MCL coexpression mm9:589

Phase1 CAGE Peaks

	Short description
Mm9::chr10:12684247..12684278,-	p3@Stx11
Mm9::chr11:70265457..70265476,+	p2@Med11
Mm9::chr13:42147384..42147441,+	p1@Hivep1
Mm9::chr19:46379199..46379301,+	p1@Nfkb2
Mm9::chr19:46380172..46380231,+	p2@Nfkb2
Mm9::chr19:46380235..46380277,+	p3@Nfkb2
Mm9::chr1:179726582..179726645,-	p1@Adss
Mm9::chr3:135354452..135354475,-	p5@Nfkb1
Mm9::chr6:140573180..140573187,-	p@chr6:140573180..140573187 -
Mm9::chr7:20214704..20214800,-	p1@Relb
Mm9::chr7:29551464..29551487,-	p2@Nfkbib
Mm9::chr9:7872886..7872909,-	p3@Birc3

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:0048535	lymph node development	0.00570946332167024
GO:0048534	hemopoietic or lymphoid organ development	0.0128876724140671
GO:0002520	immune system development	0.0128876724140671
GO:0045083	negative regulation of interleukin-12 biosynthetic process	0.0130337800136663
GO:0006355	regulation of transcription, DNA-dependent	0.0130337800136663
GO:0002250	adaptive immune response	0.0130337800136663
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0130337800136663
GO:0006351	transcription, DNA-dependent	0.0130337800136663
GO:0032774	RNA biosynthetic process	0.0130337800136663
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0130337800136663
GO:0044424	intracellular part	0.0130337800136663
GO:0004019	adenylosuccinate synthase activity	0.0130337800136663
GO:0002266	follicular dendritic cell activation	0.0130337800136663
GO:0002268	follicular dendritic cell differentiation	0.0130337800136663
GO:0045449	regulation of transcription	0.0130337800136663
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0132348084367286
GO:0006350	transcription	0.0132348084367286
GO:0005622	intracellular	0.0132348084367286
GO:0050794	regulation of cellular process	0.0132348084367286
GO:0010468	regulation of gene expression	0.0132348084367286
GO:0045063	T-helper 1 cell differentiation	0.0137294915714405
GO:0031323	regulation of cellular metabolic process	0.0144716931784834
GO:0019222	regulation of metabolic process	0.0160142300704282
GO:0005484	SNAP receptor activity	0.0160142300704282
GO:0016070	RNA metabolic process	0.0169374732737577
GO:0016564	transcription repressor activity	0.0175102895173719
GO:0050789	regulation of biological process	0.0175102895173719
GO:0043011	myeloid dendritic cell differentiation	0.0187319398928385
GO:0042090	interleukin-12 biosynthetic process	0.0187319398928385
GO:0002467	germinal center formation	0.0187319398928385
GO:0045075	regulation of interleukin-12 biosynthetic process	0.0187319398928385
GO:0001773	myeloid dendritic cell activation	0.0187319398928385
GO:0045892	negative regulation of transcription, DNA-dependent	0.0187319398928385
GO:0048536	spleen development	0.0187319398928385
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.0187319398928385
GO:0002292	T cell differentiation during immune response	0.0187319398928385
GO:0042093	T-helper cell differentiation	0.0187319398928385
GO:0002285	lymphocyte activation during immune response	0.0187319398928385
GO:0042088	T-helper 1 type immune response	0.0187319398928385
GO:0002293	alpha-beta T cell differentiation during immune response	0.0187319398928385
GO:0002286	T cell activation during immune response	0.0187319398928385
GO:0065007	biological regulation	0.0189737725871486
GO:0002376	immune system process	0.019196031657158
GO:0002366	leukocyte activation during immune response	0.019196031657158
GO:0002263	cell activation during immune response	0.019196031657158
GO:0005634	nucleus	0.0193334072601023
GO:0010467	gene expression	0.0197681334926949
GO:0042036	negative regulation of cytokine biosynthetic process	0.0197681334926949
GO:0001775	cell activation	0.0197681334926949
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0211063835598012
GO:0016481	negative regulation of transcription	0.0213149087903502
GO:0003700	transcription factor activity	0.0213149087903502
GO:0032615	interleukin-12 production	0.0213149087903502
GO:0016566	specific transcriptional repressor activity	0.0213149087903502
GO:0048523	negative regulation of cellular process	0.0217987727723372
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0228427797082627
GO:0048519	negative regulation of biological process	0.0257071905748928
GO:0031324	negative regulation of cellular metabolic process	0.0286053142831292
GO:0003677	DNA binding	0.0286053142831292
GO:0043231	intracellular membrane-bound organelle	0.0300439899962125
GO:0043227	membrane-bound organelle	0.0300439899962125
GO:0000119	mediator complex	0.0319093911503508
GO:0046632	alpha-beta T cell differentiation	0.0319093911503508
GO:0009892	negative regulation of metabolic process	0.0323932094042333
GO:0006944	membrane fusion	0.0323932094042333
GO:0017148	negative regulation of translation	0.0357783254503515
GO:0005515	protein binding	0.0357783254503515
GO:0031327	negative regulation of cellular biosynthetic process	0.0365618912224776
GO:0002274	myeloid leukocyte activation	0.0374096624706259
GO:0046631	alpha-beta T cell activation	0.0423011722615465
GO:0009890	negative regulation of biosynthetic process	0.0430412916192999

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
hematopoietic cell	3.05e-09	32
hematopoietic oligopotent progenitor cell	3.05e-09	32
hematopoietic stem cell	3.05e-09	32
angioblastic mesenchymal cell	3.05e-09	32
hematopoietic multipotent progenitor cell	3.05e-09	32
connective tissue cell	1.62e-08	46
mesenchymal cell	1.62e-08	46
motile cell	1.90e-08	54
leukocyte	1.37e-07	17
nongranular leukocyte	1.37e-07	17

