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MCL coexpression mm9:185: Difference between revisions

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{{MCL_coexpression_mm9
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fiber part;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0030016;myofibril;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0043292;contractile fiber;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0030018;Z disc;0.000219674389835757;68828,14201,170947!GO:0031674;I band;0.000269104593422744;68828,14201,170947!GO:0015629;actin cytoskeleton;0.00160500281119455;17901,17879,14201,22004!GO:0044430;cytoskeletal part;0.0055326680755427;17901,68828,17879,14201,22004!GO:0007517;muscle development;0.0198485050763202;17260,17879,14201!GO:0007507;heart development;0.0198485050763202;17260,21676,14936!GO:0007275;multicellular organismal development;0.020504372274795;17879,14201,21676,14936,19091,17260,20660,14199!GO:0007010;cytoskeleton organization and biogenesis;0.0214133097494737;17901,68828,17879,14201!GO:0003983;UTP:glucose-1-phosphate uridylyltransferase activity;0.0214133097494737;216558!GO:0051748;UDP-sugar pyrophosphorylase activity;0.0214133097494737;216558!GO:0005856;cytoskeleton;0.0285012800517676;17901,68828,17879,14201,22004!GO:0016459;myosin complex;0.0285012800517676;17901,17879!GO:0048513;organ development;0.0289571979001108;17260,17879,14201,21676,14936,19091!GO:0003779;actin binding;0.0299638512855307;17879,14201,22004!GO:0004692;cGMP-dependent protein kinase activity;0.0299638512855307;19091!GO:0004373;glycogen (starch) synthase activity;0.0299638512855307;14936!GO:0003953;NAD+ nucleosidase activity;0.0398662947341668;11875!GO:0005515;protein binding;0.0398662947341668;68828,17879,14201,22004,21676,170947,14936,19091,17260,242083,208643!GO:0003012;muscle system process;0.0398662947341668;17879,22004!GO:0006936;muscle contraction;0.0398662947341668;17879,22004!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0460527909081036;19091!GO:0005862;muscle thin filament tropomyosin;0.0460527909081036;22004!GO:0032502;developmental process;0.0486883141716843;17879,14201,21676,14936,19091,17260,20660,14199!GO:0008092;cytoskeletal protein binding;0.0486883141716843;17879,14201,22004!GO:0048731;system 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|coexpression_dpi_cluster_scores_mean=0.0151458860311508,-0.0143980042507619,-0.0127316698802874,-0.0259652694836633,-0.0192429814203123,-0.0120792973007584,-0.0110933778322028,-0.00443192076059126,0.00660330491955441,0.00168841581625915,-0.00973931681892148,-0.00956058795781387,-0.00550601926419077,-0.00568927534096473,0.00914945209188595,0.00379431046177728,-0.00895765401474589,-0.00494582328399607,-0.00518734152029746,0.00102193553499469,0.0390358522545156,-0.00093736159075543,-0.00356209406137669,-0.0170550148081858,-0.0174223746135943,-0.00734235887258309,-0.0280905620527605,-0.0157118744242961,-0.0238930338129053,-0.0244751998239771,-0.0131681282781145,0.00925223253248428,0.00606495628617376,0.00862561781034452,-0.0151147334009583,-0.0245453185796854,-0.0157370147490627,-0.00295645463978544,-0.000839600463357571,-0.00287757804443722,-0.000321624215076295,-0.00045875524937085,0.00260991939095141,0.00512899866022159,0.00574903206300502,0.00906675921361798,0.0164229619132641,0.0103934195120438,0.0147168249161116,0.0153478671087726,0.0178102037192066,0.0193035598388556,-0.00574171765185547,-0.00270513162545667,-0.00235654825274309,0.0172139504545765,0.0121236605106606,0.