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MCL coexpression mm9:108: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.

Latest revision as of 14:42, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128185807..128185839,+p@chr10:128185807..128185839
+
Mm9::chr10:16144923..16144933,-p@chr10:16144923..16144933
-
Mm9::chr10:61246669..61246707,-p1@H2afy2
Mm9::chr10:61246709..61246722,-p2@H2afy2
Mm9::chr10:75384307..75384370,-p1@Smarcb1
Mm9::chr10:79612403..79612430,+p1@Midn
Mm9::chr10:79613193..79613227,+p3@Midn
Mm9::chr10:79613230..79613258,+p6@Midn
Mm9::chr10:79642176..79642209,+p3@Efna2
Mm9::chr10:79642238..79642276,+p2@Efna2
Mm9::chr10:82323234..82323295,+p2@Txnrd1
Mm9::chr11:102635386..102635436,+p3@Adam11
Mm9::chr11:120094272..120094294,+p2@Bahcc1
Mm9::chr11:60727277..60727318,-p1@Gm16515
Mm9::chr11:61307675..61307763,-p1@Mapk7
Mm9::chr11:69229647..69229669,-p@chr11:69229647..69229669
-
Mm9::chr11:69614276..69614297,+p@chr11:69614276..69614297
+
Mm9::chr11:69651505..69651540,-p3@Nlgn2
Mm9::chr11:97560869..97560886,-p6@Pcgf2
Mm9::chr11:97560948..97561012,-p1@Pcgf2
Mm9::chr13:56804721..56804792,+p2@Smad5
Mm9::chr14:70553492..70553540,-p1@2610301G19Rik
Mm9::chr14:76814736..76814781,+p4@Tsc22d1
Mm9::chr14:76814784..76814803,+p7@Tsc22d1
Mm9::chr15:75447105..75447159,+p1@Zfp41
Mm9::chr15:76755836..76755867,-p1@Zfp647
Mm9::chr15:79376971..79376996,-p1@Ddx17
Mm9::chr15:99532709..99532743,+p1@Smarcd1
Mm9::chr16:94592057..94592160,-p1@Pigp
Mm9::chr17:35031460..35031518,+p1@Zbtb12
Mm9::chr17:35031524..35031539,+p4@Zbtb12
Mm9::chr17:35972387..35972425,-p@chr17:35972387..35972425
-
Mm9::chr17:35975164..35975188,-p1@Tubb5
Mm9::chr17:37139472..37139514,+p1@Zfp57
Mm9::chr17:37140628..37140631,+p2@Zfp57
Mm9::chr17:56615885..56615903,-p3@Ptprs
Mm9::chr17:56615909..56615916,-p8@Ptprs
Mm9::chr18:34811357..34811395,-p1@Cdc23
Mm9::chr18:37906625..37906677,+p1@Pcdhga10
Mm9::chr18:37911255..37911306,+p1@Pcdhgb7
Mm9::chr19:46574657..46574687,+p@chr19:46574657..46574687
+
Mm9::chr19:46574691..46574720,+p@chr19:46574691..46574720
+
Mm9::chr19:7491617..7491719,+p2@2700081O15Rik
Mm9::chr19:7492076..7492140,+p1@2700081O15Rik
Mm9::chr1:120286000..120286042,+p1@Clasp1
Mm9::chr1:173934221..173934235,-p@chr1:173934221..173934235
-
Mm9::chr1:173934269..173934280,-p@chr1:173934269..173934280
-
Mm9::chr1:192803074..192803111,-p1@Vash2
Mm9::chr1:192803140..192803151,-p4@Vash2
Mm9::chr1:88483700..88483731,+p1@Cops7b
Mm9::chr2:152222298..152222320,-p@chr2:152222298..152222320
-
Mm9::chr2:152223783..152223812,-p4@Sox12
Mm9::chr2:152223852..152223872,-p7@Sox12
Mm9::chr2:152223881..152223933,-p3@Sox12
Mm9::chr2:160556994..160557036,+p1@Plcg1
Mm9::chr2:164860270..164860320,-p1@Ncoa5
Mm9::chr2:165213716..165213732,-p2@Zfp334
Mm9::chr2:17970414..17970449,-p1@2810030E01Rik
Mm9::chr2:26170979..26170986,+p7@Gpsm1
Mm9::chr2:27331142..27331218,-p1@Brd3
Mm9::chr2:28695794..28695878,-p1@Gtf3c4
Mm9::chr2:4803250..4803298,+p3@Sephs1
Mm9::chr2:78709277..78709299,+p6@Ube2e3
Mm9::chr3:104855866..104855905,-p2@Cttnbp2nl
Mm9::chr3:38784234..38784253,+p@chr3:38784234..38784253
+
Mm9::chr3:88335826..88335917,+p1@Mex3a
Mm9::chr3:88336236..88336318,+p2@Mex3a
Mm9::chr3:88336634..88336687,+p@chr3:88336634..88336687
+
Mm9::chr3:88341286..88341299,+p@chr3:88341286..88341299
+
Mm9::chr3:94914935..94915009,+p1@Vps72
Mm9::chr3:97101729..97101756,-p3@ENSMUST00000110986
p3@uc008qou.1
Mm9::chr3:97101775..97101839,-p1@ENSMUST00000110986
p1@uc008qou.1
Mm9::chr3:97101844..97101861,-p2@ENSMUST00000110986
