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MCL coexpression mm9:238: Difference between revisions

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{{MCL_coexpression_mm9
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somatic muscle development;0.0450262913742367;22288!GO:0007525;somatic muscle development;0.0450262913742367;22288!GO:0045176;apical protein localization;0.047395152381351;15165!GO:0008105;asymmetric protein localization;0.047395152381351;15165!GO:0030552;cAMP binding;0.047395152381351;15165!GO:0030054;cell junction;0.047395152381351;22288,108030!GO:0016010;dystrophin-associated glycoprotein complex;0.047395152381351;22288!GO:0031594;neuromuscular junction;0.047395152381351;22288!GO:0016208;AMP binding;0.047395152381351;15165!GO:0005624;membrane fraction;0.047395152381351;22288,108030!GO:0030551;cyclic nucleotide binding;0.0486781652053827;15165!GO:0000267;cell 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|coexpression_dpi_cluster_scores_mean=0.0360521222970974,-0.0104798320372894,-0.00901960587964407,-0.00561840253779484,-0.00148845167592318,-0.00334197072632947,-0.00484195650727142,-0.0126917733440084,-0.0154146859443257,-0.00967477501887174,-0.0150880428757798,-0.0170491207754562,-0.0150882255074233,-0.01600919285917,-0.00357871974339697,-0.00789756048595707,-0.0170491207754562,-0.0134143954409446,-0.0110349813670106,-0.0126597262080029,0.236454847955999,-0.0138139165241843,-0.0170491207754562,-0.00906937865675629,0.00617860087789276,-0.0170491207754562,-0.0126043380349396,-0.0122065673707017,-0.00657596787268465,-0.00727307373895626,-0.0100096784717317,-0.0170491207754562,-0.0170491207754562,-0.0170491207754562,0.00108466161654376,-0.0120286679781336,-0.00624621203795507,-0.0127108629401493,-0.00988495834454478,-0.0170491207754562,-0.0113087264318748,-0.0105892392579816,-0.00722765318131735,-0.00541724640398795,-0.000411281131215834,0.00885750061519409,-0.00987760464753811,-0.0121544774580759,0.0119124610496424,0.00265091940042226,-0.00748342164930232,-0.00599342953747513,-0.015124492140772,-0.0170491207754562,-0.0170491207754562,-0.0113676977017275,0.00420381014715834,0.00393057467120593,0.0859638076475758,0.119400282732859,0.0870039096863467,-0.013428259368552,-0.0170491207754562,-0.0170491207754562,-0.0170491207754562,-0.0170491207754562,0.0199865317114306,0.046450328381618,0.0591145233665431,0.0431212425366962,0.0527974783257997,0.123009411332147,0.131984012226244,0.0784764326079582,0.0347558458382031,0.0670884601639554,0.185158756984908,0.247110242315753,0.259305435495641,0.0940347992936798,0.0812120618971309,0.150019248643185,0.154629389895961,0.350905517581851,0.342574369634764,0.296319102897809,0.325977402867213,0.166295240989991,0.0498855218023103,0.0974876063945256,0.0177001954805196,0.0107773949592304,-0.0106119244560567,-0.0116937776320269,-0.00671645241989984,0.00759482615828599,0.0368596637619586,-0.00195913372004755,-0.0027210094449565,-0.0132946412985454,0.0459163292723883,-0.0170491207754562,-0.0170491207754562,-0.0170491207754562,0.0137646838265918,0.0155191092902146,0.00421576701366983,0.0354970311523545,0.00610443350858635,0.0553544530821312,0.0467248340820833,0.029113536265132,0.021458455623283,0.0378949072021135,0.0739581294975329,-0.00120299618993392,0.0182608991918123,0.0143659226786031,-0.00918564596381887,0.0164889803316899,0.00865355349018241,0.0612351478