Coexpression cluster:C343

Full id: C343_CD4_mycosis_kidney_signet_hairy_b_Mast

Phase1 CAGE Peaks

Hg19::chr12:12654214..12654217,-	p@chr12:12654214..12654217 -
Hg19::chr12:12654228..12654244,-	p@chr12:12654228..12654244 -
Hg19::chr12:12654246..12654268,-	p@chr12:12654246..12654268 -
Hg19::chr12:12654286..12654294,-	p@chr12:12654286..12654294 -
Hg19::chr12:9807687..9807696,+	p@chr12:9807687..9807696 +
Hg19::chr13:42967639..42967658,+	p@chr13:42967639..42967658 +
Hg19::chr14:34682595..34682600,-	p@chr14:34682595..34682600 -
Hg19::chr14:34682624..34682671,-	p@chr14:34682624..34682671 -
Hg19::chr16:3119260..3119271,+	p@chr16:3119260..3119271 +
Hg19::chr16:78812540..78812565,+	p@chr16:78812540..78812565 +
Hg19::chr16:78996801..78996806,+	p@chr16:78996801..78996806 +
Hg19::chr17:53392505..53392514,+	p@chr17:53392505..53392514 +
Hg19::chr17:62144141..62144166,-	p@chr17:62144141..62144166 -
Hg19::chr17:62144174..62144202,-	p@chr17:62144174..62144202 -
Hg19::chr18:9088659..9088670,-	p@chr18:9088659..9088670 -
Hg19::chr18:9091167..9091184,-	p@chr18:9091167..9091184 -
Hg19::chr18:9095000..9095021,+	p@chr18:9095000..9095021 +
Hg19::chr1:117087364..117087378,+	p@chr1:117087364..117087378 +
Hg19::chr1:209925409..209925446,+	p@chr1:209925409..209925446 +
Hg19::chr1:64117070..64117080,+	p12@PGM1
Hg19::chr22:30552802..30552806,+	p@chr22:30552802..30552806 +
Hg19::chr2:39444239..39444249,+	p@chr2:39444239..39444249 +
Hg19::chr2:39444261..39444268,+	p@chr2:39444261..39444268 +
Hg19::chr3:4846563..4846612,+	p@chr3:4846563..4846612 +
Hg19::chr3:4948148..4948153,-	p4@LOC100507582
Hg19::chr3:4948161..4948169,-	p2@LOC100507582
Hg19::chr3:4948180..4948195,-	p1@LOC100507582
Hg19::chr3:53778674..53778721,+	p@chr3:53778674..53778721 +
Hg19::chr3:53880588..53880603,+	p1@IL17RB
Hg19::chr5:131993856..131993873,+	p1@IL13
Hg19::chr5:66500832..66500867,+	p@chr5:66500832..66500867 +
Hg19::chr7:148907246..148907250,+	p@chr7:148907246..148907250 +
Hg19::chr8:97296304..97296346,+	p@chr8:97296304..97296346 +

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:0005144	interleukin-13 receptor binding	0.0127152316779048
GO:0004614	phosphoglucomutase activity	0.0127152316779048
GO:0006952	defense response	0.0209988476158347
GO:0016868	intramolecular transferase activity, phosphotransferases	0.04233920409943
GO:0004907	interleukin receptor activity	0.04233920409943
GO:0019965	interleukin binding	0.04233920409943
GO:0005126	hematopoietin/interferon-class (D200-domain) cytokine receptor binding	0.0486485150110909
GO:0016866	intramolecular transferase activity	0.0486485150110909
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0486485150110909

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	1.39e-11	25
pro-T cell	1.39e-11	25
mature alpha-beta T cell	2.66e-11	18
alpha-beta T cell	2.66e-11	18
immature T cell	2.66e-11	18
mature T cell	2.66e-11	18
immature alpha-beta T cell	2.66e-11	18
leukocyte	2.40e-09	140
lymphocyte	1.22e-08	53
common lymphoid progenitor	1.22e-08	53
lymphoid lineage restricted progenitor cell	2.21e-08	52
CD8-positive, alpha-beta T cell	3.13e-08	11
hematopoietic lineage restricted progenitor cell	2.42e-07	124

Uber Anatomy

Ontology term	p-value	n
adult organism	1.85e-35	115
neural tube	7.68e-19	57
neural rod	7.68e-19	57
future spinal cord	7.68e-19	57
neural keel	7.68e-19	57
anterior neural tube	3.14e-15	42
regional part of forebrain	7.48e-15	41
forebrain	7.48e-15	41
future forebrain	7.48e-15	41
regional part of brain	4.56e-14	59
central nervous system	1.05e-13	82
gray matter	9.02e-13	34
brain grey matter	9.02e-13	34
telencephalon	1.12e-12	34
regional part of telencephalon	2.34e-12	33
cerebral hemisphere	6.80e-12	32
regional part of nervous system	1.13e-11	94
nervous system	1.13e-11	94
brain	5.18e-11	69
future brain	5.18e-11	69
neural plate	5.77e-11	86
presumptive neural plate	5.77e-11	86
neurectoderm	6.58e-10	90
regional part of cerebral cortex	3.14e-09	22
cerebral cortex	3.32e-09	25
pallium	3.32e-09	25
pre-chordal neural plate	1.17e-08	61
neocortex	2.06e-08	20
blood	9.23e-08	15
haemolymphatic fluid	9.23e-08	15
organism substance	9.23e-08	15

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	5	3.69057602913691	0.0105877801731713	0.0391010315949729

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.