Mostyn A, Symonds ME. Early programming of adipose tissue function: a large-animal perspective: symposium on ‘Frontiers in adipose tissue biology’. Proc Nutr Soc. 2009;68(4):393–400. https://doi.org/10.1017/S002966510999022X.
Article
PubMed
Google Scholar
Sharkey D, Gardner DS, Fainberg HP, Sébert S, Bos P, Wilson V, et al. Maternal nutrient restriction during pregnancy differentially alters the unfolded protein response in adipose and renal tissue of obese juvenile offspring. FASEB J. 2009;23(5):1314–24. https://doi.org/10.1096/fj.08-114330.
Article
CAS
PubMed
Google Scholar
Moreno-Mendez E, Quintero-Fabian S, Fernandez-Mejia C, Lazo-de-la-Vega-Monroy ML. Early-life programming of adipose tissue. Nutr Res Rev. 2020;33:244–59.
Grundy SM. Adipose tissue and metabolic syndrome: too much, too little or neither. Eur J Clin Investig. 2015;45(11):1209–17. https://doi.org/10.1111/eci.12519.
Article
CAS
Google Scholar
Stenkula KG, Erlanson-Albertsson C. Adipose cell size: importance in health and disease. Am J Phys Regul Integr Comp Phys. 2018;315(2):R284–R95. https://doi.org/10.1152/ajpregu.00257.2017.
Article
CAS
Google Scholar
Tan CY, Vidal-Puig A. Adipose tissue expandability: the metabolic problems of obesity may arise from the inability to become more obese: Portland Press Limited; 2008.
Manolopoulos K, Karpe F, Frayn K. Gluteofemoral body fat as a determinant of metabolic health. Int J Obes. 2010;34(6):949–59. https://doi.org/10.1038/ijo.2009.286.
Article
CAS
Google Scholar
Moreno-Indias I, Tinahones FJ. Impaired adipose tissue expandability and lipogenic capacities as ones of the main causes of metabolic disorders. J Diab Res. 2015;2015:1–12. https://doi.org/10.1155/2015/970375.
Article
Google Scholar
Pellegrinelli V, Carobbio S, Vidal-Puig A. Adipose tissue plasticity: how fat depots respond differently to pathophysiological cues. Diabetologia. 2016;59(6):1075–88. https://doi.org/10.1007/s00125-016-3933-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Björntorp P. Body fat distribution, insulin resistance, and metabolic diseases. Nutrition. 1997;13(9):795–803. https://doi.org/10.1016/S0899-9007(97)00191-3.
Article
PubMed
Google Scholar
Samara A, Ventura E, Alfadda A, Goran M. Use of MRI and CT for fat imaging in children and youth: what have we learned about obesity, fat distribution and metabolic disease risk? Obes Rev. 2012;13(8):723–32. https://doi.org/10.1111/j.1467-789X.2012.00994.x.
Article
CAS
PubMed
Google Scholar
Shuster A, Patlas M, Pinthus J, Mourtzakis M. The clinical importance of visceral adiposity: a critical review of methods for visceral adipose tissue analysis. Br J Radiol. 2012;85(1009):1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fang L, Guo F, Zhou L, Stahl R, Grams J. The cell size and distribution of adipocytes from subcutaneous and visceral fat is associated with type 2 diabetes mellitus in humans. Adipocyte. 2015;4(4):273–9. https://doi.org/10.1080/21623945.2015.1034920.
Article
CAS
PubMed
PubMed Central
Google Scholar
Foster MC, Hwang S-J, Porter SA, Massaro JM, Hoffmann U, Fox CS. Fatty kidney, hypertension, and chronic kidney disease: the Framingham heart study. Hypertension. 2011;58(5):784–90. https://doi.org/10.1161/HYPERTENSIONAHA.111.175315.
Article
CAS
PubMed
Google Scholar
Ahmad S, Lyngman LK, Mansouryar M, Dhakal R, Agerholm JS, Khanal P, et al. Depot and sex-specific implications for adipose tissue expandability and functional traits in adulthood of late prenatal and early postnatal malnutrition in a precocial sheep model. Physiol Rep. 2020;8(19):e14600.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khanal P, Johnsen L, Axel AMD, Hansen PW, Kongsted AH, Lyckegaard NB, et al. Long-term impacts of foetal malnutrition followed by early postnatal obesity on fat distribution pattern and metabolic adaptability in adult sheep. PLoS One. 2016;11(6):e0156700.
Article
PubMed
PubMed Central
Google Scholar
Khanal P, Husted SV, Axel A-MD, Johnsen L, Pedersen KL, Mortensen MS, et al. Late gestation over-and undernutrition predispose for visceral adiposity in response to a post-natal obesogenic diet, but with differential impacts on glucose–insulin adaptations during fasting in lambs. Acta Physiol. 2014;210(1):110–26. https://doi.org/10.1111/apha.12129.
Article
CAS
Google Scholar
Clément K, Langin D. Regulation of inflammation-related genes in human adipose tissue. J Intern Med. 2007;262(4):422–30. https://doi.org/10.1111/j.1365-2796.2007.01851.x.
Article
CAS
PubMed
Google Scholar
Duffield JA, Vuocolo T, Tellam R, McFarlane JR, Kauter KG, Muhlhausler BS, et al. Intrauterine growth restriction and the sex specific programming of leptin and peroxisome proliferator-activated receptor γ (PPARγ) mRNA expression in visceral fat in the lamb. Pediatr Res. 2009;66(1):59–65. https://doi.org/10.1203/PDR.0b013e3181a7c121.