618776,0.0194069202241679,0.547544598238047,0.557511738511314,0.00924605213274575,-0.0156449399500406,-0.0170491207754562,-0.00946163522348633,0.457798750923139,0.49503972376585,0.238357706525167,0.537208928891384,0.606679467803392,0.367194754772594,0.49414711919507,0.0266536531784162,0.0245931876566955,0.0188136587617375,0.385007908833309,0.078031404463111,0.0707910551442348,0.0977092506603158,0.277434714825334,0.400598971901788,0.546133782467975,0.508848443948554,0.848415369597313,-0.0101788305369788,0.0487192233328835,0.0284690693544547,0.00511044714895726,0.0797966204729952,0.0174843185402278,0.0220044284412176,0.0283054818374906,-0.0170491207754562,-0.0170491207754562,-0.0139456830176062,0.0166394585715412,0.0242828268315213,0.0186499252821136,0.0172937552429501,0.012884316786562,0.0151580813449379,0.0152432529541291,0.00683520206571558,0.015848854285227,0.00548873505106271,0.0463546753407053,0.0374745601235242,0.0377843234298546,0.0496859224046918,0.0423020975120473,0.476494602790019,0.22124731008206,0.00133495638570388,-0.00651315491329772,0.0246426311368641,0.0467888915154519,0.0290676549903236,0.014157839785548,0.0373051928597928,0.0277092259874053,0.00704421300985849,0.0235113163426614,0.031874690590527,0.0238056232105272,0.0406286696553091,0.0116297069260057,0.01528918808899,0.0278819146911881,-0.012739078271517,0.0143308891754514,-0.0170491207754562,0.0120042732807632,0.0167653769381048,0.0159638474077621,0.0190193240276169,0.0214724119320786,0.027816771874068,0.0137986760733386,0.0170659565291834,-0.00773213247686777,-0.00402842465352413,0.00624765509504583,-0.01475726000717,-0.00948381225309883,-0.00270460789474853,-0.0114094433031485,-0.0089817952320245,-0.00658310902774747,-0.000240191769213641,0.00403083964668486,0.00424085980827249,0.0181964124655257,0.0148030092817289,0.00374239946117636,0.0642038838997109,0.0300377257034901,0.0307868502643864,0.053651017042188,0.0480460203822028,0.0345434704352919,0.0511163436525895,0.0728848654862736,0.0607813255718127,0.0678870561701061,0.0661845255427991,0.0629524787942859,0.0758272261195832,0.0577493026531502,-0.0170491207754562,0.00243387406753745,0.0211195619559602,-0.00351799517738173,0.347343597545356,0.400179608640284,-0.01164671417919,0.00865501696783527,0.0927242827056772,0.0420735960526134,0.0898681255962692,0.0234618788517366,0.0117652382652079,0.0101680830042626,0.057373492127132,0.0968490127496885,0.0705331978508159,0.663884301966064,0.0504780761951693,0.00849823645722,0.02301665953498,0.0534962216757768,-0.0170491207754562,0.00167639779612679,0.01435571709768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|gostat_on_MCL_coexpression=GO:0007527;adult somatic muscle development;0.0450262913742367;22288!GO:0007525;somatic muscle development;0.0450262913742367;22288!GO:0045176;apical protein localization;0.047395152381351;15165!GO:0008105;asymmetric protein localization;0.047395152381351;15165!GO:0030552;cAMP binding;0.047395152381351;15165!GO:0030054;cell junction;0.047395152381351;22288,108030!GO:0016010;dystrophin-associated glycoprotein complex;0.047395152381351;22288!GO:0031594;neuromuscular junction;0.047395152381351;22288!GO:0016208;AMP binding;0.047395152381351;15165!GO:0005624;membrane fraction;0.047395152381351;22288,108030!GO:0030551;cyclic nucleotide binding;0.0486781652053827;15165!GO:0000267;cell fraction;0.0486781652053827;22288,108030!