018411428700261,-0.00722671973391691,-0.00523757490017768,0.00131688107899058,0.0170856144632957,0.0151752543689596,0.0160010086135833,0.0248274500497612,0.0261596573224407,0.0237018154582492,0.0191680717207844,-0.00622769016083106,-0.00699983042280258,-0.00253210270644285,0.00364190374412598,0.0035889247853827,-0.00828781626425683,-0.0108609434377358,-0.00899779387007481,0.00176674151531098,-0.00916350649855537,-0.00839633773929591,-0.00622916876355611,-0.00804952939029333,-0.0133205808047028,-0.0052286765636445,-0.00577486179815748,-0.00207143904601187,0.00902010922487267,0.0154429978336562,-0.0069197950121107,0.00593349112127216,0.00506451867194969,0.021297545290576,0.00655094014721239,0.00964710664583276,-0.0246195063116489,-0.0146963623325949,-0.0138778695592396,0.657235921765969,0.0240635021774051,0.0141043608933872,0.015243835278064,0.0211530893914271,0.0253022289051507,0.00575551518054721,0.00631639056793565,0.000305069435857939,-0.0035064058984752,-0.00802467835298335,0.169494489325346,0.0112640275332432,0.0225050821593339,0.0244405659141957,0.0238511766122055,0.0217601515018677,0.0110560019544038,0.0644080662359775,0.0289483671794382,0.0182632610343352,0.12998432506753,0.395097908661102,0.463018631666397,0.624379030557238,0.49884840033889,0.0176479719941648,-0.0085246584327422,-0.00764040670571143,-0.00557140853244548,-0.0098780261247782,-0.0148322940193207,-0.00868532553306776,0.00560449072657437,-0.00599333487841876,-0.0082386594852793,0.00391901950477603,0.00482292367203262,-0.000254918664058108,-0.00312985924743348,0.027070333518983,0.416294523397018,0.0303643530890508,0.319432233032862,0.0229302771015862,0.0331921591088221,0.0577131069417854,0.0810715181572728,0.0774844912133239,0.0864890899533162,0.0878827899127183,0.239236591925821,0.0135945032060143,0.0644680154621673,0.068632943836479,0.0968305569826419,0.0628095625674319,0.162265682582411,0.111069109932189,0.00638485197826416,-0.0173351142175044,-0.0145651629077008,-0.0151816712386588,0.0397886119625107,0.0345525777185536,0.0293750928923634,0.0419518358610164,0.0348935773944775,0.0377227520141503,0.0445124080645653,0.053672817676849,0.0543817132298967,0.0663355026976129,0.114749125936177,0.173335034996348,0.209884217654793,0.219484536628291,0.260262596918865,0.000512327921491898,-0.00765947690357474,-0.00902010241992287,-0.00559883260997544,0.0183541763308846,0.0119134862256367,0.0177605449134154,0.00857500946194951,0.0176281993684052,0.0129666828010949,0.0140735513163034,0.00567849043734853,0.00224596717139212,-0.000887126022729276,0.00204147293551566,0.0170608868526271,0.0161140086045338,0.0130511093008861,0.0148605253240832,0.0142750221633143,0.0051098626919138,0.0119934248478298,0.00918300859932866,0.0015889923710704,0.0120101480530729,0.00816846604319804,0.0169988646879983,0.0153514225335786,-0.00983784762775467,-0.000749693928807559,-0.000888397600281391,-0.00812824763028448,0.00687668963075015,0.0016644575515709,0.0119956645072372,0.0152791667206983,-0.00678572329712911,0.0210319426279049,0.0973463675268937,0.0523508901292837,0.0774605277424601,0.00233296677240402,0.123163841409745,-0.0145600259984212,0.0227536183547283,0.0231171976343899,0.00390186861974397,0.00843687540580945,0.000797168073404589,0.00494397682344332,0.0174364965142222,0.0260816496158642,0.0463680584690392,0.0379718255248559,0.0459567077900164,0.106487421083342,0.142308717616565,0.0215934519129955,0.00861803956420271,0.00876881571184706,0.0843065083297163,0.0563970392657224,0.0127066949835929,0.0163394288964854,0.0200742245984297,1.09701443146729,0.003205902546269,0.00902580422431869,0.00307884894533318,0.00609863105428924,0.010202022318174,0.0105487187967996,0.0166495841290237,0.0128166906353103,0.00908413688991595,0.00724621505342164,0.042761165587351,0.0340781437374549,0.0424452065867123,0.05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|gostat_on_MCL_coexpression=GO:0030017;sarcomere;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0044449;contractile