MCL coexpression mm9:765

Phase1 CAGE Peaks

	Short description
Mm9::chr10:57909488..57909491,+	p3@Ranbp2
Mm9::chr10:61957572..61957584,-	p@chr10:61957572..61957584 -
Mm9::chr10:61957587..61957611,-	p@chr10:61957587..61957611 -
Mm9::chr10:61957621..61957632,-	p@chr10:61957621..61957632 -
Mm9::chr10:61957717..61957729,-	p@chr10:61957717..61957729 -
Mm9::chr10:61960605..61960621,-	p@chr10:61960605..61960621 -
Mm9::chr10:61970485..61970512,-	p1@Srgn
Mm9::chr17:57244824..57244844,+	p1@Tnfsf9
Mm9::chr2:167877446..167877452,-	p@chr2:167877446..167877452 -

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:0033371	T cell secretory granule organization and biogenesis	0.00143811976113516
GO:0033366	protein localization in secretory granule	0.00143811976113516
GO:0033377	maintenance of protein localization in T cell secretory granule	0.00143811976113516
GO:0033374	protein localization in T cell secretory granule	0.00143811976113516
GO:0033365	protein localization in organelle	0.00143811976113516
GO:0033370	maintenance of protein localization in mast cell secretory granule	0.00143811976113516
GO:0033382	maintenance of granzyme B localization in T cell secretory granule	0.00143811976113516
GO:0033375	protease localization in T cell secretory granule	0.00143811976113516
GO:0033373	maintenance of protease localization in mast cell secretory granule	0.00143811976113516
GO:0033367	protein localization in mast cell secretory granule	0.00143811976113516
GO:0033364	mast cell secretory granule organization and biogenesis	0.00143811976113516
GO:0042629	mast cell granule	0.00143811976113516
GO:0033368	protease localization in mast cell secretory granule	0.00143811976113516
GO:0033363	secretory granule organization and biogenesis	0.00143811976113516
GO:0033380	granzyme B localization in T cell secretory granule	0.00143811976113516
GO:0033379	maintenance of protease localization in T cell secretory granule	0.00143811976113516
GO:0050709	negative regulation of protein secretion	0.00383456581097931
GO:0050710	negative regulation of cytokine secretion	0.00383456581097931
GO:0050707	regulation of cytokine secretion	0.00605391414152312
GO:0050663	cytokine secretion	0.00690108397284551
GO:0045185	maintenance of protein localization	0.00940902219581238
GO:0051605	protein maturation via proteolysis	0.00940902219581238
GO:0051604	protein maturation	0.00999937901019018
GO:0016050	vesicle organization and biogenesis	0.0110381045952215
GO:0051048	negative regulation of secretion	0.0110381045952215
GO:0050708	regulation of protein secretion	0.0123811320450737
GO:0051235	maintenance of localization	0.0127734838112938
GO:0005164	tumor necrosis factor receptor binding	0.014268718486589
GO:0032813	tumor necrosis factor receptor superfamily binding	0.014268718486589
GO:0045184	establishment of protein localization	0.0176249390066471
GO:0008104	protein localization	0.0192594749502943
GO:0051649	establishment of cellular localization	0.0192594749502943
GO:0051641	cellular localization	0.0192594749502943
GO:0033036	macromolecule localization	0.0192594749502943
GO:0009306	protein secretion	0.0196914644386767
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0216923192976312
GO:0016859	cis-trans isomerase activity	0.0217256151948936
GO:0051028	mRNA transport	0.0271176221182818
GO:0050658	RNA transport	0.0271176221182818
GO:0051236	establishment of RNA localization	0.0271176221182818
GO:0050657	nucleic acid transport	0.0271176221182818
GO:0006403	RNA localization	0.0271176221182818
GO:0005643	nuclear pore	0.0271176221182818
GO:0051046	regulation of secretion	0.0271176221182818
GO:0065002	intracellular protein transport across a membrane	0.027333537098526
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.027333537098526
GO:0046930	pore complex	0.027333537098526
GO:0044453	nuclear membrane part	0.0291457452728465
GO:0031965	nuclear membrane	0.0294837957638816
GO:0001503	ossification	0.0421947015982399
GO:0031214	biomineral formation	0.0421947015982399
GO:0001816	cytokine production	0.0435725434786286
GO:0046849	bone remodeling	0.0444679453359891
GO:0005515	protein binding	0.0449187407769357
GO:0005635	nuclear envelope	0.0449187407769357
GO:0048771	tissue remodeling	0.0493916889321265

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	1.19e-16	32
hematopoietic oligopotent progenitor cell	1.19e-16	32
hematopoietic stem cell	1.19e-16	32
angioblastic mesenchymal cell	1.19e-16	32
hematopoietic multipotent progenitor cell	1.19e-16	32
hematopoietic lineage restricted progenitor cell	2.12e-11	25
lymphoid lineage restricted progenitor cell	6.08e-11	12
connective tissue cell	3.34e-10	46
mesenchymal cell	3.34e-10	46
leukocyte	5.72e-10	17
nongranular leukocyte	5.72e-10	17
T cell	5.72e-10	11
pro-T cell	5.72e-10	11
lymphocyte	7.90e-10	13
common lymphoid progenitor	7.90e-10	13
common myeloid progenitor	2.98e-08	19
motile cell	3.62e-08	54
mature alpha-beta T cell	5.71e-08	9
alpha-beta T cell	5.71e-08	9
immature T cell	5.71e-08	9
mature T cell	5.71e-08	9
immature alpha-beta T cell	5.71e-08	9
nucleate cell	2.37e-07	16
CD4-positive, alpha-beta T cell	4.65e-07	8

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	5.79e-18	48
immune system	5.79e-18	48
hematopoietic system	1.13e-15	45
blood island	1.13e-15	45
mixed endoderm/mesoderm-derived structure	3.12e-13	35
hemopoietic organ	4.94e-11	29
immune organ	4.94e-11	29
connective tissue	3.34e-10	46
lateral plate mesoderm	7.09e-10	87
thymus	1.14e-09	23
neck	1.14e-09	23
respiratory system epithelium	1.14e-09	23
hemolymphoid system gland	1.14e-09	23
pharyngeal epithelium	1.14e-09	23
thymic region	1.14e-09	23
pharyngeal gland	1.14e-09	23
entire pharyngeal arch endoderm	1.14e-09	23
thymus primordium	1.14e-09	23
early pharyngeal endoderm	1.14e-09	23
respiratory tract	1.29e-09	41
respiratory system	3.28e-09	42
pharynx	4.69e-09	24
gland of gut	4.69e-09	24
upper respiratory tract	4.69e-09	24
chordate pharynx	4.69e-09	24
pharyngeal arch system	4.69e-09	24
pharyngeal region of foregut	4.69e-09	24
mesoderm	1.95e-08	120
mesoderm-derived structure	1.95e-08	120
presumptive mesoderm	1.95e-08	120
segment of respiratory tract	1.68e-07	27

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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