}}

Latest revision as of 14:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:106708946..106708957,+p5@Lin7a
Mm9::chr10:108127268..108127272,-p@chr10:108127268..108127272
-
Mm9::chr10:108156533..108156569,-p@chr10:108156533..108156569
-
Mm9::chr10:108233957..108233960,-p@chr10:108233957..108233960
-
Mm9::chr10:12334395..12334415,-p@chr10:12334395..12334415
-
Mm9::chr11:71949239..71949277,-p2@Pitpnm3
Mm9::chr11:71949307..71949338,-p1@Pitpnm3
Mm9::chr11:81406616..81406620,-p@chr11:81406616..81406620
-
Mm9::chr11:81672225..81672230,-p@chr11:81672225..81672230
-
Mm9::chr11:81715436..81715440,-p@chr11:81715436..81715440
-
Mm9::chr12:68310507..68310511,-p@chr12:68310507..68310511
-
Mm9::chr12:90228593..90228596,+p@chr12:90228593..90228596
+
Mm9::chr13:118391246..118391289,+p1@Hcn1
Mm9::chr13:118391309..118391320,+p3@Hcn1
Mm9::chr13:118455291..118455321,+p@chr13:118455291..118455321
+
Mm9::chr13:118760390..118760404,+p@chr13:118760390..118760404
+
Mm9::chr13:83941333..83941334,+p@chr13:83941333..83941334
+
Mm9::chr15:30428335..30428338,+p@chr15:30428335..30428338
+
Mm9::chr16:67016500..67016503,-p@chr16:67016500..67016503
-
Mm9::chr16:67072872..67072875,-p@chr16:67072872..67072875
-
Mm9::chr16:67183079..67183083,-p@chr16:67183079..67183083
-
Mm9::chr16:67197782..67197787,-p@chr16:67197782..67197787
-
Mm9::chr16:67278513..67278517,-p@chr16:67278513..67278517
-
Mm9::chr16:67546202..67546209,-p@chr16:67546202..67546209
-
Mm9::chr16:67584380..67584385,-p@chr16:67584380..67584385
-
Mm9::chr16:67588908..67588910,-p@chr16:67588908..67588910
-
Mm9::chr16:96924395..96924401,-p@chr16:96924395..96924401
-
Mm9::chr1:81184077..81184080,+p@chr1:81184077..81184080
+
Mm9::chr2:32680478..32680482,-p@chr2:32680478..32680482
-
Mm9::chr2:77544119..77544130,-p@chr2:77544119..77544130
-
Mm9::chr5:14521703..14521719,+p@chr5:14521703..14521719
+
Mm9::chr6:9055073..9055074,+p@chr6:9055073..9055074
+
Mm9::chr7:64989729..64989734,+p@chr7:64989729..64989734
+
Mm9::chr7:72597794..72597797,-p@chr7:72597794..72597797
-
Mm9::chr7:99384678..99384683,+p@chr7:99384678..99384683
+


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:0007527adult somatic muscle development0.0450262913742367
GO:0007525somatic muscle development0.0450262913742367
GO:0045176apical protein localization0.047395152381351
GO:0008105asymmetric protein localization0.047395152381351
GO:0030552cAMP binding0.047395152381351
GO:0030054cell junction0.047395152381351
GO:0016010dystrophin-associated glycoprotein complex0.047395152381351
GO:0031594neuromuscular junction0.047395152381351
GO:0016208AMP binding0.047395152381351
GO:0005624membrane fraction0.047395152381351
GO:0030551cyclic nucleotide binding0.0486781652053827
GO:0000267cell fraction0.0486781652053827



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
neurectoderm3.13e-3364
neural plate3.13e-3364
presumptive neural plate3.13e-3364
ecto-epithelium3.97e-2873
pre-chordal neural plate8.38e-2649
regional part of nervous system2.37e-2554
neural tube2.53e-2552
neural rod2.53e-2552
future spinal cord2.53e-2552
neural keel2.53e-2552
ectoderm-derived structure5.16e-2395
