MCL coexpression mm9:298

Phase1 CAGE Peaks

	Short description
Mm9::chr10:20032330..20032345,+	p3@Bclaf1
Mm9::chr10:40602879..40602936,-	p1@Cdc40
Mm9::chr10:7512695..7512734,+	p1@Ppil4
Mm9::chr11:104303623..104303641,-	p4@1700081L11Rik
Mm9::chr11:23795208..23795280,-	p1@Papolg
Mm9::chr11:51076623..51076699,+	p1@Clk4
Mm9::chr12:82046510..82046528,+	p1@Gm12966 p1@Srsf5
Mm9::chr13:112280043..112280098,-	p1@Gpbp1
Mm9::chr18:67884180..67884213,-	p2@Ptpn2
Mm9::chr1:55084221..55084250,-	p1@Sf3b1
Mm9::chr1:58480851..58480872,-	p1@Clk1
Mm9::chr1:58480886..58480908,-	p2@Clk1
Mm9::chr2:10002227..10002245,+	p1@Kin
Mm9::chr2:156005871..156005937,-	p1@Rbm39
Mm9::chr2:34657856..34657911,+	p1@uc008jiw.1
Mm9::chr3:30501539..30501575,+	p@chr3:30501539..30501575 +
Mm9::chr5:148241729..148241793,+	p1@Pan3
Mm9::chr5:20457587..20457642,-	p1@Rsbn1l
Mm9::chr5:22939123..22939162,-	p1@uc008wpw.1 p1@uc008wpx.1
Mm9::chr5:53981912..53981942,+	p1@Rbpj
Mm9::chr5:87233306..87233322,+	p2@Ythdc1
Mm9::chr5:9161692..9161762,-	p1@Dmtf1
Mm9::chr6:120314411..120314466,+	p2@Kdm5a
Mm9::chr7:80686605..80686623,-	p2@Chd2
Mm9::chr7:80686624..80686644,-	p1@Chd2
Mm9::chr8:72240749..72240811,-	p1@Zfp869
Mm9::chrX:39503903..39503928,+	p3@Stag2

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:0005634	nucleus	3.76419046431649e-05
GO:0043283	biopolymer metabolic process	0.000311836934344768
GO:0043170	macromolecule metabolic process	0.000497536975592701
GO:0043231	intracellular membrane-bound organelle	0.000586687245999991
GO:0043227	membrane-bound organelle	0.000586687245999991
GO:0003676	nucleic acid binding	0.000746427899461023
GO:0016070	RNA metabolic process	0.000774831726398036
GO:0016485	protein processing	0.00127511598646046
GO:0006397	mRNA processing	0.0019505498710537
GO:0044238	primary metabolic process	0.0019505498710537
GO:0044237	cellular metabolic process	0.0019505498710537
GO:0010467	gene expression	0.0019505498710537
GO:0043229	intracellular organelle	0.0019505498710537
GO:0043226	organelle	0.0019505498710537
GO:0016071	mRNA metabolic process	0.0019505498710537
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00383249314735907
GO:0003677	DNA binding	0.00418382364513257
GO:0044424	intracellular part	0.00494269684193766
GO:0006396	RNA processing	0.00494269684193766
GO:0006350	transcription	0.00494269684193766
GO:0046777	protein amino acid autophosphorylation	0.00615239353534538
GO:0016540	protein autoprocessing	0.00660974729994499
GO:0005622	intracellular	0.00668764818428192
GO:0018212	peptidyl-tyrosine modification	0.0143628569552499
GO:0018108	peptidyl-tyrosine phosphorylation	0.0143628569552499
GO:0006355	regulation of transcription, DNA-dependent	0.0143628569552499
GO:0006351	transcription, DNA-dependent	0.0145152041548976
GO:0032774	RNA biosynthetic process	0.0145152041548976
GO:0045449	regulation of transcription	0.0160271656701653
GO:0003723	RNA binding	0.0160271656701653
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0172785291018028
GO:0010468	regulation of gene expression	0.0218552790271866
GO:0031323	regulation of cellular metabolic process	0.026685242233463
GO:0018193	peptidyl-amino acid modification	0.0288652314441864
GO:0004652	polynucleotide adenylyltransferase activity	0.0288652314441864
GO:0019222	regulation of metabolic process	0.0300666077364779
GO:0048505	regulation of timing of cell differentiation	0.0332166159399697
GO:0040034	regulation of development, heterochronic	0.0332166159399697
GO:0016486	peptide hormone processing	0.0430581140249115
GO:0018210	peptidyl-threonine modification	0.0430581140249115
GO:0018107	peptidyl-threonine phosphorylation	0.0430581140249115
GO:0001837	epithelial to mesenchymal transition	0.0480139548102052

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	7.61e-08	13
common lymphoid progenitor	7.61e-08	13
lymphoid lineage restricted progenitor cell	8.35e-08	12
T cell	3.77e-07	11
pro-T cell	3.77e-07	11

Uber Anatomy

Ontology term	p-value	n
anterior region of body	5.67e-08	43
craniocervical region	1.40e-07	36
respiratory tract	1.97e-07	41
respiratory system	2.68e-07	42
hemopoietic organ	2.73e-07	29
immune organ	2.73e-07	29
mixed endoderm/mesoderm-derived structure	6.56e-07	35

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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