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MCL coexpression mm9:156: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-

Latest revision as of 14:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127114099..127114115,+p2@Tmem194
Mm9::chr10:127114120..127114155,+p1@Tmem194
Mm9::chr10:41529686..41529721,-p2@Cep57l1
Mm9::chr10:79727780..79727831,+p2@Dazap1
Mm9::chr10:85484848..85484873,+p4@Fbxo7
Mm9::chr10:90633386..90633390,-p8@Tmpo
Mm9::chr11:102110156..102110202,+p1@BC030867
Mm9::chr11:106860775..106860787,-p1@Gm10184
p1@Gm10259
p1@Kpna2
Mm9::chr11:106860796..106860817,-p2@Kpna2
Mm9::chr11:117710587..117710596,+p2@Birc5
Mm9::chr11:69727510..69727580,+p1@Gps2
Mm9::chr11:72951747..72951812,-p1@Gsg2
Mm9::chr11:75161763..75161825,-p1@Rpa1
Mm9::chr12:4233904..4233925,-p4@Cenpo
Mm9::chr12:4233927..4233951,-p1@Cenpo
Mm9::chr13:49748083..49748123,-p2@Cenpp
Mm9::chr13:49748125..49748150,-p1@Cenpp
Mm9::chr13:51740679..51740701,+p1@Cks2
p1@Gm19945
p1@LOC100044750
p1@LOC100046104
Mm9::chr14:47380242..47380301,+p1@Cdkn3
Mm9::chr14:66424669..66424683,+p6@Pbk
Mm9::chr15:57743779..57743833,+p1@Wdr67
Mm9::chr17:23863395..23863441,+p1@Pkmyt1
Mm9::chr17:56179773..56179843,+p1@Chaf1a
Mm9::chr18:74367425..74367444,-p1@Ska1
Mm9::chr19:6085053..6085146,+p1@Cdca5
Mm9::chr19:9973917..9973929,-p2@Incenp
Mm9::chr19:9974159..9974182,+p@chr19:9974159..9974182
+
Mm9::chr1:136859130..136859145,+p2@Ube2t
Mm9::chr1:136859148..136859204,+p1@Ube2t
Mm9::chr1:193399416..193399428,-p2@Dtl
Mm9::chr1:193645371..193645447,+p1@Nek2
Mm9::chr2:109120938..109120955,+p2@Kif18a
Mm9::chr2:118423945..118423962,+p3@Bub1b
Mm9::chr2:156832775..156832818,-p1@Dsn1
Mm9::chr2:164595392..164595403,+p2@Ube2c
Mm9::chr2:172196014..172196040,-p1@Aurka
Mm9::chr3:116297877..116297949,+p1@Sass6
Mm9::chr3:134875521..134875549,+p2@Cenpe
Mm9::chr3:27052787..27052798,-p3@Ect2
Mm9::chr3:40603935..40603972,+p1@Plk4
Mm9::chr3:68808891..68808943,+p1@Smc4
Mm9::chr4:114672761..114672775,+p3@Stil
Mm9::chr4:116855228..116855241,-p3@Kif2c
Mm9::chr4:118109871..118109880,-p3@Cdc20
Mm9::chr4:118109936..118109959,-p2@Cdc20
Mm9::chr4:133742934..133743005,-p1@Ccdc21
Mm9::chr4:148511645..148511704,-p1@Apitd1
Mm9::chr4:41411849..41411925,-p1@Kif24
Mm9::chr5:116295238..116295310,+p1@Cit
Mm9::chr5:151325221..151325245,+p1@Brca2
Mm9::chr5:23536467..23536525,-p1@Fam126a
Mm9::chr5:33994988..33995005,-p2@Slbp
Mm9::chr5:34001199..34001212,+p2@Tacc3
Mm9::chr5:46061123..46061140,+p2@Ncapg
Mm9::chr5:65726820..65726831,-p2@Rfc1
Mm9::chr5:8422695..8422727,-p2@Dbf4
Mm9::chr6:113481669..113481715,+p1@Fancd2
Mm9::chr6:124959016..124959061,+p3@Zfp384
Mm9::chr6:128312937..128313076,+p1@Foxm1
Mm9::chr6:146526474..146526492,+p2@Fgfr1op2
Mm9::chr7:129302936..129303015,+p1@Plk1
Mm9::chr7:52071756..52071776,+p1@Il4i1
p1@Nup62-il4i1
p1@Nup62
Mm9::chr8:119445635..119445652,+p2@Cenpn
Mm9::chr8:119445654..119445663,+p3@Cenpn
Mm9::chr8:23296293..23296312,-p2@Ckap2
Mm9::chr8:87396086..87396140,+p1@Syce2
Mm9::chr9:106183681..106183741,+p1@Poc1a
Mm9::chr9:64005854..64005856,-p@chr9:64005854..64005856
-
Mm9::chr9:70269340..70269399,-p1@Ccnb2
Mm9::chr9:72286386..72286405,+p2@Mns1


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:0007049cell cycle1.44782132470443e-24
GO:0022403cell cycle phase9.77219291633224e-18
GO:0022402cell cycle process1.1758897859158e-17
GO:0000279M phase1.1758897859158e-17
GO:0000278mitotic cell cycle2.45226822637973e-13
GO:0051301cell division3.75670463651151e-13
GO:0000775chromosome, pericentric region9.46731588926466e-12
GO:0005694chromosome8.60132120126306e-11
GO:0007067mitosis1.04544677580719e-10
GO:0000087M phase of mitotic cell cycle1.04544677580719e-10
GO:0044427chromosomal part2.62217631071725e-09
GO:0043232intracellular non-membrane-bound organelle1.265689423572e-08
GO:0043228non-membrane-bound organelle1.265689423572e-08
GO:0051327M phase of meiotic cell cycle6.18200776936742e-08
GO:0007126meiosis6.18200776936742e-08
GO:0051321meiotic cell cycle6.38670679162396e-08
