Network analysis for the identification of differentially expressed hub genes using myogenin knock-down muscle satellite cells

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Malik, Adeel ^a,b   Lee, Eun Ju ^a   Jan, Arif Tasleem ^a   Ahmad, Sarafraz ^a   Cho, Kyung Hyun ^a   Kim, Jihoe ^a   Choi, Inho ^a  

^a Yeungnam University   (South Korea)

^b PERDANA UNIVERSITY   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA CATENIN; BETA CATENIN; MESSENGER RNA; MYOGENIN; MYOSTATIN; PHOSPHATE; MYOG PROTEIN, HUMAN;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BOVINE; CELL CYCLE; CELL DIFFERENTIATION; CELL DIVISION; CELL INTERACTION; CONTROLLED STUDY; CTNNA2 GENE; DEG GENE; DNA REPLICATION; DOWN REGULATION; ECM GENE; ENZYME METABOLISM; EXTRACELLULAR MATRIX; GENE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENE SILENCING; HUB GENE; IN VITRO STUDY; MOLECULAR BIOLOGY; MOUSE; MSTN GENE; MUSCLE DEVELOPMENT; MYOBLAST; MYOTUBE; NONHUMAN; PROTEIN EXPRESSION; RNA SEQUENCE; SKELETAL MUSCLE SATELLITE CELL; UPREGULATION; ANIMAL; CELL LINE; CYTOLOGY; GENETICS; HUMAN; METABOLISM;

ANIMALS; CATTLE; CELL LINE; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; GENE REGULATORY NETWORKS; HUMANS; MYOGENIN; SATELLITE CELLS, SKELETAL MUSCLE;

EID: 84941363958     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0133597     Document Type: Article

References (56)

