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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 14:44, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128184776..128184800,-p@chr10:128184776..128184800
-
Mm9::chr10:128258801..128258829,+p2@Sarnp
Mm9::chr10:19987074..19987116,+p@chr10:19987074..19987116
+
Mm9::chr10:20881210..20881226,-p8@Myb
Mm9::chr10:41472017..41472073,-p@chr10:41472017..41472073
-
Mm9::chr10:41990727..41990747,-p@chr10:41990727..41990747
-
Mm9::chr10:79613557..79613570,+p10@Midn
Mm9::chr11:106249380..106249419,-p2@Icam2
Mm9::chr11:106249420..106249431,-p3@Icam2
Mm9::chr11:106611786..106611800,-p4@Pecam1
Mm9::chr11:115324117..115324139,-p@chr11:115324117..115324139
-
Mm9::chr11:49016787..49016800,+p3@Zfp62
Mm9::chr11:62272010..62272050,-p2@Ncor1
Mm9::chr11:62387979..62388024,+p2@Trpv2
Mm9::chr11:62388025..62388054,+p5@Trpv2
Mm9::chr11:62388075..62388086,+p7@Trpv2
Mm9::chr11:6488230..6488234,+p@chr11:6488230..6488234
+
Mm9::chr11:82880750..82880793,-p@chr11:82880750..82880793
-
Mm9::chr11:98407142..98407159,-p5@Ikzf3
Mm9::chr11:98407164..98407177,-p8@Ikzf3
Mm9::chr11:98407210..98407221,-p7@Ikzf3
Mm9::chr12:114664203..114664241,-p@chr12:114664203..114664241
-
Mm9::chr12:70576554..70576575,-p2@5830428M24Rik
Mm9::chr12:80081745..80081804,-p2@Tmem229b
Mm9::chr13:20277272..20277279,+p17@Elmo1
Mm9::chr13:24508497..24508537,+p5@Cmah
Mm9::chr13:24509523..24509546,+p@chr13:24509523..24509546
+
Mm9::chr13:35281129..35281136,+p@chr13:35281129..35281136
+
Mm9::chr14:79915425..79915501,+p1@Elf1
Mm9::chr15:59451643..59451659,+p@chr15:59451643..59451659
+
Mm9::chr15:80402967..80402990,+p2@Grap2
Mm9::chr15:80541722..80541770,+p1@Tnrc6b
Mm9::chr15:8394164..8394209,-p3@Nipbl
Mm9::chr17:71824625..71824680,-p1@Smchd1
Mm9::chr17:84580073..84580090,-p@chr17:84580073..84580090
-
Mm9::chr17:84586009..84586031,-p@chr17:84586009..84586031
-
Mm9::chr18:24364108..24364133,+p11@Galnt1
Mm9::chr18:34381287..34381313,-p1@Gm10548
Mm9::chr18:34937244..34937300,+p@chr18:34937244..34937300
+
Mm9::chr18:78338818..78338829,-p3@Slc14a1
Mm9::chr18:78338876..78338893,-p2@Slc14a1
Mm9::chr18:78338906..78338915,-p4@Slc14a1
Mm9::chr19:25127044..25127101,+p1@Dock8
Mm9::chr19:8894247..8894280,-p5@Ttc9c
Mm9::chr1:133904862..133904893,+p6@Elk4
Mm9::chr1:133904901..133904934,+p3@Elk4
Mm9::chr1:135586667..135586674,-p6@Lax1
Mm9::chr1:157883011..157883020,-p11@Tor1aip1
Mm9::chr1:173847569..173847603,+p2@Slamf6
Mm9::chr1:38721779..38721790,-p6@Aff3
Mm9::chr1:38721792..38721845,-p1@Aff3
Mm9::chr1:46951476..46951503,+p@chr1:46951476..46951503
+
Mm9::chr1:88256128..88256165,+p1@C130036L24Rik
Mm9::chr2:121332451..121332469,+p2@Wdr76
Mm9::chr2:44166131..44166132,+p@chr2:44166131..44166132
+
Mm9::chr2:6642696..6642730,-p6@Celf2
Mm9::chr3:103190802..103190814,+p@chr3:103190802..103190814
+
Mm9::chr3:130814435..130814449,+p@chr3:130814435..130814449
+
Mm9::chr3:146444315..146444395,-p1@Prkacb
Mm9::chr3:152591853..152591864,+p@chr3:152591853..152591864
+
Mm9::chr3:152593008..152593012,+p@chr3:152593008..152593012
+
Mm9::chr3:60276744..60276759,+p7@Mbnl1
Mm9::chr4:102792072..102792091,+p5@Mier1
Mm9::chr4:123250215..123250231,-p@chr4:123250215..123250231
-
Mm9::chr4:129236052..129236065,-p10@Lck
Mm9::chr4:137439830..137439880,-p1@ENSMUST00000155349
p1@ENSMUST00000156022
Mm9::chr5:105924474..105924494,+p@chr5:105924474..105924494
+
Mm9::chr5:117959951..117959963,+p@chr5:117959951..117959963
+
Mm9::chr5:141476588..141476603,-p2@Card11
Mm9::chr5:37438659..37438696,+p2@Jakmip1
Mm9::chr5:66254802..66254889,+p1@Rhoh
Mm9::chr5:77695390..77695414,+p2@Rest
Mm9::chr5:96593138..96593161,-p5@Cnot6l
Mm9::chr5:96593166..96593220,-p2@Cnot6l
Mm9::chr6:117850421..117850435,+p15@Hnrnpf
Mm9::chr6:47586869..47586882,-p@chr6:47586869..47586882
-
Mm9::chr6:48689458..48689462,-p@chr6:48689458..48689462
-
Mm9::chr6:57531054..57531109,+p1@Herc6
Mm9::chr6:57531119..57531132,+p4@Herc6
Mm9::chr6:87482995..87483032,-p4@Arhgap25
Mm9::chr7:142843956..142843985,-p1@5830432E09Rik
Mm9::chr7:148282731..148282745,-p@chr7:148282731..148282745
-
Mm9::chr7:150813953..150813968,+p1@uc009kpq.1
p1@uc009kpr.1
Mm9::chr7:17428319..17428365,+p2@Prkd2
Mm9::chr7:52156943..52156963,-p5@Ap2a1
Mm9::chr7:52997400..52997421,+p@chr7:52997400..52997421
+
Mm9::chr7:71144109..71144114,-p@chr7:71144109..71144114
-
Mm9::chr7:75420856..75420911,+p1@ENSMUST00000153805
Mm9::chr7:87171047..87171078,+p1@Zfp710
Mm9::chr8:108583550..108583595,+p2@Nfatc3
Mm9::chr8:74126069..74126107,+p2@Fam129c
Mm9::chr8:74247186..74247197,-p4@Fcho1
Mm9::chr9:21156409..21156413,+p@chr9:21156409..21156413
+
Mm9::chr9:21936079..21936109,-p@chr9:21936079..21936109
-
Mm9::chr9:32503590..32503680,+p1@Ets1
Mm9::chr9:53344724..53344798,-p1@Atm
Mm9::chrX:130697516..130697537,-p@chrX:130697516..130697537
-
Mm9::chrX:98469445..98469487,+p2@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

