MCL coexpression mm9:321

Phase1 CAGE Peaks

	Short description
Mm9::chr10:62486608..62486619,-	p2@Hnrnph3
Mm9::chr11:50641183..50641244,-	p1@Zfp354c
Mm9::chr14:22319053..22319105,+	p2@Myst4
Mm9::chr16:48994044..48994062,-	p1@Dzip3
Mm9::chr18:65740410..65740452,+	p@chr18:65740410..65740452 +
Mm9::chr1:137327004..137327065,-	p1@Ipo9
Mm9::chr2:121097091..121097133,-	p1@Trp53bp1
Mm9::chr2:13995774..13995818,+	p2@Stam
Mm9::chr2:165213745..165213815,-	p1@Zfp334
Mm9::chr3:129763728..129763744,-	p4@Sec24b
Mm9::chr4:137772539..137772565,+	p1@Hp1bp3
Mm9::chr4:155043228..155043272,-	p2@Mib2
Mm9::chr4:54960870..54960926,+	p1@Zfp462
Mm9::chr4:83132361..83132382,-	p2@Psip1
Mm9::chr5:111308807..111308861,+	p1@Ttc28
Mm9::chr5:31754831..31754876,+	p1@Zfp512
Mm9::chr5:53225284..53225351,+	p2@Anapc4
Mm9::chr7:17199897..17199955,-	p1@Grlf1
Mm9::chr7:30568977..30569047,+	p1@Zfp30
Mm9::chr8:108939219..108939296,+	p1@Zfp90
Mm9::chr8:86707764..86707815,-	p@chr8:86707764..86707815 -
Mm9::chr9:45714452..45714520,-	p1@Rnf214
Mm9::chrX:143988594..143988630,-	p1@Lrch2
Mm9::chrX:148235416..148235455,+	p2@Huwe1
Mm9::chrX:148235556..148235626,+	p5@Huwe1

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:0043283	biopolymer metabolic process	0.00794587097948635
GO:0003677	DNA binding	0.00794587097948635
GO:0043170	macromolecule metabolic process	0.0113426159567994
GO:0005634	nucleus	0.0113426159567994
GO:0003676	nucleic acid binding	0.0113426159567994
GO:0006355	regulation of transcription, DNA-dependent	0.0116253998330533
GO:0006351	transcription, DNA-dependent	0.0116253998330533
GO:0032774	RNA biosynthetic process	0.0116253998330533
GO:0008270	zinc ion binding	0.0116253998330533
GO:0045449	regulation of transcription	0.0121275033569461
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0125967280283161
GO:0006350	transcription	0.0126131748376515
GO:0010468	regulation of gene expression	0.0145568400482656
GO:0031323	regulation of cellular metabolic process	0.0176996880778582
GO:0006512	ubiquitin cycle	0.0189891975018616
GO:0019222	regulation of metabolic process	0.0196114607507608
GO:0044238	primary metabolic process	0.0196114607507608
GO:0044237	cellular metabolic process	0.0196114607507608
GO:0016070	RNA metabolic process	0.0197265385463275
GO:0046914	transition metal ion binding	0.0222689625102905
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0234264727644384
GO:0051100	negative regulation of binding	0.0234264727644384
GO:0043392	negative regulation of DNA binding	0.0234264727644384
GO:0004406	H3/H4 histone acetyltransferase activity	0.0323117080144102
GO:0044427	chromosomal part	0.0385349237162417
GO:0065003	macromolecular complex assembly	0.0407551671595038
GO:0006334	nucleosome assembly	0.0407551671595038
GO:0010467	gene expression	0.0407551671595038
GO:0016874	ligase activity	0.0407551671595038
GO:0004842	ubiquitin-protein ligase activity	0.0407551671595038
GO:0000786	nucleosome	0.0407551671595038
GO:0006610	ribosomal protein import into nucleus	0.0407551671595038
GO:0008639	small protein conjugating enzyme activity	0.0413391853083521
GO:0031497	chromatin assembly	0.0416704877530539
GO:0005694	chromosome	0.0437425671811541
GO:0043231	intracellular membrane-bound organelle	0.0437425671811541
GO:0019787	small conjugating protein ligase activity	0.0437425671811541
GO:0043227	membrane-bound organelle	0.0437425671811541
GO:0022607	cellular component assembly	0.0437425671811541
GO:0033036	macromolecule localization	0.0437425671811541
GO:0065004	protein-DNA complex assembly	0.0437425671811541
GO:0008536	Ran GTPase binding	0.0437425671811541
GO:0016881	acid-amino acid ligase activity	0.0467068866387382
GO:0050821	protein stabilization	0.0467068866387382
GO:0042393	histone binding	0.0467068866387382
GO:0006333	chromatin assembly or disassembly	0.0467102769164932
GO:0043687	post-translational protein modification	0.0483164904506294
GO:0031647	regulation of protein stability	0.0483164904506294
GO:0016573	histone acetylation	0.0483164904506294

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
neuron	5.58e-16	33
neuronal stem cell	5.58e-16	33
neuroblast	5.58e-16	33
electrically signaling cell	5.58e-16	33
electrically responsive cell	4.77e-13	39
electrically active cell	4.77e-13	39
CNS neuron (sensu Vertebrata)	1.05e-12	23
neuroblast (sensu Vertebrata)	1.05e-12	23
ectodermal cell	8.33e-10	44
neurectodermal cell	8.33e-10	44
neural cell	1.00e-09	43
non-terminally differentiated cell	3.36e-08	49

Uber Anatomy

Ontology term	p-value	n
neurectoderm	3.81e-21	64
neural plate	3.81e-21	64
presumptive neural plate	3.81e-21	64
central nervous system	5.23e-21	73
nervous system	5.16e-20	75
ectoderm-derived structure	5.40e-20	95
ectoderm	5.40e-20	95
presumptive ectoderm	5.40e-20	95
ecto-epithelium	1.05e-18	73
structure with developmental contribution from neural crest	6.84e-18	92
pre-chordal neural plate	2.58e-17	49
regional part of nervous system	3.94e-17	54
neural tube	2.45e-16	52
neural rod	2.45e-16	52
future spinal cord	2.45e-16	52
neural keel	2.45e-16	52
brain	3.67e-14	47
future brain	3.67e-14	47
anterior neural tube	7.35e-14	40
regional part of brain	1.36e-13	46
regional part of forebrain	1.91e-13	39
forebrain	1.91e-13	39
future forebrain	1.91e-13	39
gray matter	6.95e-13	34
brain grey matter	1.78e-10	29
regional part of telencephalon	1.78e-10	29
telencephalon	1.78e-10	29
multi-cellular organism	4.95e-09	333
embryo	2.37e-08	320
cerebral cortex	4.66e-07	21
cerebral hemisphere	4.66e-07	21
pallium	4.66e-07	21

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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