GO:0000793condensed chromosome9.56985388378011e-08
GO:0030496midbody6.78530907114803e-07
GO:0004674protein serine/threonine kinase activity7.30829495754949e-07
GO:0005634nucleus3.62053258431639e-06
GO:0044446intracellular organelle part3.7693393557102e-06
GO:0044422organelle part3.95679878990212e-06
GO:0007059chromosome segregation5.08436914316912e-06
GO:0004672protein kinase activity1.34923448539993e-05
GO:0051726regulation of cell cycle1.56939896772251e-05
GO:0000910cytokinesis1.58585477378526e-05
GO:0015630microtubule cytoskeleton3.39123823793808e-05
GO:0016773phosphotransferase activity, alcohol group as acceptor5.25615099083774e-05
GO:0016301kinase activity8.87708698217631e-05
GO:0043687post-translational protein modification0.000180430799812609
GO:0000070mitotic sister chromatid segregation0.000252030120370413
GO:0000819sister chromatid segregation0.000252030120370413
GO:0044430cytoskeletal part0.000294355970171273
GO:0016772transferase activity, transferring phosphorus-containing groups0.000294355970171273
GO:0005874microtubule0.000294355970171273
GO:0000166nucleotide binding0.000494032795681147
GO:0043229intracellular organelle0.000494032795681147
GO:0043226organelle0.000494032795681147
GO:0003777microtubule motor activity0.000505422407726698
GO:0005524ATP binding0.000556982811378001
GO:0006260DNA replication0.000556982811378001
GO:0000801central element0.000582992732372436
GO:0006464protein modification process0.000582992732372436
GO:0032559adenyl ribonucleotide binding0.000582992732372436
GO:0006468protein amino acid phosphorylation0.000585366207086157
GO:0006996organelle organization and biogenesis0.000737750600726981
GO:0000794condensed nuclear chromosome0.000774884105448121
GO:0007127meiosis I0.000774884105448121
GO:0043412biopolymer modification0.000785149151412593
GO:0000228nuclear chromosome0.000796153639353472
GO:0030554adenyl nucleotide binding0.000814291696431081
GO:0051276chromosome organization and biogenesis0.00109393948773557
GO:0016310phosphorylation0.00113744853852033
GO:0007017microtubule-based process0.00151388958990548
GO:0005622intracellular0.00154075664745744
GO:0000074regulation of progression through cell cycle0.00154075664745744
GO:0005856cytoskeleton0.00155377679311978
GO:0005875microtubule associated complex0.00195060377001823
GO:0006259DNA metabolic process0.00311908774026783
GO:0006793phosphorus metabolic process0.00335251251295851
GO:0006796phosphate metabolic process0.00335251251295851
GO:0032553ribonucleotide binding0.00352423973104953
GO:0032555purine ribonucleotide binding0.00352423973104953
GO:0007129synapsis0.00408235542320438
GO:0044424intracellular part0.00413716403331301
GO:0017076purine nucleotide binding0.00489846206117519
GO:0044454nuclear chromosome part0.00720823581324697
GO:0000776kinetochore0.00786979640958395
GO:0000795synaptonemal complex0.00871570269389151
GO:0043231intracellular membrane-bound organelle0.00913973487769127
GO:0043227membrane-bound organelle0.00917190599941111
GO:0007346regulation of progression through mitotic cell cycle0.0103568536863254
GO:0016538cyclin-dependent protein kinase regulator activity0.0112770017115633
GO:0043283biopolymer metabolic process0.0117384447574178
GO:0007018microtubule-based movement0.0120179366875721
GO:0016740transferase activity0.0173676526985089
GO:0042772DNA damage response, signal transduction resulting in transcription0.0173676526985089
GO:0008054cyclin catabolic process0.0173676526985089
GO:0006978DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator0.0173676526985089
GO:0048478replication fork protection0.0173676526985089
GO:0031625ubiquitin protein ligase binding0.0173676526985089
GO:0030705cytoskeleton-dependent intracellular transport0.0177134065082344
GO:0005635nuclear envelope0.0230199955487026
GO:0006974response to DNA damage stimulus0.0273197900990334
GO:0000940outer kinetochore of condensed chromosome0.0307105649515775
GO:0008334histone mRNA metabolic process0.0307105649515775
