Coexpression cluster:C2295

Full id: C2295_CD4_CD8_cerebellum_Small_pituitary_Mast_cord

Phase1 CAGE Peaks

Hg19::chr14:45553296..45553340,+	p1@PRPF39
Hg19::chr15:101142365..101142395,-	p1@LINS
Hg19::chr3:56591184..56591255,+	p1@CCDC66
Hg19::chr5:64859094..64859136,+	p1@PPWD1

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:0008380	RNA splicing	0.00102948989227113
GO:0006397	mRNA processing	0.00102948989227113
GO:0016071	mRNA metabolic process	0.00107790320168466
GO:0006396	RNA processing	0.0019070019214864
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0291609777648741
GO:0016859	cis-trans isomerase activity	0.0291609777648741
GO:0005681	spliceosome	0.0373329756484199

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
nucleate cell	1.36e-18	55
lymphocyte	1.85e-17	53
common lymphoid progenitor	1.85e-17	53
lymphoid lineage restricted progenitor cell	3.21e-17	52
mature alpha-beta T cell	3.72e-11	18
alpha-beta T cell	3.72e-11	18
immature T cell	3.72e-11	18
mature T cell	3.72e-11	18
immature alpha-beta T cell	3.72e-11	18
T cell	7.04e-11	25
pro-T cell	7.04e-11	25
hematopoietic stem cell	8.34e-11	168
angioblastic mesenchymal cell	8.34e-11	168
hematopoietic cell	9.08e-10	177
hematopoietic oligopotent progenitor cell	9.69e-10	161
hematopoietic multipotent progenitor cell	9.69e-10	161
CD8-positive, alpha-beta T cell	3.26e-08	11
hematopoietic lineage restricted progenitor cell	1.04e-07	120
leukocyte	6.99e-07	136
nongranular leukocyte	8.91e-07	115

Uber Anatomy

Ontology term	p-value	n
adult organism	2.14e-23	114
neural tube	1.96e-17	56
neural rod	1.96e-17	56
future spinal cord	1.96e-17	56
neural keel	1.96e-17	56
regional part of nervous system	3.41e-16	53
regional part of brain	3.41e-16	53
nervous system	4.93e-16	89
regional part of forebrain	2.25e-15	41
forebrain	2.25e-15	41
anterior neural tube	2.25e-15	41
future forebrain	2.25e-15	41
central nervous system	3.08e-15	81
brain	1.08e-13	68
future brain	1.08e-13	68
brain grey matter	1.74e-12	34
gray matter	1.74e-12	34
telencephalon	2.64e-12	34
regional part of telencephalon	1.05e-11	32
cerebral hemisphere	1.28e-11	32
neurectoderm	4.37e-10	86
neural plate	2.62e-09	82
presumptive neural plate	2.62e-09	82
regional part of cerebral cortex	4.05e-09	22
cerebral cortex	1.44e-08	25
pallium	1.44e-08	25
neocortex	3.96e-08	20
pre-chordal neural plate	2.15e-07	61

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
ATF3#467	3	16.8473808945066	0.000340998682365564	0.00346368035280851
BRCA1#672	2	10.0921153216119	0.013771396990026	0.0484657949265846
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160682830980134
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234593972284355
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185729913642328
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319972216726937
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00484877851195379
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186288042898462
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.007672128799321
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508546098684727
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618551162098486
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119604772038238
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434811162983708
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795117021018123
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321603060372145
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243742135629798

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.