MCL coexpression mm9:734

Phase1 CAGE Peaks

	Short description
Mm9::chr15:34425057..34425102,+	p1@Pop1
Mm9::chr15:8059322..8059356,+	p1@Nup155
Mm9::chr17:35378730..35378782,+	p1@Ddx39b
Mm9::chr19:47165238..47165290,+	p1@Pdcd11
Mm9::chr4:129318235..129318295,-	p1@Txlna
Mm9::chr4:148000865..148000884,-	p1@Tardbp
Mm9::chr4:62069804..62069899,+	p1@Prpf4
Mm9::chr6:35127610..35127627,+	p1@Nup205
Mm9::chr8:113370670..113370698,-	p1@Sf3b3
Mm9::chr8:126473101..126473187,-	p1@Nup133

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:0005487	nucleocytoplasmic transporter activity	0.000749205781920186
GO:0051028	mRNA transport	0.00407034741706452
GO:0050658	RNA transport	0.00407034741706452
GO:0051236	establishment of RNA localization	0.00407034741706452
GO:0050657	nucleic acid transport	0.00407034741706452
GO:0006403	RNA localization	0.00407034741706452
GO:0005643	nuclear pore	0.00407034741706452
GO:0065002	intracellular protein transport across a membrane	0.00407034741706452
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.00407034741706452
GO:0046930	pore complex	0.00407034741706452
GO:0044453	nuclear membrane part	0.00429391984070031
GO:0031965	nuclear membrane	0.00429391984070031
GO:0044428	nuclear part	0.00746703842105303
GO:0006913	nucleocytoplasmic transport	0.00746703842105303
GO:0051169	nuclear transport	0.00746703842105303
GO:0017056	structural constituent of nuclear pore	0.00764090439970906
GO:0005635	nuclear envelope	0.00886461988172955
GO:0005681	spliceosome	0.0143799144534344
GO:0046540	U4/U6 x U5 tri-snRNP complex	0.0160755416039761
GO:0008380	RNA splicing	0.0197360766737931
GO:0051649	establishment of cellular localization	0.0243803738730018
GO:0051641	cellular localization	0.0244002357987189
GO:0004526	ribonuclease P activity	0.0248546207161951
GO:0006397	mRNA processing	0.0248546207161951
GO:0006406	mRNA export from nucleus	0.0248546207161951
GO:0030532	small nuclear ribonucleoprotein complex	0.0248546207161951
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0248546207161951
GO:0004549	tRNA-specific ribonuclease activity	0.0261400419890448
GO:0016071	mRNA metabolic process	0.027836696568666
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0284511320653779
GO:0006405	RNA export from nucleus	0.0294935597533027
GO:0012505	endomembrane system	0.0328158581290779
GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	0.0369009904895174
GO:0032991	macromolecular complex	0.0382548377726184
GO:0016893	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0382548377726184
GO:0051168	nuclear export	0.0388742433313261
GO:0006396	RNA processing	0.0398025270092647
GO:0031975	envelope	0.0437951567695661
GO:0031967	organelle envelope	0.0437951567695661
GO:0006886	intracellular protein transport	0.0448957993436601
GO:0016070	RNA metabolic process	0.0499137677017831

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
nucleate cell	1.39e-07	16

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	1.06e-09	29
immune organ	1.06e-09	29
anterior region of body	2.15e-09	43
primordium	2.09e-08	134
thymus	1.70e-07	23
neck	1.70e-07	23
respiratory system epithelium	1.70e-07	23
hemolymphoid system gland	1.70e-07	23
pharyngeal epithelium	1.70e-07	23
thymic region	1.70e-07	23
pharyngeal gland	1.70e-07	23
entire pharyngeal arch endoderm	1.70e-07	23
thymus primordium	1.70e-07	23
early pharyngeal endoderm	1.70e-07	23
respiratory tract	5.02e-07	41
mixed endoderm/mesoderm-derived structure	6.08e-07	35
pharynx	6.25e-07	24
upper respiratory tract	6.25e-07	24
chordate pharynx	6.25e-07	24
pharyngeal arch system	6.25e-07	24
pharyngeal region of foregut	6.25e-07	24
craniocervical region	7.77e-07	36
segment of respiratory tract	8.81e-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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