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MCL coexpression mm9:449: Difference between revisions

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{{MCL_coexpression_mm9
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polymerase II transcription factor activity, enhancer binding;1.30825649872795e-06;17927,17877,17928!GO:0007517;muscle development;2.24385378621871e-06;17930,17927,17877,17928!GO:0003702;RNA polymerase II transcription factor activity;3.14894467472946e-05;17927,17877,17928!GO:0007519;skeletal muscle development;4.64273339264029e-05;17927,17877,17928!GO:0014706;striated muscle development;7.90474854121923e-05;17927,17877,17928!GO:0048741;skeletal muscle fiber development;0.00221721181591798;17927,17928!GO:0048747;muscle fiber development;0.00221721181591798;17927,17928!GO:0048513;organ development;0.00221721181591798;17930,17927,17877,17928!GO:0048625;myoblast cell fate commitment;0.00369210929248125;17927!GO:0007518;myoblast cell fate determination;0.00369210929248125;17927!GO:0048731;system development;0.00369210929248125;17930,17927,17877,17928!GO:0048856;anatomical structure development;0.00617794943570449;17930,17927,17877,17928!GO:0003700;transcription factor activity;0.00822184566576725;17927,17877,17928!GO:0007275;multicellular organismal development;0.00822184566576725;17930,17927,17877,17928!GO:0016070;RNA metabolic process;0.00895309312046242;17927,17877,78651,17928!GO:0001952;regulation of cell-matrix adhesion;0.0157891795918016;17877!GO:0010467;gene expression;0.0157891795918016;17927,17877,78651,17928!GO:0003676;nucleic acid binding;0.0157891795918016;17927,17877,78651,17928!GO:0008307;structural constituent of muscle;0.0157891795918016;17930!GO:0032502;developmental process;0.0167022049410475;17930,17927,17877,17928!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0187434878481659;17927,17877,78651,17928!GO:0048704;embryonic skeletal morphogenesis;0.0187434878481659;17877!GO:0032982;myosin filament;0.0203009953927489;17930!GO:0005863;striated muscle thick filament;0.0203009953927489;17930!GO:0005859;muscle myosin complex;0.0209858061922863;17930!GO:0016460;myosin II complex;0.0222023357894868;17930!GO:0048706;embryonic skeletal development;0.0222023357894868;17877!GO:0048705;skeletal morphogenesis;0.0286850449302073;17877!GO:0001709;cell fate determination;0.0286850449302073;17927!GO:0048869;cellular developmental process;0.0286850449302073;17927,17877,17928!GO:0030154;cell differentiation;0.0286850449302073;17927,17877,17928!GO:0006402;mRNA catabolic process;0.0286850449302073;78651!GO:0006941;striated muscle contraction;0.0286850449302073;17930!GO:0006355;regulation of transcription, DNA-dependent;0.0286850449302073;17927,17877,17928!GO:0043229;intracellular organelle;0.0286850449302073;17930,17927,17877,78651,17928!GO:0006351;transcription, DNA-dependent;0.0286850449302073;17927,17877,17928!GO:0043226;organelle;0.0286850449302073;17930,17927,17877,78651,17928!GO:0032774;RNA biosynthetic process;0.0286850449302073;17927,17877,17928!GO:0006401;RNA catabolic process;0.0286850449302073;78651!GO:0003677;DNA binding;0.0286850449302073;17927,17877,17928!GO:0005634;nucleus;0.0286850449302073;17927,17877,78651,17928!GO:0001756;somitogenesis;0.0286850449302073;17877!GO:0032501;multicellular organismal process;0.0286850449302073;17930,17927,17877,17928!GO:0045449;regulation of transcription;0.0286850449302073;17927,17877,17928!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0288343685554405;17927,17877,17928!GO:0045445;myoblast differentiation;0.0288343685554405;17927!GO:0043283;biopolymer metabolic process;0.0288343685554405;17927,17877,78651,17928!GO:0006350;transcription;0.0288343685554405;17927,17877,17928!GO:0032991;macromolecular complex;0.0293743797132572;17930,17927,78651!GO:0010468;regulation of gene expression;0.0303893002783488;17927,17877,17928!GO:0035282;segmentation;0.0307669318902937;17877!GO:0030155;regulation of cell adhesion;0.0321065380895143;17877!GO:0031323;regulation of cellular metabolic process;0.0321065380895143;17927,17877,17928!GO:0019222;regulation of metabolic process;0.0348980828944188;17927,17877,17928!GO:0030198;extracellular matrix organization and biogenesis;0.0379645308585611;17877!GO:0016459;myosin complex;0.0379645308585611;17930!GO:0046982;protein heterodimerization