Coexpression cluster:C386

Full id: C386_chronic_acute_Hodgkin_NK_thymus_liver_blood

Phase1 CAGE Peaks

Hg19::chr11:6423953..6423960,-	p19@APBB1
Hg19::chr13:113819053..113819062,+	p@chr13:113819053..113819062 +
Hg19::chr13:49070828..49070853,-	p@chr13:49070828..49070853 -
Hg19::chr14:23588816..23588836,-	p4@CEBPE
Hg19::chr15:58306192..58306225,-	p7@ALDH1A2
Hg19::chr15:58306277..58306282,-	p41@ALDH1A2
Hg19::chr15:58306295..58306302,-	p30@ALDH1A2
Hg19::chr16:89165058..89165067,+	p8@ACSF3
Hg19::chr19:7733929..7733950,+	p1@RETN
Hg19::chr19:7733964..7733984,+	p2@RETN
Hg19::chr1:198988091..198988097,-	p@chr1:198988091..198988097 -
Hg19::chr1:54751075..54751101,+	p1@ENST00000426901 p1@uc001cxi.1
Hg19::chr2:238933920..238933935,+	p7@UBE2F
Hg19::chr2:238933960..238933968,+	p9@UBE2F
Hg19::chr4:108984808..108984820,-	p@chr4:108984808..108984820 -
Hg19::chr4:145568170..145568180,-	p@chr4:145568170..145568180 -
Hg19::chr4:145568348..145568363,-	p@chr4:145568348..145568363 -
Hg19::chr4:145568421..145568432,-	p@chr4:145568421..145568432 -
Hg19::chr4:145580790..145580817,+	p@chr4:145580790..145580817 +
Hg19::chr6:26251989..26252003,+	p3@HIST1H2BH
Hg19::chr6:27841151..27841161,-	p1@AB451459
Hg19::chrX:123480125..123480142,+	p5@SH2D1A
Hg19::chrX:123480155..123480178,+	p7@SH2D1A
Hg19::chrX:123480179..123480190,+	p9@SH2D1A
Hg19::chrX:123480196..123480210,+	p8@SH2D1A
Hg19::chrX:123480214..123480227,+	p6@SH2D1A
Hg19::chrX:153200709..153200718,-	p5@NAA10
Hg19::chrX:78618558..78618574,-	p@chrX:78618558..78618574 -

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:0050760	negative regulation of thymidylate synthase biosynthetic process	0.0147572510695082
GO:0050758	regulation of thymidylate synthase biosynthetic process	0.0147572510695082
GO:0050757	thymidylate synthase biosynthetic process	0.0147572510695082
GO:0001758	retinal dehydrogenase activity	0.0331969733939237
GO:0004028	3-chloroallyl aldehyde dehydrogenase activity	0.0493885243935911
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.0493885243935911
GO:0001540	beta-amyloid binding	0.0493885243935911
GO:0030225	macrophage differentiation	0.0493885243935911
GO:0007090	regulation of S phase of mitotic cell cycle	0.0493885243935911
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0493885243935911
GO:0033261	regulation of progression through S phase	0.0493885243935911
GO:0006776	vitamin A metabolic process	0.0493885243935911
GO:0000084	S phase of mitotic cell cycle	0.0493885243935911
GO:0051246	regulation of protein metabolic process	0.0493885243935911
GO:0006775	fat-soluble vitamin metabolic process	0.0493885243935911
GO:0030426	growth cone	0.0493885243935911
GO:0030427	site of polarized growth	0.0493885243935911

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
T cell	5.28e-11	25
pro-T cell	5.28e-11	25

Uber Anatomy

Ontology term	p-value	n
thymus	4.21e-29	4
hemolymphoid system gland	4.21e-29	4
thymic region	4.21e-29	4
pharyngeal gland	4.21e-29	4
thymus primordium	4.21e-29	4
pharyngeal epithelium	8.63e-20	6
hemopoietic organ	4.02e-17	7
immune organ	4.02e-17	7
neck	2.66e-12	10
gland of gut	2.66e-12	10
chordate pharynx	2.66e-12	10
pharyngeal region of foregut	2.66e-12	10
pharynx	2.83e-11	11
entire pharyngeal arch endoderm	2.83e-11	11
early pharyngeal endoderm	2.83e-11	11
pharyngeal arch system	2.95e-07	18
upper respiratory tract	6.38e-07	19

Disease

Ontology term	p-value	n
hematologic cancer	2.03e-09	51
immune system cancer	2.03e-09	51
leukemia	2.73e-07	39

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
GATA2#2624	11	5.00693746675335	4.20328319157111e-06	0.000133268577184121
TAL1#6886	12	12.8008357189029	3.62005246867039e-11	4.14101489348814e-09

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.