p2@uc008qou.1
Mm9::chr4:120597555..120597637,-p1@Dem1
Mm9::chr4:129419519..129419556,-p1@Khdrbs1
Mm9::chr4:147504884..147504939,+p2@Mad2l2
Mm9::chr4:14791238..14791297,+p2@Tmem55a
Mm9::chr4:148892304..148892318,+p4@Ctnnbip1
Mm9::chr4:41082602..41082671,+p4@Ube2r2
Mm9::chr5:108494537..108494559,-p@chr5:108494537..108494559
-
Mm9::chr5:108890433..108890444,+p4@Pcgf3
Mm9::chr5:137748749..137748804,-p2@Srrt
Mm9::chr5:137974398..137974426,-p2@Gnb2
Mm9::chr5:141124972..141125006,-p1@Ttyh3
Mm9::chr5:143579262..143579320,-p1@Tnrc18
Mm9::chr5:21151796..21151850,+p1@Armc10
Mm9::chr5:24107676..24107722,-p4@Smarcd3
Mm9::chr5:34892244..34892280,+p2@Sh3bp2
Mm9::chr5:39075982..39076052,-p1@Zfp518b
Mm9::chr5:91360115..91360138,+p2@Mthfd2l
Mm9::chr6:87931623..87931639,-p1@H1fx
Mm9::chr7:112936020..112936037,-p2@Dchs1
Mm9::chr7:112936058..112936069,-p3@Dchs1
Mm9::chr7:112936081..112936153,-p1@Dchs1
Mm9::chr7:128178095..128178232,+p1@Mettl9
Mm9::chr7:137836100..137836140,+p4@Tacc2
Mm9::chr7:27980665..27980693,-p3@Gm5161
p4@Snrpa
Mm9::chr7:52124941..52124944,-p9@Ptov1
Mm9::chr7:52124957..52124988,-p2@Ptov1
Mm9::chr7:6124135..6124158,+p2@Zfp444
Mm9::chr7:87171256..87171280,+p4@Zfp710
Mm9::chr7:88005795..88005858,+p1@Zscan2
Mm9::chr7:89079517..89079536,-p2@Hdgfrp3
Mm9::chr7:90015837..90015867,+p1@Mex3b
Mm9::chr8:86521512..86521553,+p3@Samd1
Mm9::chr8:92872242..92872285,-p1@Tox3
Mm9::chr9:106789390..106789425,-p1@Rbm15b
Mm9::chr9:21420674..21420725,+p1@Smarca4
Mm9::chr9:21420744..21420755,+p3@Smarca4
Mm9::chr9:21420812..21420815,+p6@Smarca4
Mm9::chr9:44134615..44134659,+p2@Dpagt1
Mm9::chr9:64988982..64989005,+p1@Igdcc3


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:0005634nucleus3.15892471530941e-08
GO:0006350transcription1.81634119877763e-07
GO:0010468regulation of gene expression3.68979121648299e-07
GO:0045449regulation of transcription4.06331862039578e-07
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process6.05984590256704e-07
GO:0006355regulation of transcription, DNA-dependent9.17927765930472e-07
GO:0006351transcription, DNA-dependent1.060866475235e-06
GO:0032774RNA biosynthetic process1.060866475235e-06
GO:0019222regulation of metabolic process1.39904230341091e-06
GO:0031323regulation of cellular metabolic process4.04875665017288e-06
GO:0000792heterochromatin6.27932474364799e-06
GO:0043283biopolymer metabolic process1.3271587679848e-05
GO:0050789regulation of biological process1.76227075149709e-05
GO:0050794regulation of cellular process2.11669458286095e-05
GO:0005720nuclear heterochromatin3.51529592662672e-05
GO:0010467gene expression3.6371338529627e-05
GO:0016568chromatin modification4.28447824998891e-05
GO:0065007biological regulation4.45921775069015e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process7.13967497693972e-05
GO:0043231intracellular membrane-bound organelle7.36960617296392e-05
GO:0043227membrane-bound organelle7.36960617296392e-05
GO:0016070RNA metabolic process7.39233263127378e-05
GO:0000790nuclear chromatin7.98236461854426e-05
GO:0043170macromolecule metabolic process9.52431606098504e-05
GO:0044238primary metabolic process0.000159122765132399
GO:0001739sex chromatin0.000160042875407345
GO:0000803sex chromosome0.000199864708894719
GO:0043229intracellular organelle0.000250861175813654
GO:0043226organelle0.000250861175813654
GO:0044237cellular metabolic process0.000503601991882903
GO:0006325establishment and/or maintenance of chromatin architecture0.000547852626210717
GO:0006323DNA packaging0.000640400642748319