fiber part;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0030016;myofibril;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0043292;contractile fiber;9.36064978987318e-07;68828,17879,14201,22004,170947!GO:0030018;Z disc;0.000219674389835757;68828,14201,170947!GO:0031674;I band;0.000269104593422744;68828,14201,170947!GO:0015629;actin cytoskeleton;0.00160500281119455;17901,17879,14201,22004!GO:0044430;cytoskeletal part;0.0055326680755427;17901,68828,17879,14201,22004!GO:0007517;muscle development;0.0198485050763202;17260,17879,14201!GO:0007507;heart development;0.0198485050763202;17260,21676,14936!GO:0007275;multicellular organismal development;0.020504372274795;17879,14201,21676,14936,19091,17260,20660,14199!GO:0007010;cytoskeleton organization and biogenesis;0.0214133097494737;17901,68828,17879,14201!GO:0003983;UTP:glucose-1-phosphate uridylyltransferase activity;0.0214133097494737;216558!GO:0051748;UDP-sugar pyrophosphorylase activity;0.0214133097494737;216558!GO:0005856;cytoskeleton;0.0285012800517676;17901,68828,17879,14201,22004!GO:0016459;myosin complex;0.0285012800517676;17901,17879!GO:0048513;organ development;0.0289571979001108;17260,17879,14201,21676,14936,19091!GO:0003779;actin binding;0.0299638512855307;17879,14201,22004!GO:0004692;cGMP-dependent protein kinase activity;0.0299638512855307;19091!GO:0004373;glycogen (starch) synthase activity;0.0299638512855307;14936!GO:0003953;NAD+ nucleosidase activity;0.0398662947341668;11875!GO:0005515;protein binding;0.0398662947341668;68828,17879,14201,22004,21676,170947,14936,19091,17260,242083,208643!GO:0003012;muscle system process;0.0398662947341668;17879,22004!GO:0006936;muscle contraction;0.0398662947341668;17879,22004!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0460527909081036;19091!GO:0005862;muscle thin filament tropomyosin;0.0460527909081036;22004!GO:0032502;developmental process;0.0486883141716843;17879,14201,21676,14936,19091,17260,20660,14199!GO:0008092;cytoskeletal protein binding;0.0486883141716843;17879,14201,22004!GO:0048731;system development;0.0493006131586607;17260,17879,14201,21676,14936,19091!
}}

Latest revision as of 14:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:122608843..122608894,-p@chr10:122608843..122608894
-
Mm9::chr10:20611321..20611361,-p@chr10:20611321..20611361
-
Mm9::chr10:36348041..36348054,+p@chr10:36348041..36348054
+
Mm9::chr11:21270681..21270692,-p5@Ugp2
Mm9::chr11:66926940..66926976,-p@chr11:66926940..66926976
-
Mm9::chr11:67013593..67013609,+p1@Myh1
Mm9::chr11:67029448..67029459,-p@chr11:67029448..67029459
-
Mm9::chr11:87975881..87975888,+p16@Cuedc1
Mm9::chr13:83518057..83518059,-p@chr13:83518057..83518059
-
Mm9::chr13:83643136..83643158,+p7@Mef2c
Mm9::chr14:31693672..31693685,+p@chr14:31693672..31693685
+
Mm9::chr15:24236671..24236673,-p@chr15:24236671..24236673
-
Mm9::chr15:76993404..76993415,-p@chr15:76993404..76993415
-
Mm9::chr16:20678283..20678329,+p11@Eif4g1
Mm9::chr16:57352884..57352895,+p11@Filip1l
Mm9::chr17:7342812..7342832,+p@chr17:7342812..7342832
+
Mm9::chr18:60751417..60751432,-p2@Myoz3
