Coexpression cluster:C1361

Full id: C1361_CD4_cord_mycosis_hairy_CD8_Whole_thymus

Phase1 CAGE Peaks

Hg19::chr12:48277143..48277154,-	p10@VDR
Hg19::chr3:32993065..32993074,+	p3@CCR4
Hg19::chr3:32993109..32993124,+	p2@CCR4
Hg19::chr3:32993128..32993144,+	p1@CCR4
Hg19::chr6:106547062..106547071,+	p25@PRDM1
Hg19::chr6:106547079..106547114,+	p9@PRDM1

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:0006874	cellular calcium ion homeostasis	0.00136204756176744
GO:0055074	calcium ion homeostasis	0.00136204756176744
GO:0006875	cellular metal ion homeostasis	0.00136204756176744
GO:0055065	metal ion homeostasis	0.00136204756176744
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.00148645142072713
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.00148645142072713
GO:0002507	tolerance induction	0.00148645142072713
GO:0008434	vitamin D3 receptor activity	0.00148645142072713
GO:0030003	cellular cation homeostasis	0.00148645142072713
GO:0055080	cation homeostasis	0.00148645142072713
GO:0055082	cellular chemical homeostasis	0.00168846236759857
GO:0006873	cellular ion homeostasis	0.00168846236759857
GO:0050801	ion homeostasis	0.00197790247834568
GO:0016481	negative regulation of transcription	0.00218128597867069
GO:0048878	chemical homeostasis	0.00219248957442734
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00229301767600982
GO:0019725	cellular homeostasis	0.0029054511865854
GO:0031324	negative regulation of cellular metabolic process	0.0029054511865854
GO:0009892	negative regulation of metabolic process	0.00360186242986817
GO:0042592	homeostatic process	0.00414451130338411
GO:0004945	angiotensin type II receptor activity	0.00505645008471668
GO:0001595	angiotensin receptor activity	0.00505645008471668
GO:0050892	intestinal absorption	0.005373846714639
GO:0022600	digestive system process	0.00978228687467743
GO:0019957	C-C chemokine binding	0.0114043882617499
GO:0016493	C-C chemokine receptor activity	0.0114043882617499
GO:0065008	regulation of biological quality	0.0120006251142817
GO:0004950	chemokine receptor activity	0.0146652234547873
GO:0001764	neuron migration	0.0146652234547873
GO:0001637	G-protein chemoattractant receptor activity	0.0146652234547873
GO:0048523	negative regulation of cellular process	0.0146652234547873
GO:0019956	chemokine binding	0.0146652234547873
GO:0048519	negative regulation of biological process	0.0150382652472423
GO:0003700	transcription factor activity	0.0233294294183521
GO:0051480	cytosolic calcium ion homeostasis	0.0239906100823015
GO:0007204	elevation of cytosolic calcium ion concentration	0.0239906100823015
GO:0048731	system development	0.0245253645526278
GO:0065007	biological regulation	0.0286460422766611
GO:0007586	digestion	0.0300320435974881
GO:0019955	cytokine binding	0.0305105407580529
GO:0048856	anatomical structure development	0.0342634993280422
GO:0003707	steroid hormone receptor activity	0.034322657953198
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0363790715162824
GO:0042330	taxis	0.0382503179965157
GO:0006935	chemotaxis	0.0382503179965157
GO:0001653	peptide receptor activity	0.0382503179965157
GO:0008528	peptide receptor activity, G-protein coupled	0.0382503179965157
GO:0007275	multicellular organismal development	0.0382503179965157
GO:0004879	ligand-dependent nuclear receptor activity	0.0384307489624711
GO:0007626	locomotory behavior	0.0441245460901082
GO:0006816	calcium ion transport	0.0441245460901082
GO:0045892	negative regulation of transcription, DNA-dependent	0.0475574799163466
GO:0042277	peptide binding	0.0475574799163466
GO:0001501	skeletal development	0.0475574799163466

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	5.72e-33	25
pro-T cell	5.72e-33	25
mature alpha-beta T cell	2.93e-26	18
alpha-beta T cell	2.93e-26	18
immature T cell	2.93e-26	18
mature T cell	2.93e-26	18
immature alpha-beta T cell	2.93e-26	18
lymphoid lineage restricted progenitor cell	2.22e-25	52
lymphocyte	1.06e-24	53
common lymphoid progenitor	1.06e-24	53
leukocyte	2.18e-24	136
nucleate cell	2.00e-23	55
nongranular leukocyte	1.01e-20	115
hematopoietic cell	1.89e-20	177
hematopoietic stem cell	3.35e-19	168
angioblastic mesenchymal cell	3.35e-19	168
CD8-positive, alpha-beta T cell	2.16e-18	11
hematopoietic lineage restricted progenitor cell	7.91e-18	120
hematopoietic oligopotent progenitor cell	6.89e-17	161
hematopoietic multipotent progenitor cell	6.89e-17	161
CD4-positive, alpha-beta T cell	2.24e-11	6
circulating cell	2.32e-11	6

Uber Anatomy

Ontology term	p-value	n
blood	8.75e-21	15
haemolymphatic fluid	8.75e-21	15
organism substance	8.75e-21	15
hemolymphoid system	9.16e-12	108
hematopoietic system	3.28e-11	98
blood island	3.28e-11	98
adult organism	1.64e-07	114

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
BATF#10538	3	12.1789008961518	0.0012598148712534	0.00846188213639677
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287485098928736
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318857114208124
MEF2A#4205	4	12.495487273096	0.000111333627719979	0.001545808660655
STAT2#6773	3	32.6318855932203	6.94270331437341e-05	0.00110112223454798
TAL1#6886	3	14.9343083387201	0.000695218440592151	0.005598143308944

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.