MCL coexpression mm9:224

Phase1 CAGE Peaks

	Short description
Mm9::chr10:79957600..79957618,+	p1@Onecut3
Mm9::chr10:91627904..91627922,-	p1@Rmst
Mm9::chr12:47821823..47821831,-	p@chr12:47821823..47821831 -
Mm9::chr12:47919122..47919142,-	p@chr12:47919122..47919142 -
Mm9::chr13:95587649..95587666,+	p@chr13:95587649..95587666 +
Mm9::chr15:98918857..98918860,-	p@chr15:98918857..98918860 -
Mm9::chr16:72027952..72027965,+	p@chr16:72027952..72027965 +
Mm9::chr17:37182755..37182764,+	p18@Gabbr1
Mm9::chr19:47098299..47098310,+	p@chr19:47098299..47098310 +
Mm9::chr19:47098414..47098424,+	p@chr19:47098414..47098424 +
Mm9::chr1:122498955..122498968,+	p1@En1
Mm9::chr1:122498982..122498991,+	p3@En1
Mm9::chr1:122499088..122499099,+	p2@En1
Mm9::chr1:140739042..140739054,-	p2@Lhx9
Mm9::chr1:19093112..19093124,+	p1@Tfap2d
Mm9::chr1:78193687..78193692,-	p1@Pax3
Mm9::chr2:181333948..181333966,-	p2@Samd10
Mm9::chr2:181333971..181333985,-	p3@Samd10
Mm9::chr2:28771056..28771092,-	p1@Barhl1
Mm9::chr2:28771380..28771413,-	p2@Barhl1
Mm9::chr3:17226363..17226378,-	p@chr3:17226363..17226378 -
Mm9::chr4:115612528..115612533,-	p1@Dmbx1
Mm9::chr4:130348020..130348047,+	p8@Sdc3
Mm9::chr4:53792566..53792578,+	p1@Tal2
Mm9::chr5:120881766..120881780,-	p@chr5:120881766..120881780 -
Mm9::chr5:120881900..120881914,+	p1@Lhx5
Mm9::chr5:120881918..120881921,+	p5@Lhx5
Mm9::chr5:120881939..120881946,+	p2@Lhx5
Mm9::chr5:137994829..137994836,+	p2@Actl6b
Mm9::chr6:138375256..138375268,-	p8@Lmo3
Mm9::chr6:138375597..138375621,-	p11@Lmo3
Mm9::chr7:116314043..116314071,-	p1@Lmo1
Mm9::chr7:17400821..17400830,-	p4@Fkrp
Mm9::chr7:56892217..56892221,-	p1@Dbx1
Mm9::chr7:58877078..58877091,+	p6@Slc17a6
Mm9::chr9:102619607..102619633,+	p5@Amotl2
Mm9::chr9:41254760..41254771,+	p@chr9:41254760..41254771 +
Mm9::chr9:99776566..99776612,-	p1@Sox14
Mm9::chr9:99776617..99776631,-	p2@Sox14