GO:0000785chromatin0.000762772902849071
GO:0001835blastocyst hatching0.00100365454975742
GO:0035188hatching0.00100365454975742
GO:0044454nuclear chromosome part0.00113380249672702
GO:0003677DNA binding0.0013785314832874
GO:0000228nuclear chromosome0.00194399302459289
GO:0016514SWI/SNF complex0.00224193530759556
GO:0005694chromosome0.00252093377276147
GO:0003676nucleic acid binding0.00305265673105741
GO:0051276chromosome organization and biogenesis0.00351885106715107
GO:0044424intracellular part0.0045768620305623
GO:0044428nuclear part0.0045768620305623
GO:0044427chromosomal part0.00612706227195036
GO:0005622intracellular0.0112371619048192
GO:0016585chromatin remodeling complex0.0228530859712625
GO:0046831regulation of RNA export from nucleus0.034499835106343
GO:0003975UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity0.034499835106343
GO:0045090retroviral genome replication0.034499835106343
GO:0008963phospho-N-acetylmuramoyl-pentapeptide-transferase activity0.034499835106343
GO:0007088regulation of mitosis0.0375799132490187
GO:0006259DNA metabolic process0.0436105060817978
GO:0003682chromatin binding0.0445383486760207
GO:0001824blastocyst development0.0458278280095512
GO:0008430selenium binding0.0458278280095512
GO:0009892negative regulation of metabolic process0.0474749508064222



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>


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)
MA0003.118.289
MA0004.11.83707
MA0006.13.12763
MA0007.10.448276
MA0009.10.0612679
MA0014.116.6733
MA0017.10.0143055
MA0019.10.65408
MA0024.11.5536
MA0025.10.165497
MA0027.11.37997
MA0028.10.612677
MA0029.10.161831
MA0030.10.379974
MA0031.10.589672
MA0038.10.0323731
MA0040.10.0654871
MA0041.10.00130293
MA0042.10.000975472
MA0043.10.664753
MA0046.10.0738138
MA0048.11.81259
MA0050.10.0335149
MA0051.10.0352645
MA0052.10.0682899
MA0055.10.162931
MA0056.10
MA0057.112.2241
MA0058.14.09502
MA0059.12.68657
MA0060.10.913244
MA0061.10.533428
MA0063.10
MA0066.10.34239
MA0067.10.232206
MA0068.13.50696
MA0069.10.0684094
MA0070.10.0650422
MA0071.10.0331824
MA0072.10.062178
MA0073.143.4752
MA0074.10.439657
MA0076.10.650383
MA0077.10.446955
MA0078.10.131538
MA0081.10.445704
MA0083.10.0977058
MA0084.10.475311
MA0087.10.0801732
MA0088.11.76932
MA0089.10
MA0090.10.148961
MA0091.10.0634745
MA0092.10.551598
MA0093.13.10552
MA0095.10
MA0098.10
MA0100.10.40795
MA0101.10.165002
MA0103.10.00644654
MA0105.13.05487
MA0106.10.486464
MA0107.10.035936
MA0108.20.021509
MA0109.10
MA0111.10.284394
MA0113.10.0396188
MA0114.10.0864832
MA0115.10.0992504
MA0116.12.77885
MA0117.10.290328
MA0119.10.554567
MA0122.10.645398
MA0124.10.199034
MA0125.10.156605
MA0130.10
MA0131.11.32048
MA0132.10
MA0133.10
MA0135.10.11432
MA0136.10.0757037
MA0139.15.04927
MA0140.10.407641
MA0141.10.0254036
MA0142.10.12791
MA0143.10.263943
MA0144.10.144493
MA0145.10.88788
MA0146.110.21
MA0147.16.25049
MA0148.10.0657204
MA0149.11.5248
MA0062.20.949799
MA0035.20.135724
MA0039.210.1924
MA0138.20.618245
MA0002.20.041551
MA0137.20.0992968
MA0104.28.6942
MA0047.20.204339
MA0112.20.65215
MA0065.21.02876
MA0150.10.0452099
MA0151.10
MA0152.10.204493
MA0153.10.122178
MA0154.10.273718
MA0155.14.01768
MA0156.10.0452994
MA0157.10.258054
MA0158.10
MA0159.11.27549
MA0160.10.0263222
MA0161.10
MA0162.112.5056
MA0163.119.3793
MA0164.10.309223
MA0080.20.0717589
MA0018.20.329605
MA0099.20.360652
MA0079.295.688
MA0102.20.518907
MA0258.10.107363
MA0259.12.57367
MA0442.10
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