MCL coexpression mm9:434

Phase1 CAGE Peaks

	Short description
Mm9::chr10:13589556..13589587,-	p@chr10:13589556..13589587 -
Mm9::chr11:23646730..23646750,-	p@chr11:23646730..23646750 -
Mm9::chr11:23648455..23648462,-	p@chr11:23648455..23648462 -
Mm9::chr17:34256262..34256285,-	p@chr17:34256262..34256285 -
Mm9::chr17:71200529..71200556,-	p1@Tgif1
Mm9::chr17:71200558..71200572,-	p4@Tgif1
Mm9::chr17:71200676..71200704,+	p@chr17:71200676..71200704 +
Mm9::chr17:71201050..71201078,-	p9@Tgif1
Mm9::chr18:3281015..3281028,-	p18@Crem
Mm9::chr18:3281725..3281740,-	p3@Crem
Mm9::chr18:3281750..3281776,-	p2@Crem
Mm9::chr1:173848007..173848014,+	p@chr1:173848007..173848014 +
Mm9::chr3:21852105..21852114,+	p@chr3:21852105..21852114 +
Mm9::chr3:30993641..30993651,+	p7@Skil
Mm9::chr4:32337706..32337718,-	p@chr4:32337706..32337718 -
Mm9::chr6:122290517..122290528,-	p15@Phc1
Mm9::chr9:44413016..44413033,+	p3@Ddx6

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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GO ID	GO name	FDR corrected p-value
GO:0044451	nucleoplasm part	0.0220916838479725
GO:0005654	nucleoplasm	0.0220916838479725
GO:0008432	JUN kinase binding	0.0220916838479725
GO:0031981	nuclear lumen	0.0220916838479725
GO:0031974	membrane-enclosed lumen	0.0220916838479725
GO:0043233	organelle lumen	0.0220916838479725
GO:0007283	spermatogenesis	0.0233882010690361
GO:0048232	male gamete generation	0.0233882010690361
GO:0005634	nucleus	0.0277644688566074
GO:0044428	nuclear part	0.0277644688566074
GO:0007276	gamete generation	0.0277644688566074
GO:0019953	sexual reproduction	0.03423568125556
GO:0001739	sex chromatin	0.03423568125556
GO:0000803	sex chromosome	0.0344347483300447
GO:0003724	RNA helicase activity	0.0346065965449581
GO:0003676	nucleic acid binding	0.0403273692115077
GO:0005667	transcription factor complex	0.0436719040086291
GO:0000003	reproduction	0.0436719040086291
GO:0005720	nuclear heterochromatin	0.0436719040086291
GO:0043565	sequence-specific DNA binding	0.0436719040086291

Relative expression of the co-expression cluster over median <br>Analyst:

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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
hematopoietic cell	9.86e-25	32
hematopoietic oligopotent progenitor cell	9.86e-25	32
hematopoietic stem cell	9.86e-25	32
angioblastic mesenchymal cell	9.86e-25	32
hematopoietic multipotent progenitor cell	9.86e-25	32
lymphoid lineage restricted progenitor cell	1.44e-22	12
T cell	1.33e-20	11
pro-T cell	1.33e-20	11
lymphocyte	1.39e-20	13
common lymphoid progenitor	1.39e-20	13
mature alpha-beta T cell	5.48e-18	9
alpha-beta T cell	5.48e-18	9
immature T cell	5.48e-18	9
mature T cell	5.48e-18	9
immature alpha-beta T cell	5.48e-18	9
leukocyte	2.03e-17	17
nongranular leukocyte	2.03e-17	17
connective tissue cell	4.81e-17	46
mesenchymal cell	4.81e-17	46
hematopoietic lineage restricted progenitor cell	5.55e-17	25
motile cell	2.24e-16	54
nucleate cell	4.00e-16	16
CD4-positive, alpha-beta T cell	4.43e-16	8
thymocyte	2.66e-12	6
double negative thymocyte	2.66e-12	6
naive T cell	2.66e-12	6
double-positive, alpha-beta thymocyte	2.66e-12	6
CD4-positive, alpha-beta thymocyte	2.66e-12	6
naive thymus-derived CD4-positive, alpha-beta T cell	2.66e-12	6
DN4 thymocyte	2.66e-12	6
DN1 thymic pro-T cell	2.66e-12	6
DN2 thymocyte	2.66e-12	6
DN3 thymocyte	2.66e-12	6
immature single positive thymocyte	2.66e-12	6
early T lineage precursor	2.66e-12	6
mature CD4 single-positive thymocyte	2.66e-12	6
resting double-positive thymocyte	2.66e-12	6
double-positive blast	2.66e-12	6
CD69-positive double-positive thymocyte	2.66e-12	6
CD69-positive, CD4-positive single-positive thymocyte	2.66e-12	6
CD4-positive, CD8-intermediate double-positive thymocyte	2.66e-12	6
CD24-positive, CD4 single-positive thymocyte	2.66e-12	6
stem cell	8.45e-10	97
animal cell	3.20e-08	115
eukaryotic cell	3.20e-08	115
common myeloid progenitor	5.55e-08	19
somatic stem cell	6.61e-08	91
multi fate stem cell	6.61e-08	91
somatic cell	8.04e-08	118

Uber Anatomy

Ontology term	p-value	n
connective tissue	4.81e-17	46

TFBS overrepresentation<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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