Mm9::chr19:30699939..30699952,-p@chr19:30699939..30699952
-
Mm9::chr19:43602850..43602863,+p@chr19:43602850..43602863
+
Mm9::chr1:12982731..12982747,-p@chr1:12982731..12982747
-
Mm9::chr1:185863421..185863436,+p@chr1:185863421..185863436
+
Mm9::chr1:66992035..66992057,-p8@Myl1
Mm9::chr1:94009904..94009911,-p@chr1:94009904..94009911
-
Mm9::chr2:181314020..181314044,+p1@ENSMUST00000126672
Mm9::chr2:181314061..181314072,+p2@ENSMUST00000126672
Mm9::chr2:69507955..69507970,+p3@Kbtbd10
Mm9::chr3:122820113..122820116,-p@chr3:122820113..122820116
-
Mm9::chr3:69352872..69352898,+p4@Ppm1l
Mm9::chr4:124377615..124377628,+p3@Fhl3
Mm9::chr4:124377944..124377972,+p1@Fhl3
Mm9::chr4:128964917..128964929,+p5@Sync
Mm9::chr4:133712837..133712847,-p5@Ccdc21
Mm9::chr4:137591803..137591812,+p@chr4:137591803..137591812
+
Mm9::chr4:148688115..148688131,-p@chr4:148688115..148688131
-
Mm9::chr4:43528040..43528062,-p@chr4:43528040..43528062
-
Mm9::chr4:43536708..43536719,-p10@Tpm2
Mm9::chr4:57262011..57262022,-p@chr4:57262011..57262022
-
Mm9::chr4:73596402..73596419,-p@chr4:73596402..73596419
-
Mm9::chr4:73596683..73596694,-p3@2310002L09Rik
Mm9::chr4:73596718..73596737,-p2@2310002L09Rik
Mm9::chr4:73596738..73596757,-p1@2310002L09Rik
Mm9::chr6:108888660..108888701,-p@chr6:108888660..108888701
-
Mm9::chr6:128247107..128247125,-p@chr6:128247107..128247125
-
Mm9::chr7:109248409..109248420,-p4@Art5
Mm9::chr7:119885584..119885594,+p8@Tead1
Mm9::chr7:52693378..52693403,+p@chr7:52693378..52693403
+
Mm9::chr7:52699829..52699843,+p@chr7:52699829..52699843
+
Mm9::chr7:83374655..83374680,+p1@Agbl1
Mm9::chr7:83374741..83374752,+p2@Agbl1
Mm9::chr9:41793716..41793730,-p@chr9:41793716..41793730
-
Mm9::chr9:65112980..65112994,+p1@Cilp
Mm9::chr9:72541001..72541016,+p@chr9:72541001..72541016
+
Mm9::chr9:77195696..77195713,-p3@2310046A06Rik
Mm9::chrX:54032726..54032742,+p10@Fhl1


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:0030017sarcomere9.36064978987318e-07
GO:0044449contractile fiber part9.36064978987318e-07
GO:0030016myofibril9.36064978987318e-07
GO:0043292contractile fiber9.36064978987318e-07
GO:0030018Z disc0.000219674389835757
GO:0031674I band0.000269104593422744
GO:0015629actin cytoskeleton0.00160500281119455
GO:0044430cytoskeletal part0.0055326680755427
GO:0007517muscle development0.0198485050763202
GO:0007507heart development0.0198485050763202
GO:0007275multicellular organismal development0.020504372274795
GO:0007010cytoskeleton organization and biogenesis0.0214133097494737
GO:0003983UTP:glucose-1-phosphate uridylyltransferase activity0.0214133097494737
GO:0051748UDP-sugar pyrophosphorylase activity0.0214133097494737
GO:0005856cytoskeleton0.0285012800517676
GO:0016459myosin complex0.0285012800517676
GO:0048513organ development0.0289571979001108
GO:0003779actin binding0.0299638512855307
GO:0004692cGMP-dependent protein kinase activity0.0299638512855307
GO:0004373glycogen (starch) synthase activity0.0299638512855307
GO:0003953NAD+ nucleosidase activity0.0398662947341668
GO:0005515protein binding0.0398662947341668
GO:0003012muscle system process0.0398662947341668
GO:0006936muscle contraction0.0398662947341668
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0460527909081036
GO:0005862muscle thin filament tropomyosin0.0460527909081036
GO:0032502developmental process0.0486883141716843
GO:0008092cytoskeletal protein binding0.0486883141716843
GO:0048731system development0.0493006131586607



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
hindlimb bud1.36e-085
stylopod1.36e-085
lower limb segment1.36e-085
