Coexpression cluster:C1768

Full id: C1768_testis_CD8_Natural_embryonic_Eosinophils_CD4_CD14

Phase1 CAGE Peaks

Hg19::chr16:85833874..85833901,+	p@chr16:85833874..85833901 +
Hg19::chr1:114471972..114472000,+	p3@HIPK1
Hg19::chr21:34915147..34915178,-	p3@GART
Hg19::chr21:34915181..34915204,-	p4@GART
Hg19::chr5:34839260..34839339,+	p1@TTC23L

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:0004644	phosphoribosylglycinamide formyltransferase activity	0.0027375485694101
GO:0004641	phosphoribosylformylglycinamidine cyclo-ligase activity	0.0027375485694101
GO:0004637	phosphoribosylamine-glycine ligase activity	0.00456231233278836
GO:0046040	IMP metabolic process	0.00456231233278836
GO:0006189	'de novo' IMP biosynthetic process	0.00456231233278836
GO:0006188	IMP biosynthetic process	0.00456231233278836
GO:0009113	purine base biosynthetic process	0.00547461362960894
GO:0016882	cyclo-ligase activity	0.00602172041914822
GO:0006144	purine base metabolic process	0.00602172041914822
GO:0016742	hydroxymethyl-, formyl- and related transferase activity	0.00602172041914822
GO:0046112	nucleobase biosynthetic process	0.00696697213612794
GO:0009112	nucleobase metabolic process	0.00855181734683608
GO:0009168	purine ribonucleoside monophosphate biosynthetic process	0.00855181734683608
GO:0009167	purine ribonucleoside monophosphate metabolic process	0.00855181734683608
GO:0009127	purine nucleoside monophosphate biosynthetic process	0.00855181734683608
GO:0009126	purine nucleoside monophosphate metabolic process	0.00855181734683608
GO:0004372	glycine hydroxymethyltransferase activity	0.00901422339566733
GO:0009161	ribonucleoside monophosphate metabolic process	0.00945183586136322
GO:0009156	ribonucleoside monophosphate biosynthetic process	0.00945183586136322
GO:0046148	pigment biosynthetic process	0.00945183586136322
GO:0009124	nucleoside monophosphate biosynthetic process	0.00945183586136322
GO:0009123	nucleoside monophosphate metabolic process	0.00945183586136322
GO:0042440	pigment metabolic process	0.00999197011681788
GO:0019748	secondary metabolic process	0.0120815856858232
GO:0005524	ATP binding	0.0245517609060341
GO:0032559	adenyl ribonucleotide binding	0.0245517609060341
GO:0030554	adenyl nucleotide binding	0.0253718292786105
GO:0046483	heterocycle metabolic process	0.0253718292786105
GO:0009152	purine ribonucleotide biosynthetic process	0.0262962846519019
GO:0009150	purine ribonucleotide metabolic process	0.0262962846519019
GO:0009260	ribonucleotide biosynthetic process	0.0262962846519019
GO:0016740	transferase activity	0.0262962846519019
GO:0006164	purine nucleotide biosynthetic process	0.0262962846519019
GO:0006163	purine nucleotide metabolic process	0.0262962846519019
GO:0009259	ribonucleotide metabolic process	0.0262962846519019
GO:0032553	ribonucleotide binding	0.0262962846519019
GO:0032555	purine ribonucleotide binding	0.0262962846519019
GO:0006725	aromatic compound metabolic process	0.0262962846519019
GO:0017076	purine nucleotide binding	0.0273848872620982
GO:0009165	nucleotide biosynthetic process	0.0347732572115841
GO:0000166	nucleotide binding	0.0351870221378261
GO:0008168	methyltransferase activity	0.0351870221378261
GO:0016741	transferase activity, transferring one-carbon groups	0.0352528252605742
GO:0009117	nucleotide metabolic process	0.042096473073867
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0439173729042794
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0439173729042794

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
leukocyte	1.73e-24	140
CD14-positive, CD16-negative classical monocyte	7.38e-23	42
classical monocyte	3.23e-22	45
hematopoietic lineage restricted progenitor cell	1.78e-20	124
hematopoietic stem cell	1.88e-19	172
angioblastic mesenchymal cell	1.88e-19	172
nongranular leukocyte	1.25e-18	119
hematopoietic cell	3.28e-18	182
hematopoietic oligopotent progenitor cell	6.84e-17	165
hematopoietic multipotent progenitor cell	6.84e-17	165
myeloid leukocyte	2.48e-14	76
myeloid lineage restricted progenitor cell	1.79e-12	70
granulocyte monocyte progenitor cell	6.07e-12	71
macrophage dendritic cell progenitor	9.44e-12	65
monopoietic cell	8.22e-11	63
monocyte	8.22e-11	63
monoblast	8.22e-11	63
promonocyte	8.22e-11	63
myeloid cell	5.44e-10	112
common myeloid progenitor	5.44e-10	112
lymphoid lineage restricted progenitor cell	1.41e-07	52
lymphocyte	2.44e-07	53
common lymphoid progenitor	2.44e-07	53

Uber Anatomy

Ontology term	p-value	n
neural tube	3.18e-12	57
neural rod	3.18e-12	57
future spinal cord	3.18e-12	57
neural keel	3.18e-12	57
hematopoietic system	3.57e-11	102
blood island	3.57e-11	102
central nervous system	1.65e-10	82
bone marrow	7.92e-10	80
regional part of forebrain	8.71e-10	41
forebrain	8.71e-10	41
future forebrain	8.71e-10	41
regional part of brain	1.52e-09	59
anterior neural tube	2.82e-09	42
hemolymphoid system	3.92e-09	112
brain	5.83e-09	69
future brain	5.83e-09	69
bone element	1.78e-08	86
regional part of nervous system	2.09e-08	94
nervous system	2.09e-08	94
gray matter	5.55e-08	34
brain grey matter	5.55e-08	34
telencephalon	8.49e-08	34
regional part of telencephalon	1.55e-07	33
cerebral hemisphere	2.41e-07	32

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.