GO IDGO nameFDR corrected p-value
GO:0003676nucleic acid binding6.04249900836944e-05
GO:0016070RNA metabolic process0.000144609430801015
GO:0043283biopolymer metabolic process0.000144609430801015
GO:0050789regulation of biological process0.000144609430801015
GO:0043170macromolecule metabolic process0.000147915531054353
GO:0019222regulation of metabolic process0.000214075200626794
GO:0050794regulation of cellular process0.000319364604303831
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000418549991844582
GO:0031323regulation of cellular metabolic process0.00044431535329671
GO:0003677DNA binding0.00044431535329671
GO:0065007biological regulation0.000549174522709008
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000564970487741933
GO:0005634nucleus0.000740222579883123
GO:0010468regulation of gene expression0.000844361037870367
GO:0006355regulation of transcription, DNA-dependent0.00107438648694831
GO:0006351transcription, DNA-dependent0.00111405541609713
GO:0032774RNA biosynthetic process0.00111405541609713
GO:0010467gene expression0.00120754781530943
GO:0045449regulation of transcription0.00135665362047548
GO:0044238primary metabolic process0.00152869350552634
GO:0006350transcription0.00176016174777587
GO:0003700transcription factor activity0.00185708016705504
GO:0044237cellular metabolic process0.00552146585177274
GO:0050851antigen receptor-mediated signaling pathway0.0414713688806204
GO:0050776regulation of immune response0.0449529524925541
GO:0002682regulation of immune system process0.0449529524925541
GO:0021542dentate gyrus development0.0449529524925541
GO:0030338CMP-N-acetylneuraminate monooxygenase activity0.0449529524925541
GO:0005521lamin binding0.0449529524925541
GO:0002429immune response-activating cell surface receptor signaling pathway0.0449529524925541
GO:0001756somitogenesis0.0449529524925541
GO:0048518positive regulation of biological process0.0449529524925541
GO:0043231intracellular membrane-bound organelle0.0449529524925541
GO:0043227membrane-bound organelle0.0449529524925541
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0449904172636834
GO:0002757immune response-activating signal transduction0.0489777847153195