activity;0.0392486596754975;78651!GO:0042692;muscle cell differentiation;0.0398010198410609;17927!GO:0007160;cell-matrix adhesion;0.0398010198410609;17877!GO:0030017;sarcomere;0.0409223218011252;17930!GO:0031589;cell-substrate adhesion;0.0409223218011252;17877!GO:0044449;contractile fiber part;0.0414550571125855;17930!GO:0030016;myofibril;0.0440876304488212;17930!GO:0044424;intracellular part;0.0440876304488212;17930,17927,17877,78651,17928!GO:0043292;contractile fiber;0.0440876304488212;17930!GO:0003012;muscle system process;0.0460741289802003;17930!GO:0006936;muscle contraction;0.0460741289802003;17930!GO:0005200;structural constituent of cytoskeleton;0.0481049369305937;17930!GO:0005622;intracellular;0.0490378524892453;17930,17927,17877,78651,17928!GO:0009952;anterior/posterior pattern 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|gostat_on_MCL_coexpression=GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;1.30825649872795e-06;17927,17877,17928!GO:0007517;muscle development;2.24385378621871e-06;17930,17927,17877,17928!GO:0003702;RNA polymerase II transcription factor activity;3.14894467472946e-05;17927,17877,17928!GO:0007519;skeletal muscle development;4.64273339264029e-05;17927,17877,17928!GO:0014706;striated muscle development;7.90474854121923e-05;17927,17877,17928!GO:0048741;skeletal muscle fiber development;0.00221721181591798;17927,17928!GO:0048747;muscle fiber development;0.00221721181591798;17927,17928!GO:0048513;organ development;0.00221721181591798;17930,17927,17877,17928!GO:0048625;myoblast cell fate commitment;0.00369210929248125;17927!GO:0007518;myoblast cell fate determination;0.00369210929248125;17927!GO:0048731;system development;0.00369210929248125;17930,17927,17877,17928!GO:0048856;anatomical structure development;0.00617794943570449;17930,17927,17877,17928!GO:0003700;transcription factor activity;0.00822184566576725;17927,17877,17928!GO:0007275;multicellular organismal development;0.00822184566576725;17930,17927,17877,17928!GO:0016070;RNA metabolic process;0.00895309312046242;17927,17877,78651,17928!GO:0001952;regulation of cell-matrix adhesion;0.0157891795918016;17877!GO:0010467;gene expression;0.0157891795918016;17927,17877,78651,17928!GO:0003676;nucleic acid binding;0.0157891795918016;17927,17877,78651,17928!GO:0008307;structural constituent of muscle;0.0157891795918016;17930!GO:0032502;developmental process;0.0167022049410475;17930,17927,17877,17928!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0187434878481659;17927,17877,78651,17928!GO:0048704;embryonic skeletal morphogenesis;0.0187434878481659;17877!GO:0032982;myosin filament;0.0203009953927489;17930!GO:0005863;striated muscle thick filament;0.0203009953927489;17930!GO:0005859;muscle myosin complex;0.0209858061922863;17930!GO:0016460;myosin II complex;0.0222023357894868;17930!GO:0048706;embryonic skeletal development;0.0222023357894868;17877!GO:0048705;skeletal morphogenesis;0.0286850449302073;17877!GO:0001709;cell fate determination;0.0286850449302073;17927!GO:0048869;cellular developmental process;0.0286850449302073;17927,17877,17928!GO:0030154;cell differentiation;0.0286850449302073;17927,17877,17928!GO:0006402;mRNA catabolic process;0.0286850449302073;78651!GO:0006941;striated muscle contraction;0.0286850449302073;17930!GO:0006355;regulation of transcription, DNA-dependent;0.0286850449302073;17927,17877,17928!GO:0043229;intracellular organelle;0.0286850449302073;17930,17927,17877,78651,17928!GO:0006351;transcription, DNA-dependent;0.0286850449302073;17927,17877,17928!GO:0043226;organelle;0.0286850449302073;17930,17927,17877,78651,17928!GO:0032774;RNA biosynthetic process;0.0286850449302073;17927,17877,17928!GO:0006401;RNA catabolic process;0.0286850449302073;78651!GO:0003677;DNA binding;0.0286850449302073;17927,17877,17928!GO:0005634;nucleus;0.0286850449302073;17927,17877,78651,17928!GO:0001756;somitogenesis;0.0286850449302073;17877!GO:0032501;multicellular organismal process;0.0286850449302073;17930,17927,17877,17928!GO:0045449;regulation of transcription;0.0286850449302073;17927,17877,17928!