1. Meadows E, Cho JH, Flynn JM, Klein WH (2008) Myogenin regulates a distinct genetic program in adult muscle stem cells. Dev Biol 322: 406-14. doi:10.1016/j.ydbio.2008.07.024 PMID: 18721801.
2. Olson EN, Brennan TJ, Chakraborty T, Cheng TC, Cserjesi P, Edmondson D, et al. (1991) Molecular control of myogenesis: Antagonism between growth and differentiation. Mol Cell Biochem 104: 7-13. PMID: 1922004.
3. Mohun T. Muscle differentiation. Curr Opin Cell Biol 4: 923-928. PMID: 1485959.
4. Andrés V, Walsh K (1996) Myogenin expression, cell cycle withdrawal, and phenotypic differentiation are temporally separable events that precede cell fusion upon myogenesis. J Cell Biol 132: 657-66. PMID: 8647896.
5. Moran JL, Li Y, Hill AA, Mounts WM, Miller CP (2002) Gene expression changes during mouse skeletal myoblast differentiation revealed by transcriptional profiling. Physiol Genomics 10: 103-11. PMID: 12181367.
6. Janot M, Audfray A, Loriol C, Germot A, Maftah A, Dupuy F (2009) Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates. BMC Genomics 10: 483. doi:10.1186/1471-2164-10-483 PMID: 19843320.
7. Rajan S, Chu Pham Dang H, Djambazian H, Zuzan H, Ketela T, et al. (2012) Analysis of early C2C12 myogenesis identifies stably and differentially expressed transcriptional regulators whose knock-down inhibits myoblast differentiation. Physiol Genomics 2: 183-197. doi:10.1152/physiolgenomics.00093.2011PMID: 22147266.
8. Rudnicki MA, Schnegelsberg PNJ, Stead RH, Braun T, Arnold HH, Jaenisch R (1993) MyoD or Myf-5 is required for the formation of skeletal muscle. Cell 75: 1351-1359. PMID: 8269513.
9. Rawls A, Morris JH, Rudnicki M, Braun T, Arnold HH, Klein WH, et al. (1995) Myogenin's functions do not overlap with those of MyoD or Myf-5 during mouse embryogenesis. Dev Biol 172: 37-50. PMID: 7589813.
10. Cao Y, Kumar RM, Penn BH, Berkes CA, Kooperberg C, Boyer LA, et al. (2006) Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. EMBO J 25: 502- 511. PMID: 16437161.
11. Wang Y, Jaenisch R (1997) Myogenin can substitute for Myf5 in promoting myogenesis but less efficiently. Development 124: 2507-2513. PMID: 9216993.
12. Rajan S, Chu Pham Dang H, Djambazian H, Zuzan H, Fedyshyn Y, Ketela T, et al. (2012) Analysis of early C2C12 myogenesis identifies stably and differentially expressed transcriptional regulators whose knock-down inhibits myoblast differentiation. Physiol Genomics 2: 183-197. doi:10.1152/physiolgenomics.00093.2011 PMID: 22147266.
13. Kablar B, Asakura A, Krastel K, Ying C, May LL, Goldhamer DJ, et al. (1998) MyoD and Myf-5 define the specification of musculature of distinct embryonic origin. Biochem Cell Biol 76: 1079-1091. PMID: 10392718.
14. Kassar-Duchossoy L, Gayraud-Morel B, Gomès D, Rocancourt D, Buckingham M, Shinin V, et al. (2004) Mrf4 determines skeletal muscle identity in Myf5:Myod double-mutant mice. Nature 431: 466- 471. PMID: 15386014.
15. Bischoff R. (1994) The satellite cell and muscle regeneration. Engel A. (Ed.), Myology, Mc-Graw Hill, New York 1: 97-118.
16. Charge SB, Rudnicki MA (2004) Cellular and molecular regulation of muscle regeneration. Physiol Rev 84: 209-238. PMID: 14715915.
17. Cossu G, Molinaro M (1987) Cell heterogeneity in the myogenic lineage. Curr Top Dev Biol 23: 185- 208. PMID: 3330504.
18. Gibson MC, Schultz E (1983) Age-related differences in absolute numbers of skeletal muscle satellite cells. Muscle Nerve 6: 574-580. PMID: 6646160.
19. Schultz E, Jaryszak DL, Valliere CR (1985) Response of satellite cells to focal skeletal muscle injury. Muscle Nerve 8: 217-222. PMID: 4058466.
20. Lee EJ, Lee HJ, Kamli MR, Pokharel S, Bhat AR, Lee YH, et al. (2012) Depot-specific gene expression profiles during differentiation and transdifferentiation of bovine muscle satellite cells, and differentiation of preadipocytes. Genomics 100: 195-202. doi:10.1016/j.ygeno.2012.06.005 PMID: 22728265.
21. Lee EJ, Kamli MR, Pokharel S, Malik A, Tareq KM, Roof BA, et al. (2013) Expressed sequence tags for bovine muscle satellite cells, myotube formed-cells and adipocyte-like cells. PLOS ONE 8: e79780. doi:10.1371/journal.pone.0079780 PMID: 24224006.
22. Lee EJ, Bhat AR, Kaml MR, Pokharel S, Chun T, Lee YH, et al. (2013) Transthyretin is a key regulator of myoblast differentiation. PLOS ONE 8: e63627. doi:10.1371/journal.pone.0063627 PMID: 23717457.
23. Lee EJ, Malik A, Pokharel S, Ahmad S, Mir BA, Cho KH, et al. (2014) Identification of genes differentially expressed in myogenin knock-down bovine muscle satellite cells during differentiation through RNA sequencing analysis. PLOS ONE 9: e92447. doi:10.1371/journal.pone.0092447 PMID: 24647404.
24. Sterrenburg E, Turk R, Hoen PA, van Deutekom JC, Boer JM, van Ommen GJ, et al. (2004) Largescale gene expression analysis of human skeletal myoblast differentiation. Neuromuscul Disord 14: 507-518. PMID: 15336692.
25. Shen X, Collier JM, Hlaing M, Zhang L, Delshad EH, Bristow J, et al. (2003) Genome-wide examination of myoblast cell cycle withdrawal during differentiation. Dev Dyn 1: 128-138. PMID: 12508234.