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.89e-17	48
immune system	1.89e-17	48
hematopoietic system	1.36e-15	45
blood island	1.36e-15	45
lateral plate mesoderm	1.61e-14	87
mixed endoderm/mesoderm-derived structure	4.55e-11	35
endoderm-derived structure	1.38e-10	118
endoderm	1.38e-10	118
presumptive endoderm	1.38e-10	118
mesoderm	1.60e-10	120
mesoderm-derived structure	1.60e-10	120
presumptive mesoderm	1.60e-10	120
hemopoietic organ	2.31e-10	29
immune organ	2.31e-10	29
digestive system	2.85e-10	116
digestive tract	2.85e-10	116
primitive gut	2.85e-10	116
segment of respiratory tract	6.29e-10	27
respiratory system	1.36e-09	42
subdivision of digestive tract	2.10e-09	114
respiratory tract	2.55e-09	41
gland of gut	4.29e-09	24
pharynx	6.31e-09	24
upper respiratory tract	6.31e-09	24
chordate pharynx	6.31e-09	24
pharyngeal arch system	6.31e-09	24
pharyngeal region of foregut	6.31e-09	24
thymus	7.81e-09	23
neck	7.81e-09	23
respiratory system epithelium	7.81e-09	23
hemolymphoid system gland	7.81e-09	23
pharyngeal epithelium	7.81e-09	23
thymic region	7.81e-09	23
pharyngeal gland	7.81e-09	23
entire pharyngeal arch endoderm	7.81e-09	23
thymus primordium	7.81e-09	23
early pharyngeal endoderm	7.81e-09	23
connective tissue	1.62e-08	46
organ component layer	1.34e-07	24
organ segment	4.56e-07	35
musculoskeletal system	5.62e-07	32

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)
MA0003.1	5.27524
MA0004.1	0.303605
MA0006.1	0.960584
MA0007.1	0.290695
MA0009.1	0.709264
MA0014.1	5.47643
MA0017.1	0.546298
MA0019.1	0.535691
MA0024.1	0.667197
MA0025.1	0.936082
MA0027.1	2.34178
MA0028.1	0.173587
MA0029.1	0.64639
MA0030.1	0.65267
MA0031.1	0.618697
MA0038.1	0.432665
MA0040.1	0.721328
MA0041.1	0.239557
MA0042.1	0.228771
MA0043.1	0.802848
MA0046.1	0.743934
MA0048.1	0.382561
MA0050.1	0.337476
MA0051.1	0.440863
MA0052.1	0.729105
MA0055.1	0.10681
MA0056.1	0
MA0057.1	0.983678
MA0058.1	0.635024
MA0059.1	0.233271
MA0060.1	0.713464
MA0061.1	15.1152
MA0063.1	0
MA0066.1	0.422624
MA0067.1	1.04514
MA0068.1	1.43405
MA0069.1	0.729433
MA0070.1	0.720077
MA0071.1	0.336739
MA0072.1	0.711905
MA0073.1	0.486225
MA0074.1	1.01196
MA0076.1	0.200996
MA0077.1	0.691048
MA0078.1	0.471303
MA0081.1	0.252371
MA0083.1	0.802078
MA0084.1	1.3693
MA0087.1	0.760279
MA0088.1	1.49046
MA0089.1	0
MA0090.1	0.753315
MA0091.1	0.315003
MA0092.1	0.753925
MA0093.1	0.531567
MA0095.1	0
MA0098.1	0
MA0100.1	0.989129
MA0101.1	13.4863
MA0103.1	0.19444
MA0105.1	9.32904
MA0106.1	4.19338
MA0107.1	19.7892
MA0108.2	0.557195
MA0109.1	0
MA0111.1	0.286331
MA0113.1	0.452439
MA0114.1	1.29784
MA0115.1	0.805567
MA0116.1	2.91832
MA0117.1	0.774259
MA0119.1	0.241106
MA0122.1	0.793507
MA0124.1	0.992825
MA0125.1	0.920215
MA0130.1	0
MA0131.1	0.531427
MA0132.1	0
MA0133.1	0
MA0135.1	0.838263
MA0136.1	0.408073
MA0139.1	1.53598
MA0140.1	0.379562
MA0141.1	0.603844
MA0142.1	0.604892
MA0143.1	0.467531
MA0144.1	0.406018
MA0145.1	0.109043
MA0146.1	4.26321
MA0147.1	0.845188
MA0148.1	0.317692
MA0149.1	0.245177
MA0062.2	0.507063
MA0035.2	0.383789
MA0039.2	10.9843
MA0138.2	0.523978
MA0002.2	0.302282
MA0137.2	0.207733
MA0104.2	0.670538
MA0047.2	0.431964
MA0112.2	0.494696
MA0065.2	1.15835
MA0150.1	0.290598
MA0151.1	0
MA0152.1	0.432062
MA0153.1	0.854464
MA0154.1	1.97011
MA0155.1	1.26717
MA0156.1	0.580656
MA0157.1	0.574484
MA0158.1	0
MA0159.1	0.145521
MA0160.1	0.320315
MA0161.1	0
MA0162.1	4.05719
MA0163.1	3.36551
MA0164.1	0.408402
MA0080.2	1.06013
MA0018.2	1.88337
MA0099.2	0.518072
MA0079.2	9.9816
MA0102.2	1.42135
MA0258.1	0.118033
MA0259.1	0.408856
MA0442.1	0