multi-limb segment region1.36e-085
pelvic appendage1.36e-085
limb segment1.36e-085
paired limb/fin segment1.36e-085
pelvic appendage bud1.36e-085
subdivision of organism along appendicular axis1.36e-085
leg1.36e-085
hindlimb1.36e-085
hindlimb stylopod1.36e-085
posterior region of body1.36e-085
pelvic complex1.36e-085
hindlimb/pelvic fin field1.36e-085
surface structure5.75e-0822
femur4.06e-074
hindlimb long bone4.06e-074
upper leg bone4.06e-074
bone of hip region4.06e-074
skeleton of limb4.06e-074
pelvic appendage skeleton4.06e-074
subdivision of skeleton4.06e-074
endochondral bone4.06e-074
bone of free limb or fin4.06e-074
bone of appendage girdle complex4.06e-074
endochondral element4.06e-074
hindlimb mesenchyme4.06e-074
limb bone4.06e-074
bone of pelvic complex4.06e-074
long bone4.06e-074
hindlimb bone4.06e-074
limb long bone4.06e-074
leg bone4.06e-074
limb mesenchyme4.06e-074
limb skeleton subdivision4.06e-074
hindlimb bone pre-cartilage condensation4.06e-074
upper leg mesenchyme4.06e-074
hindlimb cartilage element4.06e-074
limb cartilage element4.06e-074
limb bone pre-cartilage condensation4.06e-074
cartilage element4.06e-074
hindlimb skeleton4.06e-074
appendicular skeletal system4.06e-074
appendicular skeleton4.06e-074
limb of embryo4.06e-074
skeleton4.06e-074
femur cartilage element4.06e-074
femur pre-cartilage condensation4.06e-074


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)
MA0003.10.214788
MA0004.10.0892328
MA0006.10.0155406
MA0007.10.393726
MA0009.10.591589
MA0014.10.00245467
MA0017.10.966104
MA0019.10.338619
MA0024.10.177895
MA0025.10.97048
MA0027.11.69203
MA0028.10.00294766
MA0029.10.495242
MA0030.10.973798
MA0031.10.454375
MA0038.10.212097
MA0040.10.212892
MA0041.10.130255
MA0042.10.42638
MA0043.10.269674
MA0046.10.228174
MA0048.10.752056
MA0050.10.116964
MA0051.10.0614839
MA0052.17.24352
MA0055.10.737197
MA0056.10
MA0057.10.259941
MA0058.10.109899
MA0059.10.12223
MA0060.10.0425561
MA0061.10.136704
MA0063.10
MA0066.10.200976
MA0067.10.460607
MA0068.10.0378703
MA0069.10.218327
MA0070.10.212057
MA0071.10.279746
MA0072.10.206634
MA0073.10.00144677
MA0074.10.0433514
MA0076.10.00500926
MA0077.10.563199
MA0078.10.0738871
MA0081.10.298309
MA0083.10.741495
MA0084.10.748608
MA0087.10.239452
MA0088.10.107606
MA0089.10
MA0090.10.587501
MA0091.11.48871
MA0092.10.352487
MA0093.10.0637286
MA0095.10
MA0098.10
MA0100.10.358539
MA0101.10.467
MA0103.10.172623
MA0105.10.0247853
MA0106.10.56216
MA0107.10.163369
MA0108.21.21592
MA0109.10
MA0111.10.382441
MA0113.10.868376
MA0114.10.23639
MA0115.10.747285
MA0116.10.579712
MA0117.10.249244
MA0119.11.0239
MA0122.10.262941
MA0124.11.07093
MA0125.10.358609
MA0130.10
MA0131.10.101573
MA0132.10
MA0133.10
MA0135.10.295692
MA0136.10.0494027
MA0139.10.451321
MA0140.10.156085
MA0141.11.88088
MA0142.10.855712
MA0143.11.37584
MA0144.10.387694
MA0145.10.133951
MA0146.10.156724
MA0147.10.00866184
MA0148.10.24705
MA0149.10.137617
MA0062.26.56523e-05
MA0035.20.0413363
MA0039.20.00685052
MA0138.20.0979225
MA0002.20.0603574
MA0137.20.356944
MA0104.20.00279736
MA0047.20.211312
MA0112.21.65053
MA0065.21.00048
MA0150.10.648329
MA0151.10
MA0152.10.211422
MA0153.10.307841
MA0154.10.42399
MA0155.10.120663
MA0156.10.00494869
MA0157.10.782378
MA0158.10
MA0159.10.303519
MA0160.11.52286
MA0161.10
MA0162.17.30206e-05
MA0163.10.138485
MA0164.10.730123
MA0080.20.0238613
MA0018.20.195087
MA0099.20.650672
MA0079.23.19157e-07
MA0102.20.796982
MA0258.10.690998
MA0259.10.0682504
MA0442.10
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