26. Tomczak KK, Marinescu VD, Ramoni MF, Sanoudou D, Montanaro F, Han M, et al. (2004) Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J 18: 403-405. PMID: 14688207.
27. Liu QC, Zha XH, Faralli H, Yin H, Louis-Jeune C, Perdiguero E, et al. (2012) Comparative expression profiling identifies differential roles for Myogenin and p38α MAPK signaling in myogenesis. J Mol Cell Biol 4: 386-397. doi:10.1093/jmcb/mjs045PMID: 22847234.
28. Wicik Z, Sadkowski T, Jank M, Motyl T (2011) The transcriptomic signature of myostatin inhibitory influence on the differentiation of mouse C2C12 myoblasts. Pol J Vet Sci 4: 643-652. PMID: 22439337.
29. Langmead B, Trapnell C, Pop M, Salzberg SL (2010) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi:10.1186/gb-2009-10-3-r25 PMID: 19261174.
30. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38: W214-20. doi:10.1093/nar/gkq537PMID: 20576703.
31. Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118: 4947-4957. PMID: 16254242.
32. Wu XR, Zhu Y, Li Y (2005) Analyzing protein interaction networks via random graph model. Int. J. Inf. Technol 11: 125-132.
33. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2001) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432. doi:10.1093/bioinformatics/btq675 PMID: 21149340.
34. van Dongen S. Graph Clustering by Flow Simulation. Unpublished doctoral dissertation. Centre for Mathematics and Computer Science, University of Utrecht, The Netherlands. 2000a.
35. van Dongen S. MCL-an algorithm for clustering graphs. Available: http://micans.org/mcl/2000b.
36. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2. PMID: 12525261.
37. Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113. PMID: 14995526.
38. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, et al. (2011) clusterMaker: A multialgorithm clustering plugin for Cytoscape. BMC Bioinformatics 12: 436. doi:10.1186/1471-2105-12-436 PMID: 22070249.
39. Su G, Kuchinsky A, Morris JH, States DJ, Meng F (2010) GLay: community structure analysis of biological networks. Bioinformatics 26: 3135-3137. doi:10.1093/bioinformatics/btq596 PMID: 21123224.
40. Lee SH, Park BH, Sharma A, Dang CG, Lee SS Choi TJ et al. (2014) Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. Journal of Animal Science and Technology 56: 2. doi:10.1186/2055-0391-56-2.
41. Dinh P, Sotiriou C, Piccart MJ (2007) The evolution of treatment strategies: Aiming at the target. Breast 16: S10-6. PMID: 17764940.
42. Park C, Falls W, Finger JH, Longo-Guess CM, Ackerman SL (2002) Deletion in Catna2, encoding alpha N-catenin, causes cerebellar and hippocampal lamination defects and impaired startle modulation. Nat Genet 31: 279-84. PMID: 12089526.
43. Togashi H, Abe K, Mizoguchi A, Takaoka K, Chisaka O, Takeichi M (2002) Cadherin regulates dendritic spine morphogenesis. Neuron 35: 77-89. PMID: 12123610.
44. Abe T, Takagi N, Nakano M, Furuya M, Takeo S (2004) Altered Bad localization and interaction between Bad and Bcl-xL in the hippocampus after transient global ischemia. Brain Res 1009: 159-68. PMID: 15120593.
45. Kang JS, Mulieri PJ, Hu Y, Taliana L, Krauss RS (2002) BOC, an Ig superfamily member, associates with CDO to positively regulate myogenic differentiation. EMBO J 21: 114-24. PMID: 11782431.
46. Kang JS, Feinleib JL, Knox S, Ketteringham MA, Krauss RS (2003) Promyogenic members of the Ig and cadherin families associate to positively regulate differentiation. Proc Natl Acad Sci U S A. 100: 3989-94. PMID: 12634428.
47. Kang JS, Yi MJ, Zhang W, Feinleib JL, Cole F, Krauss RS (2004) Netrins and neogenin promote myotube formation. J Cell Biol 167: 493-504. PMID: 15520228.
48. Reactome pathway: http://www.reactome.org/PathwayBrowser/#REACT-21402.
49. Andrés V, Walsh K (1996) Myogenin expression, cell cycle withdrawal, and phenotypic differentiation are temporally separable events that precede cell fusion upon myogenesis. J Cell Biol 4: 657-66. PMID: 8647896.
50. Li Y, Xu Z, Li H, Xiong Y, Zuo B (2012) Differential transcriptional analysis between red and white skeletal muscle of Chinese Meishan pigs. Int J Biol Sci 6: 350-360. PMID: 20617128.
51. Monnier N, Ferreiro A, Marty I, Labarre-Vila A, Mezin P, Lunardi J (2003) A homozygous splicing mutation causing a depletion of skeletal muscle RYR1 is associated with multi-minicore disease congenital myopathy with ophthalmoplegia. Hum Mol Genet 12: 1171-8. PMID: 12719381.
52. Lee J, Lee J (2013) Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction. PLOS ONE 8:e60372. doi:10.1371/journal.pone.0060372.23577106 PMID: 23577106.
53. Malik A, Lee J, Lee J (2014) Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data. PLOS ONE 9:e95480. doi:10.1371/journal.pone.0095480PMID: 24755681.
54. Firoz A, Malik A, Singh SK, Jha V, Ali A (2014) Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data. Int J Genomics 837365. doi:10.1155/2014/837365.25121089.
55. Desaphy JF, De Luca A, Camerino DC (1998) Blockade by cAMP of native sodium channels of adult rat skeletal muscle fibers. Am J Physiol 275: C1465-72. PMID: 9843707.
56. Dinh P, Sotiriou C, Piccart MJ (2007) The evolution of treatment strategies: Aiming at the target. Breast. 16: S10-6. PMID: 17764940.