta thymocyte	5.85e-07	2
DN4 thymocyte	5.85e-07	2
DN1 thymic pro-T cell	5.85e-07	2
DN2 thymocyte	5.85e-07	2
DN3 thymocyte	5.85e-07	2
immature single positive thymocyte	5.85e-07	2
early T lineage precursor	5.85e-07	2

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	8.89e-15	7
immune organ	8.89e-15	7
blood	2.34e-14	15
haemolymphatic fluid	2.34e-14	15
organism substance	2.34e-14	15
thymus	1.08e-12	4
hemolymphoid system gland	1.08e-12	4
thymic region	1.08e-12	4
pharyngeal gland	1.08e-12	4
thymus primordium	1.08e-12	4
pharyngeal epithelium	1.84e-08	6
chordate pharynx	2.26e-07	10
pharyngeal region of foregut	2.26e-07	10

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	5	4.04839402116773	0.00459238325242163	0.0217024395701205

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.