GO:0051220cytoplasmic sequestering of protein0.0307105649515775
GO:0001716L-amino-acid oxidase activity0.0307105649515775
GO:0042994cytoplasmic sequestering of transcription factor0.0307105649515775
GO:0010225response to UV-C0.0307105649515775
GO:0008608attachment of spindle microtubules to kinetochore0.0307105649515775
GO:0006398histone mRNA 3'-end processing0.0307105649515775
GO:0009719response to endogenous stimulus0.0321817238295457
GO:0007276gamete generation0.0321817238295457
GO:0016043cellular component organization and biogenesis0.0321817238295457
GO:0044428nuclear part0.0371554930705214
GO:0007141male meiosis I0.0416594668065179
GO:0005095GTPase inhibitor activity0.0416594668065179
GO:0050774negative regulation of dendrite morphogenesis0.0416594668065179
GO:0031573intra-S DNA damage checkpoint0.0416594668065179
GO:0008518reduced folate carrier activity0.0416594668065179
GO:0007089traversing start control point of mitotic cell cycle0.0416594668065179
GO:0006512ubiquitin cycle0.0433078326437268
GO:0005083small GTPase regulator activity0.0465867594713286
GO:0007010cytoskeleton organization and biogenesis0.0465867594713286
GO:0019953sexual reproduction0.0491705653225339
GO:0030695GTPase regulator activity0.0492954483949226
GO:0033205cytokinesis during cell cycle0.0498248338747191
GO:0051224negative regulation of protein transport0.0498248338747191
GO:0046823negative regulation of nucleocytoplasmic transport0.0498248338747191
GO:0000777condensed chromosome kinetochore0.0498248338747191
GO:0042308negative regulation of protein import into nucleus0.0498248338747191
GO:0042992negative regulation of transcription factor import into nucleus0.0498248338747191
GO:0045931positive regulation of progression through mitotic cell cycle0.0498248338747191



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
primordium3.23e-07134


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)
MA0003.11.40539
MA0004.10.664995
MA0006.12.04308
MA0007.10.611716
MA0009.10.4417
MA0014.13.69101
MA0017.10.378927
MA0019.10.0625856
MA0024.16.50814
MA0025.10.290379
MA0027.11.58064
MA0028.12.16164
MA0029.10.110598
MA0030.10.113716
MA0031.10.321618
MA0038.11.25335
MA0040.10.150335
MA0041.10.0575895
MA0042.10.22529
MA0043.11.09587
MA0046.10.163356
MA0048.10.827896
MA0050.10.534642
MA0051.10.311762
MA0052.10.154763
MA0055.10.0235698
MA0056.10
MA0057.10.113862
MA0058.10.773365
MA0059.10.591937
MA0060.124.101
MA0061.11.21968
MA0063.10
MA0066.10.117158
MA0067.11.73168
MA0068.10.026325
MA0069.10.154951
MA0070.10.149628
MA0071.10.0120294
MA0072.10.145044
MA0073.15.7206e-05
MA0074.10.0923804
MA0076.12.5733
MA0077.10.825305
MA0078.10.159531
MA0081.10.283991
MA0083.10.198862
MA0084.10.648071
MA0087.10.173051
MA0088.12.43723
MA0089.10
MA0090.10.343094
MA0091.10.268395
MA0092.10.0875239
MA0093.10.524033
MA0095.10
MA0098.10
MA0100.15.91712
MA0101.11.17268
MA0103.10.414717
MA0105.10.882096
MA0106.11.48038
MA0107.10.5776
MA0108.20.0708441
MA0109.10
MA0111.10.0990902
MA0113.10.331635
MA0114.10.549546
MA0115.10.20108
MA0116.11.10358
MA0117.11.02496
MA0119.10.255297
MA0122.10.193454
MA0124.10.332586
MA0125.10.278915
MA0130.10
MA0131.15.79476
MA0132.10
MA0133.10
MA0135.10.222323
MA0136.10.105718
MA0139.11.35291
MA0140.10.0850147
MA0141.10.0375835
MA0142.10.0910287
MA0143.10.0399933
MA0144.10.272616
MA0145.10.00672333
MA0146.13.01492
MA0147.10.838993
MA0148.10.133377
MA0149.10.00323152
MA0062.24.22844
MA0035.20.0879378
MA0039.22.84679
MA0138.20.0583125
MA0002.20.29059
MA0137.20.473238
MA0104.20.841049
MA0047.20.124805
MA0112.20.0258614
MA0065.20.026241
MA0150.10.0356481
MA0151.10
MA0152.10.296975
MA0153.10.233143
MA0154.10.0918945
MA0155.10.523509
MA0156.10.28152
MA0157.10.0778671
MA0158.10
MA0159.10.0680834
MA0160.10.479842
MA0161.10
MA0162.14.16848
MA0163.10.4459
MA0164.10.484537
MA0080.20.142171
MA0018.21.60277
MA0099.20.0562189
MA0079.20.311032
MA0102.20.695093
MA0258.10.0362695
MA0259.12.87778
MA0442.10
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