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0288343685554405;17927,17877,17928!GO:0045445;myoblast differentiation;0.0288343685554405;17927!GO:0043283;biopolymer metabolic process;0.0288343685554405;17927,17877,78651,17928!GO:0006350;transcription;0.0288343685554405;17927,17877,17928!GO:0032991;macromolecular complex;0.0293743797132572;17930,17927,78651!GO:0010468;regulation of gene expression;0.0303893002783488;17927,17877,17928!GO:0035282;segmentation;0.0307669318902937;17877!GO:0030155;regulation of cell adhesion;0.0321065380895143;17877!GO:0031323;regulation of cellular metabolic process;0.0321065380895143;17927,17877,17928!GO:0019222;regulation of metabolic process;0.0348980828944188;17927,17877,17928!GO:0030198;extracellular matrix organization and biogenesis;0.0379645308585611;17877!GO:0016459;myosin complex;0.0379645308585611;17930!GO:0046982;protein heterodimerization activity;0.0392486596754975;78651!GO:0042692;muscle cell differentiation;0.0398010198410609;17927!GO:0007160;cell-matrix adhesion;0.0398010198410609;17877!GO:0030017;sarcomere;0.0409223218011252;17930!GO:0031589;cell-substrate adhesion;0.0409223218011252;17877!GO:0044449;contractile fiber part;0.0414550571125855;17930!GO:0030016;myofibril;0.0440876304488212;17930!GO:0044424;intracellular part;0.0440876304488212;17930,17927,17877,78651,17928!GO:0043292;contractile fiber;0.0440876304488212;17930!GO:0003012;muscle system process;0.0460741289802003;17930!GO:0006936;muscle contraction;0.0460741289802003;17930!GO:0005200;structural constituent of cytoskeleton;0.0481049369305937;17930!GO:0005622;intracellular;0.0490378524892453;17930,17927,17877,78651,17928!GO:0009952;anterior/posterior pattern formation;0.0498838723759717;17877!
}}

Latest revision as of 15:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:106920848..106920852,-p@chr10:106920848..106920852
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Mm9::chr10:106923133..106923146,-p1@Myf5
Mm9::chr12:74140323..74140332,+p1@uc007nvz.1
Mm9::chr15:76993525..76993544,-p@chr15:76993525..76993544
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Mm9::chr15:76993546..76993607,-p@chr15:76993546..76993607
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Mm9::chr17:45738994..45739005,-p1@Gm7325
Mm9::chr17:45739019..45739035,-p3@Gm7325
Mm9::chr17:45739045..45739057,-p2@Gm7325
Mm9::chr1:136186574..136186592,+p1@Myog
Mm9::chr1:136186599..136186608,+p3@Myog
Mm9::chr2:26927548..26927562,-p4@Tmem8c
Mm9::chr2:26927603..26927613,-p5@Tmem8c
Mm9::chr7:53631818..53631829,+p2@Myod1
Mm9::chr7:53631837..53631850,+p1@Myod1
Mm9::chr8:15060282..15060301,+p6@Myom2
Mm9::chr8:81337088..81337099,-p5@Lsm6


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:0003705RNA polymerase II transcription factor activity, enhancer binding1.30825649872795e-06
GO:0007517muscle development2.24385378621871e-06
GO:0003702RNA polymerase II transcription factor activity3.14894467472946e-05
GO:0007519skeletal muscle development4.64273339264029e-05
GO:0014706striated muscle development7.90474854121923e-05
GO:0048741skeletal muscle fiber development0.00221721181591798
GO:0048747muscle fiber development0.00221721181591798
GO:0048513organ development0.00221721181591798
GO:0048625myoblast cell fate commitment0.00369210929248125
GO:0007518myoblast cell fate determination0.00369210929248125
GO:0048731system development0.00369210929248125
GO:0048856anatomical structure development0.00617794943570449
GO:0003700transcription factor activity0.00822184566576725
GO:0007275multicellular organismal development0.00822184566576725
GO:0016070RNA metabolic process0.00895309312046242
GO:0001952regulation of cell-matrix adhesion0.0157891795918016
GO:0010467gene expression0.0157891795918016
GO:0003676nucleic acid binding0.0157891795918016
GO:0008307structural constituent of muscle0.0157891795918016
GO:0032502developmental process0.0167022049410475
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0187434878481659
GO:0048704embryonic skeletal morphogenesis0.0187434878481659
GO:0032982myosin filament0.0203009953927489
GO:0005863striated muscle thick filament0.0203009953927489
GO:0005859muscle myosin complex0.0209858061922863
GO:0016460myosin II complex0.0222023357894868
GO:0048706embryonic skeletal development0.0222023357894868
GO:0048705skeletal morphogenesis0.0286850449302073
GO:0001709cell fate determination0.0286850449302073
GO:0048869cellular developmental process0.0286850449302073
GO:0030154cell differentiation0.0286850449302073
GO:0006402mRNA catabolic process0.0286850449302073
