MCL coexpression mm9:2396

Phase1 CAGE Peaks

	Short description
Mm9::chr4:129419477..129419512,-	p2@Khdrbs1
Mm9::chr6:29998062..29998078,+	p2@Nrf1
Mm9::chr8:108160490..108160512,+	p2@Ctcf
Mm9::chrX:98469402..98469427,+	p3@Med12

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:0006355	regulation of transcription, DNA-dependent	0.00264962671142477
GO:0006351	transcription, DNA-dependent	0.00264962671142477
GO:0032774	RNA biosynthetic process	0.00264962671142477
GO:0045449	regulation of transcription	0.00264962671142477
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00264962671142477
GO:0006350	transcription	0.00264962671142477
GO:0010468	regulation of gene expression	0.00264962671142477
GO:0031323	regulation of cellular metabolic process	0.00264962671142477
GO:0019222	regulation of metabolic process	0.00264962671142477
GO:0016070	RNA metabolic process	0.00264962671142477
GO:0046831	regulation of RNA export from nucleus	0.00264962671142477
GO:0010467	gene expression	0.00493676572862241
GO:0003676	nucleic acid binding	0.00501317796555137
GO:0010216	maintenance of DNA methylation	0.00586084345170822
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00586084345170822
GO:0050794	regulation of cellular process	0.00726818264355437
GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	0.00856950403349945
GO:0050789	regulation of biological process	0.00994081576642363
GO:0006349	genetic imprinting	0.010196033647745
GO:0009048	dosage compensation, by inactivation of X chromosome	0.010196033647745
GO:0003916	DNA topoisomerase activity	0.0109891901210296
GO:0006265	DNA topological change	0.0109891901210296
GO:0007549	dosage compensation	0.0109891901210296
GO:0065007	biological regulation	0.0109891901210296
GO:0005634	nucleus	0.0114538221230214
GO:0043283	biopolymer metabolic process	0.0124452804732688
GO:0046822	regulation of nucleocytoplasmic transport	0.0129420245574463
GO:0005070	SH3/SH2 adaptor activity	0.0140866333941102
GO:0006305	DNA alkylation	0.0140866333941102
GO:0006405	RNA export from nucleus	0.0140866333941102
GO:0006306	DNA methylation	0.0140866333941102
GO:0003677	DNA binding	0.0158713381875643
GO:0006304	DNA modification	0.0158755623720686
GO:0005515	protein binding	0.0174588127541724
GO:0000119	mediator complex	0.0174588127541724
GO:0051168	nuclear export	0.0185873464027477
GO:0030674	protein binding, bridging	0.0196543615796995
GO:0006259	DNA metabolic process	0.0223176074557033
GO:0043170	macromolecule metabolic process	0.0247191938869611
GO:0007049	cell cycle	0.0275956870726719
GO:0043414	biopolymer methylation	0.0297006816389028
GO:0040029	regulation of gene expression, epigenetic	0.0297006816389028
GO:0060090	molecular adaptor activity	0.0297006816389028
GO:0032259	methylation	0.0297006816389028
GO:0050658	RNA transport	0.0301391412602402
GO:0051236	establishment of RNA localization	0.0301391412602402
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	0.0301391412602402
GO:0050657	nucleic acid transport	0.0301391412602402
GO:0006403	RNA localization	0.0301391412602402
GO:0048523	negative regulation of cellular process	0.0301391412602402
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0312926256970316
GO:0044238	primary metabolic process	0.0318401864703
GO:0048519	negative regulation of biological process	0.0318401864703
GO:0044237	cellular metabolic process	0.0318401864703
GO:0043231	intracellular membrane-bound organelle	0.0318401864703
GO:0043227	membrane-bound organelle	0.0318401864703
GO:0003713	transcription coactivator activity	0.0345795460137525
GO:0006730	one-carbon compound metabolic process	0.0384526715069959
GO:0051049	regulation of transport	0.0412136454567188
GO:0006913	nucleocytoplasmic transport	0.0441006895042575
GO:0051169	nuclear transport	0.0441006895042575
GO:0043229	intracellular organelle	0.0464795240315621
GO:0043226	organelle	0.0464795240315621

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
lymphocyte	7.80e-07	13
common lymphoid progenitor	7.80e-07	13

Uber Anatomy

Ontology term	p-value	n
anterior region of body	5.78e-12	43
hemopoietic organ	4.80e-10	29
immune organ	4.80e-10	29
craniocervical region	5.24e-10	36
thymus	2.60e-08	23
neck	2.60e-08	23
respiratory system epithelium	2.60e-08	23
hemolymphoid system gland	2.60e-08	23
pharyngeal epithelium	2.60e-08	23
thymic region	2.60e-08	23
pharyngeal gland	2.60e-08	23
entire pharyngeal arch endoderm	2.60e-08	23
thymus primordium	2.60e-08	23
early pharyngeal endoderm	2.60e-08	23
gland of gut	7.59e-08	24
pharynx	1.31e-07	24
upper respiratory tract	1.31e-07	24
chordate pharynx	1.31e-07	24
pharyngeal arch system	1.31e-07	24
pharyngeal region of foregut	1.31e-07	24
respiratory tract	3.32e-07	41
mixed endoderm/mesoderm-derived structure	3.38e-07	35
respiratory system	6.10e-07	42

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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