Relative expression of the co-expression cluster over median <br>Analyst:




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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.28e-2048
immune system1.28e-2048
hemopoietic organ1.19e-1929
immune organ1.19e-1929
hematopoietic system1.85e-1845
blood island1.85e-1845
gland of gut9.73e-1624
mixed endoderm/mesoderm-derived structure1.45e-1535
thymus3.78e-1523
neck3.78e-1523
respiratory system epithelium3.78e-1523
hemolymphoid system gland3.78e-1523
pharyngeal epithelium3.78e-1523
thymic region3.78e-1523
pharyngeal gland3.78e-1523
entire pharyngeal arch endoderm3.78e-1523
thymus primordium3.78e-1523
early pharyngeal endoderm3.78e-1523
pharynx3.55e-1424
upper respiratory tract3.55e-1424
chordate pharynx3.55e-1424
pharyngeal arch system3.55e-1424
pharyngeal region of foregut3.55e-1424
respiratory system4.73e-1442
respiratory tract1.74e-1341
segment of respiratory tract1.02e-1127
foregut4.15e-1180
lateral plate mesoderm8.54e-1087
organ segment3.07e-0835
craniocervical region7.62e-0836
endo-epithelium1.02e-0769
digestive system1.43e-07116
digestive tract1.43e-07116
primitive gut1.43e-07116
endoderm-derived structure3.41e-07118
endoderm3.41e-07118
presumptive endoderm3.41e-07118
subdivision of digestive tract6.94e-07114
mesoderm9.93e-07120
mesoderm-derived structure9.93e-07120
presumptive mesoderm9.93e-07120


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

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.67621
MA0004.10.689053
MA0006.10.143595
MA0007.10.0778773
MA0009.10.276069
MA0014.10.0893699
MA0017.10.441896
MA0019.11.17955
MA0024.10.49814
MA0025.10.19779
MA0027.11.43681
MA0028.11.92601
MA0029.10.0573756
MA0030.11.23821
MA0031.10.408875
MA0038.10.746863
MA0040.10.0856419
MA0041.11.56537
MA0042.12.09104
MA0043.10.389469
MA0046.10.0953474
MA0048.10.26747
MA0050.13.13288
MA0051.11.46749
MA0052.10.298791
MA0055.11.57485
MA0056.10
MA0057.10.268162
MA0058.10.481036
MA0059.10.369814
MA0060.10.452108
MA0061.10.815142
MA0063.10
MA0066.10.459646
MA0067.10.269528
MA0068.11.33289
MA0069.10.299173
MA0070.10.0851203
MA0071.10.130428
MA0072.11.4715
MA0073.10.840474
MA0074.10.209177
MA0076.13.11892
MA0077.10.25588
MA0078.10.362191
MA0081.11.10755
MA0083.10.122707
MA0084.10.522943
MA0087.10.102695
MA0088.10.0782412
MA0089.10
MA0090.10.23256
MA0091.10.103785
MA0092.10.372271
MA0093.10.562296
MA0095.10
MA0098.10
MA0100.10.088341
MA0101.10.0834252
MA0103.10.489254
MA0105.10.432404
MA0106.10.625057
MA0107.10.62883
MA0108.20.0317826
MA0109.10
MA0111.10.831744
MA0113.10.3234
MA0114.10.626698
MA0115.10.392987
MA0116.10.812657
MA0117.10.3532
MA0119.10.0840222
MA0122.10.37747
MA0124.11.22992
MA0125.10.551321
MA0130.10
MA0131.10.497478
MA0132.10
MA0133.10
MA0135.10.141399
MA0136.13.5151
MA0139.10.0904796
MA0140.10.0882536
MA0141.10.281717
MA0142.10.384727
MA0143.10.179907
MA0144.10.821162
MA0145.10.408923
MA0146.10.0935388
MA0147.10.30682
MA0148.10.534677
MA0149.10.0404853
MA0062.24.58886
MA0035.20.198945
MA0039.20.228214
MA0138.20.104551
MA0002.21.19536
MA0137.20.405348
MA0104.20.492644
MA0047.20.485965
MA0112.21.47181
MA0065.20.610615
MA0150.10.430047
MA0151.10
MA0152.10.486244
MA0153.10.150162
MA0154.10.526167
MA0155.10.169351
MA0156.16.32029
MA0157.10.333652
MA0158.10
MA0159.10.0528643
MA0160.10.0460532
MA0161.10
MA0162.10.264151
MA0163.11.19169
MA0164.10.420676
MA0080.27.58299
MA0018.20.0439143
MA0099.20.100425
MA0079.20.121813
MA0102.20.567661
MA0258.11.76522
MA0259.10.0668436
MA0442.10
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