GO:0006941striated muscle contraction0.0286850449302073
GO:0006355regulation of transcription, DNA-dependent0.0286850449302073
GO:0043229intracellular organelle0.0286850449302073
GO:0006351transcription, DNA-dependent0.0286850449302073
GO:0043226organelle0.0286850449302073
GO:0032774RNA biosynthetic process0.0286850449302073
GO:0006401RNA catabolic process0.0286850449302073
GO:0003677DNA binding0.0286850449302073
GO:0005634nucleus0.0286850449302073
GO:0001756somitogenesis0.0286850449302073
GO:0032501multicellular organismal process0.0286850449302073
GO:0045449regulation of transcription0.0286850449302073
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0288343685554405
GO:0045445myoblast differentiation0.0288343685554405
GO:0043283biopolymer metabolic process0.0288343685554405
GO:0006350transcription0.0288343685554405
GO:0032991macromolecular complex0.0293743797132572
GO:0010468regulation of gene expression0.0303893002783488
GO:0035282segmentation0.0307669318902937
GO:0030155regulation of cell adhesion0.0321065380895143
GO:0031323regulation of cellular metabolic process0.0321065380895143
GO:0019222regulation of metabolic process0.0348980828944188
GO:0030198extracellular matrix organization and biogenesis0.0379645308585611
GO:0016459myosin complex0.0379645308585611
GO:0046982protein heterodimerization activity0.0392486596754975
GO:0042692muscle cell differentiation0.0398010198410609
GO:0007160cell-matrix adhesion0.0398010198410609
GO:0030017sarcomere0.0409223218011252
GO:0031589cell-substrate adhesion0.0409223218011252
GO:0044449contractile fiber part0.0414550571125855
GO:0030016myofibril0.0440876304488212
GO:0044424intracellular part0.0440876304488212
GO:0043292contractile fiber0.0440876304488212
GO:0003012muscle system process0.0460741289802003
GO:0006936muscle contraction0.0460741289802003
GO:0005200structural constituent of cytoskeleton0.0481049369305937
GO:0005622intracellular0.0490378524892453
GO:0009952anterior/posterior pattern formation0.0498838723759717



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
appendage3.27e-0912
paired limb/fin3.27e-0912
limb3.27e-0912
paired limb/fin bud3.27e-0912
limb bud3.27e-0912
limb/fin field3.27e-0912
limb field3.27e-0912
surface structure5.06e-0922
appendage girdle complex3.02e-0813
forelimb7.15e-077
pectoral appendage7.15e-077
pectoral appendage bud7.15e-077
forelimb bud7.15e-077
forelimb/pectoral fin field7.15e-077


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)
MA0003.10.0557359
MA0004.10.221835
MA0006.10.105852
MA0007.10.210531
MA0009.10.599391
MA0014.10.0783947
MA0017.10.122138
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.112137
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.166538
MA0042.10.15744
MA0043.10.689898
MA0046.11.53
MA0048.11.39913
MA0050.10.701661
MA0051.10.345658
MA0052.10.618515
MA0055.11.94636
MA0056.10
MA0057.10.381022
MA0058.10.152805
MA0059.10.942177
MA0060.10.223836
MA0061.13.23261
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.650068
MA0069.10.618831
MA0070.10.609808
MA0071.10.251158
MA0072.10.601934
MA0073.11.58649
MA0074.11.47068
MA0076.10.134359
MA0077.10.581866
MA0078.10.37382
MA0081.10.177433
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.251567
MA0089.10
MA0090.11.08371
MA0091.11.22165
MA0092.10.571528
MA0093.10.11723
MA0095.10
MA0098.10
MA0100.11.43649
MA0101.12.20176
MA0103.10.805091
MA0105.10.881005
MA0106.10.380511
MA0107.11.28321
MA0108.22.00858
MA0109.10
MA0111.10.595954
MA0113.10.356344
MA0114.10.0762439
MA0115.10.692537
MA0116.11.15654
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.315568
MA0139.10.0480655
MA0140.10.289637
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.0778672
MA0145.11.7928
MA0146.10.00479338
MA0147.10.286569
MA0148.10.23425
MA0149.10.171305
MA0062.20.0332891
MA0035.20.293466
MA0039.20.989198
MA0138.20.423003
MA0002.20.049318
MA0137.20.139909
MA0104.20.0556953
MA0047.20.337465
MA0112.20.277674
MA0065.20.479069
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.11.38057
MA0155.10.32315
MA0156.10.133796
MA0157.10.47062
MA0158.10
MA0159.10.626722
MA0160.10.666246
MA0161.10
MA0162.10.00698895
MA0163.10.961593
MA0164.10.315868
MA0080.20.125629
MA0018.20.323932
MA0099.20.417463
MA0079.20.298654
MA0102.21.29919
MA0258.10.24394
MA0259.10.0787033
MA0442.10
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