ectoderm5.16e-2395
presumptive ectoderm5.16e-2395
brain5.87e-2247
future brain5.87e-2247
central nervous system2.72e-2173
regional part of brain7.38e-2146
nervous system2.65e-2075
structure with developmental contribution from neural crest1.05e-1892
anterior neural tube1.70e-1840
gray matter1.71e-1834
regional part of forebrain1.44e-1739
forebrain1.44e-1739
future forebrain1.44e-1739
brain grey matter3.97e-1529
regional part of telencephalon3.97e-1529
telencephalon3.97e-1529
occipital lobe1.45e-1210
visual cortex1.45e-1210
neocortex1.45e-1210
regional part of cerebral cortex2.92e-1117
cerebral cortex6.82e-1121
cerebral hemisphere6.82e-1121
pallium6.82e-1121
eye2.34e-089
camera-type eye2.34e-089
simple eye2.34e-089
immature eye2.34e-089
ocular region2.34e-089
visual system2.34e-089
face2.34e-089
optic cup2.34e-089
optic vesicle2.34e-089
eye primordium2.34e-089
posterior neural tube2.15e-0712
chordal neural plate2.15e-0712


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)
MA0003.10.0318092
MA0004.10.062848
MA0006.10.0155229
MA0007.10.0571705
MA0009.10.328429
MA0014.10.232858
MA0017.10.226589
MA0019.10.198145
MA0024.10.295217
MA0025.10.520387
MA0027.11.87879
MA0028.10.0173823
MA0029.10.764415
MA0030.10.283968
MA0031.10.258132
MA0038.10.814792
MA0040.10.338117
MA0041.10.614371
MA0042.10.576917
MA0043.10.405289
MA0046.10.93796
MA0048.10.0149481
MA0050.10.270889
MA0051.10.83636
MA0052.10.344399
MA0055.10.00313082
MA0056.10
MA0057.10.141547
MA0058.10.0315409
MA0059.10.0349015
MA0060.10.0297545
MA0061.10.121235
MA0063.10
MA0066.10.125212
MA0067.10.61835
MA0068.10.0799178
MA0069.10.344664
MA0070.10.337108
MA0071.10.0784611
MA0072.10.880371
MA0073.13.85152e-13
MA0074.10.346087
MA0076.10.0246789
MA0077.10.843174
MA0078.10.917137
MA0081.10.161577
MA0083.10.404641
MA0084.10.922325
MA0087.10.369857
MA0088.10.000714612
MA0089.10
MA0090.10.188011
MA0091.10.240385
MA0092.10.188341
MA0093.10.0189566
MA0095.10
MA0098.10
MA0100.10.677527
MA0101.10.147962
MA0103.10.0987072
MA0105.10.00885235
MA0106.10.159832
MA0107.10.233864
MA0108.20.213222
MA0109.10
MA0111.10.055305
MA0113.10.143312
MA0114.10.118523
MA0115.10.407576
MA0116.10.0718313
MA0117.10.381411
MA0119.10.0376401
MA0122.10.397452
MA0124.11.4001
MA0125.10.506387
MA0130.10
MA0131.10.195197
MA0132.10
MA0133.10
MA0135.10.435302
MA0136.10.372901
MA0139.10.0605993
MA0140.10.100709
MA0141.10.114542
MA0142.12.77484
MA0143.11.4545
MA0144.10.0433959
MA0145.10.0150165
MA0146.10.0118771
MA0147.10.0099166
MA0148.10.0693066
MA0149.14.98135
MA0062.20.00145284
MA0035.20.336844
MA0039.20.000112192
MA0138.20.19008
MA0002.20.143884
MA0137.20.0266693
MA0104.20.00425077
MA0047.20.40925
MA0112.20.037397
MA0065.20.0377528
MA0150.10.457668
MA0151.10
MA0152.10.409401
MA0153.10.449181
MA0154.10.0398509
MA0155.10.00160198
MA0156.10.104561
MA0157.10.640537
MA0158.10
MA0159.10.0552837
MA0160.10.52922
MA0161.10
MA0162.10.167385
MA0163.10.0026353
MA0164.10.373396
MA0080.20.0946724
MA0018.20.122026
MA0099.20.186055
MA0079.22.60004e-06
MA0102.20.972341
MA0258.10.0356434
MA0259.10.00860255
MA0442.10
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