Coexpression cluster:C1077

Full id: C1077_thymus_CD8_Natural_blood_NK_Peripheral_acute

Phase1 CAGE Peaks

Hg19::chr2:87014966..87014973,-	p@chr2:87014966..87014973 -
Hg19::chr2:87016482..87016502,-	p@chr2:87016482..87016502 -
Hg19::chr2:87017652..87017670,-	p@chr2:87017652..87017670 -
Hg19::chr2:87017971..87017982,-	p4@CD8A
Hg19::chr2:87017985..87018050,-	p1@CD8A
Hg19::chr2:87018060..87018074,-	p2@CD8A
Hg19::chr2:87018470..87018477,-	p7@CD8A
Hg19::chr2:87088995..87089018,-	p1@CD8B

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
2.25318768070372e-05	0.00285253560377091	2	136	Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-06	0.00198248117124819	2	78	Antigen processing and presentation (KEGG):04612
9.39564536136585e-06	0.00198248117124819	2	88	Hematopoietic cell lineage (KEGG):04640
1.41818283432528e-05	0.00224427433531976	2	108	T cell receptor signaling pathway (KEGG):04660
1.46039942267834e-06	0.000924432834555386	2	35	Primary immunodeficiency (KEGG):05340
0.000319827473566556	0.0337417984612716	2	511	Signaling in Immune system (Reactome):REACT_6900

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:0042288	MHC class I protein binding	1.94443489268243e-06
GO:0042101	T cell receptor complex	1.94443489268243e-06
GO:0015026	coreceptor activity	2.00335716215766e-06
GO:0001772	immunological synapse	2.00335716215766e-06
GO:0042287	MHC protein binding	2.98146683544639e-06
GO:0042110	T cell activation	4.66762578026242e-05
GO:0043235	receptor complex	5.04627150719965e-05
GO:0046649	lymphocyte activation	8.79046607733516e-05
GO:0045321	leukocyte activation	0.000105470862360653
GO:0001775	cell activation	0.000117549927603074
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.000117549927603074
GO:0007167	enzyme linked receptor protein signaling pathway	0.000220221982163654
GO:0005102	receptor binding	0.00243469536960991
GO:0006955	immune response	0.00297248539808496
GO:0005887	integral to plasma membrane	0.00332669934433345
GO:0031226	intrinsic to plasma membrane	0.00332669934433345
GO:0002376	immune system process	0.00332669934433345
GO:0044459	plasma membrane part	0.00854199414041754
GO:0007166	cell surface receptor linked signal transduction	0.00917490442452626
GO:0043234	protein complex	0.0122393426537342
GO:0004872	receptor activity	0.0133734696582529
GO:0004871	signal transducer activity	0.017635448063124
GO:0060089	molecular transducer activity	0.017635448063124
GO:0005886	plasma membrane	0.0177636571829853
GO:0032991	macromolecular complex	0.0177636571829853
GO:0007165	signal transduction	0.0299540671128367
GO:0019882	antigen processing and presentation	0.0305786064897416
GO:0007154	cell communication	0.0325209261041257
GO:0016021	integral to membrane	0.0444991702929945
GO:0031224	intrinsic to membrane	0.0444991702929945

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
CD8-positive, alpha-beta T cell	2.49e-32	11
mature alpha-beta T cell	5.12e-22	18
alpha-beta T cell	5.12e-22	18
immature T cell	5.12e-22	18
mature T cell	5.12e-22	18
immature alpha-beta T cell	5.12e-22	18
T cell	1.49e-20	25
pro-T cell	1.49e-20	25
leukocyte	8.18e-13	136
lymphoid lineage restricted progenitor cell	2.17e-12	52
lymphocyte	4.51e-12	53
common lymphoid progenitor	4.51e-12	53
nongranular leukocyte	6.05e-12	115
nucleate cell	1.80e-11	55
natural killer cell	1.38e-09	3
pro-NK cell	1.38e-09	3
single nucleate cell	3.21e-09	3
mononuclear cell	3.21e-09	3
basophil	6.57e-09	3
hematopoietic stem cell	7.15e-09	168
angioblastic mesenchymal cell	7.15e-09	168
hematopoietic lineage restricted progenitor cell	2.67e-08	120
hematopoietic cell	4.89e-08	177
hematopoietic oligopotent progenitor cell	2.93e-07	161
hematopoietic multipotent progenitor cell	2.93e-07	161

Uber Anatomy

Ontology term	p-value	n
blood	3.20e-25	15
haemolymphatic fluid	3.20e-25	15
organism substance	3.20e-25	15
adult organism	7.61e-21	114
hemolymphoid system	1.60e-11	108
hematopoietic system	4.95e-11	98
blood island	4.95e-11	98
hemopoietic organ	2.76e-10	7
immune organ	2.76e-10	7
thymus	2.58e-07	4
hemolymphoid system gland	2.58e-07	4
thymic region	2.58e-07	4
pharyngeal gland	2.58e-07	4
thymus primordium	2.58e-07	4
neck	5.61e-07	10
chordate pharynx	7.55e-07	10
pharyngeal region of foregut	7.55e-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)
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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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No analysis results for this cluster

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.