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:0003700	transcription factor activity	4.87239805828158e-07
GO:0043565	sequence-specific DNA binding	7.50904652949013e-07
GO:0006355	regulation of transcription, DNA-dependent	1.1901999276898e-06
GO:0044451	nucleoplasm part	1.1901999276898e-06
GO:0006351	transcription, DNA-dependent	1.1901999276898e-06
GO:0032774	RNA biosynthetic process	1.1901999276898e-06
GO:0045449	regulation of transcription	1.25222133356989e-06
GO:0005654	nucleoplasm	1.25222133356989e-06
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.3522715200986e-06
GO:0006350	transcription	1.40927872813406e-06
GO:0010468	regulation of gene expression	1.85839274777677e-06
GO:0031323	regulation of cellular metabolic process	2.67439720531192e-06
GO:0005667	transcription factor complex	2.71664147626017e-06
GO:0031981	nuclear lumen	2.71664147626017e-06
GO:0019222	regulation of metabolic process	3.21206305699881e-06
GO:0016070	RNA metabolic process	4.02750325884528e-06
GO:0043233	organelle lumen	5.3120582662618e-06
GO:0031974	membrane-enclosed lumen	5.3120582662618e-06
GO:0003677	DNA binding	5.89520912770347e-06
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	6.87222645177476e-06
GO:0010467	gene expression	2.23211148596962e-05
GO:0043283	biopolymer metabolic process	3.39485775885998e-05
GO:0044428	nuclear part	3.57754438809217e-05
GO:0050789	regulation of biological process	4.70755603433095e-05
GO:0043234	protein complex	0.000111908985509395
GO:0050794	regulation of cellular process	0.000111908985509395
GO:0065007	biological regulation	0.00012949928815094
GO:0003676	nucleic acid binding	0.000191543667322009
GO:0043170	macromolecule metabolic process	0.000592673197893004
GO:0032991	macromolecular complex	0.000618771760972181
GO:0005634	nucleus	0.0010018896344164
GO:0007399	nervous system development	0.00311877579333697
GO:0044238	primary metabolic process	0.00496102477809034
GO:0044237	cellular metabolic process	0.00508543312608764
GO:0043231	intracellular membrane-bound organelle	0.00530114834423677
GO:0043227	membrane-bound organelle	0.00530114834423677
GO:0007275	multicellular organismal development	0.00615939336069996
GO:0030902	hindbrain development	0.0064693499615585
GO:0007420	brain development	0.0064693499615585
GO:0044446	intracellular organelle part	0.00914043744565135
GO:0044422	organelle part	0.00914043744565135
GO:0007417	central nervous system development	0.0115634810794873
GO:0021915	neural tube development	0.0138961149319929
GO:0030917	midbrain-hindbrain boundary development	0.0197354658683251
GO:0004965	GABA-B receptor activity	0.0197354658683251
GO:0021903	rostrocaudal neural tube patterning	0.0197354658683251
GO:0043229	intracellular organelle	0.0215666072893901
GO:0043226	organelle	0.0215666072893901
GO:0032502	developmental process	0.028069917852192
GO:0048731	system development	0.0288922135031901
GO:0005313	L-glutamate transmembrane transporter activity	0.0335736911544627
GO:0021937	Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	0.0335736911544627
GO:0015172	acidic amino acid transmembrane transporter activity	0.0335736911544627
GO:0016514	SWI/SNF complex	0.0335736911544627
GO:0001504	neurotransmitter uptake	0.0384381861901399
GO:0044424	intracellular part	0.0423670894296677
GO:0021532	neural tube patterning	0.0423670894296677
GO:0021692	cerebellar Purkinje cell layer morphogenesis	0.043797599519862
GO:0021940	positive regulation of granule cell precursor proliferation	0.043797599519862
GO:0021694	cerebellar Purkinje cell layer formation	0.043797599519862
GO:0021936	regulation of granule cell precursor proliferation	0.043797599519862
GO:0021702	cerebellar Purkinje cell differentiation	0.043797599519862
GO:0048513	organ development	0.0448353612621322
GO:0009954	proximal/distal pattern formation	0.0448353612621322
GO:0021930	granule cell precursor proliferation	0.0448353612621322
GO:0021534	cell proliferation in hindbrain	0.0448353612621322
GO:0021924	cell proliferation in the external granule layer	0.0448353612621322
GO:0048856	anatomical structure development	0.0448353612621322
GO:0016564	transcription repressor activity	0.0454041794967971
GO:0030901	midbrain development	0.0454041794967971
GO:0021697	cerebellar cortex formation	0.0454041794967971
GO:0021533	cell differentiation in hindbrain	0.0454041794967971
GO:0032501	multicellular organismal process	0.0454041794967971
GO:0008283	cell proliferation	0.0454041794967971
GO:0016566	specific transcriptional repressor activity	0.047205899167591
GO:0035115	embryonic forelimb morphogenesis	0.047205899167591
GO:0005622	intracellular	0.047205899167591

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
CNS neuron (sensu Vertebrata)	3.23e-23	23
neuroblast (sensu Vertebrata)	3.23e-23	23
neuron	4.05e-14	33
neuronal stem cell	4.05e-14	33
neuroblast	4.05e-14	33
electrically signaling cell	4.05e-14	33
electrically responsive cell	5.89e-11	39
electrically active cell	5.89e-11	39
neural cell	2.32e-09	43
ectodermal cell	5.20e-09	44
neurectodermal cell	5.20e-09	44
non-terminally differentiated cell	1.73e-07	49

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	5.22e-11	54
neurectoderm	7.58e-10	64
neural plate	7.58e-10	64
presumptive neural plate	7.58e-10	64
central nervous system	1.13e-09	73
neural tube	2.60e-09	52
neural rod	2.60e-09	52
future spinal cord	2.60e-09	52
neural keel	2.60e-09	52
nervous system	3.47e-09	75
spinal cord	9.35e-09	6
dorsal region element	9.35e-09	6
dorsum	9.35e-09	6
basal ganglion	1.24e-08	8
nuclear complex of neuraxis	1.24e-08	8
aggregate regional part of brain	1.24e-08	8
collection of basal ganglia	1.24e-08	8
cerebral subcortex	1.24e-08	8
ectoderm-derived structure	2.47e-08	95
ectoderm	2.47e-08	95
presumptive ectoderm	2.47e-08	95
regional part of spinal cord	3.26e-08	5
gray matter of spinal cord	3.26e-08	5
posterior neural tube	4.16e-08	12
chordal neural plate	4.16e-08	12
ecto-epithelium	1.13e-07	73
gray matter	2.09e-07	34

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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