Article
CAS
PubMed
Google Scholar
Faulconnier Y, Chilliard Y, Torbati MM, Leroux C. The transcriptomic profiles of adipose tissues are modified by feed deprivation in lactating goats. Comp Biochem Physiol Part D Genomics Proteomics. 2011;6(2):139–49.
Article
CAS
PubMed
Google Scholar
Peñagaricano F, Wang X, Rosa GJ, Radunz AE, Khatib H. Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep. BMC Genomics. 2014;15(1):1034. https://doi.org/10.1186/1471-2164-15-1034.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grant RW, Vester Boler BM, Ridge TK, Graves TK, Swanson KS. Adipose tissue transcriptome changes during obesity development in female dogs. Physiol Genomics. 2011;43(6):295–307. https://doi.org/10.1152/physiolgenomics.00190.2010.
Article
CAS
PubMed
Google Scholar
Khanal P, Pandey D, Binti Ahmad S, Safayi S, Kadarmideen HN, Olaf NM. Differential impacts of late gestational over–and undernutrition on adipose tissue traits and associated visceral obesity risk upon exposure to a postnatal high-fat diet in adolescent sheep. Physiol Rep. 2020;8(3):e14359. https://doi.org/10.14814/phy2.14359.
Article
PubMed
PubMed Central
Google Scholar
Fuente-Martín E, Argente-Arizón P, Ros P, Argente J, Chowen JA. Sex differences in adipose tissue: it is not only a question of quantity and distribution. Adipocyte. 2013;2(3):128–34. https://doi.org/10.4161/adip.24075.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bloor ID, Sébert SP, Saroha V, Gardner DS, Keisler DH, Budge H, et al. Sex differences in metabolic and adipose tissue responses to juvenile-onset obesity in sheep. Endocrinology. 2013;154(10):3622–31. https://doi.org/10.1210/en.2013-1207.
Article
CAS
PubMed
Google Scholar
Khanal P, AM DA, Safayi S, Elbrønd VS, Nielsen MO. Prenatal over-and undernutrition differentially program small intestinal growth, angiogenesis, absorptive capacity, and endocrine function in sheep. Physiol Rep. 2020;8(12):e14498.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karastergiou K, Smith SR, Greenberg AS, Fried SK. Sex differences in human adipose tissues–the biology of pear shape. Biol Sex Differ. 2012;3(1):13. https://doi.org/10.1186/2042-6410-3-13.
Article
PubMed
PubMed Central
Google Scholar
Medrikova D, Jilkova Z, Bardova K, Janovska P, Rossmeisl M, Kopecky J. Sex differences during the course of diet-induced obesity in mice: adipose tissue expandability and glycemic control. Int J Obes. 2012;36(2):262–72. https://doi.org/10.1038/ijo.2011.87.
Article
CAS
Google Scholar
Gealekman O, Guseva N, Hartigan C, Apotheker S, Gorgoglione M, Gurav K, et al. Depot-specific differences and insufficient subcutaneous adipose tissue angiogenesis in human obesity. Circulation. 2011;123(2):186–94. https://doi.org/10.1161/CIRCULATIONAHA.110.970145.
Article
PubMed
PubMed Central
Google Scholar
Porter SA, Massaro JM, Hoffmann U, Vasan RS, O'Donnel CJ, Fox CS. Abdominal subcutaneous adipose tissue: a protective fat depot? Diabetes Care. 2009;32(6):1068–75. https://doi.org/10.2337/dc08-2280.
Article
PubMed
PubMed Central
Google Scholar
Tchkonia T, Thomou T, Zhu Y, Karagiannides I, Pothoulakis C, Jensen MD, et al. Mechanisms and metabolic implications of regional differences among fat depots. Cell Metab. 2013;17(5):644–56. https://doi.org/10.1016/j.cmet.2013.03.008.
Article
CAS
PubMed
PubMed Central
Google Scholar
O'Connell J, Lynch L, Cawood TJ, Kwasnik A, Nolan N, Geoghegan J, et al. The relationship of omental and subcutaneous adipocyte size to metabolic disease in severe obesity. PloS One. 2010;5(4):e9997.
Article
PubMed
PubMed Central
Google Scholar
Cuthbertson DJ, Steele T, Wilding JP, Halford J, Harrold JA, Hamer M, et al. What have human experimental overfeeding studies taught us about adipose tissue expansion and susceptibility to obesity and metabolic complications? Int J Obes. 2017;41(6):853–65. https://doi.org/10.1038/ijo.2017.4.
Article
CAS
Google Scholar
Sniderman AD, Bhopal R, Prabhakaran D, Sarrafzadegan N, Tchernof A. Why might south Asians be so susceptible to central obesity and its atherogenic consequences? The adipose tissue overflow hypothesis. Int J Epidemiol. 2007;36(1):220–5. https://doi.org/10.1093/ije/dyl245.
Article
PubMed
Google Scholar
Sarr O, Gondret F, Jamin A, Le Huërou-Luron I, Louveau I. A high-protein neonatal formula induces a temporary reduction of adiposity and changes later adipocyte physiology. Am J Phys Regul Integr Comp Phys. 2011;300(2):R387–R97. https://doi.org/10.1152/ajpregu.00459.2010.
Article
CAS
Google Scholar
Gondret F, Vincent A, Houée-Bigot M, Siegel A, Lagarrigue S, Louveau I, et al. Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location. BMC Genomics. 2016;17(1):120. https://doi.org/10.1186/s12864-016-2438-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gemmell R, Alexander G. Ultrastructural development of adipose tissue in foetal sheep. Aust J Biol Sci. 1978;31(5):505–16. https://doi.org/10.1071/BI9780505.
Article
CAS
PubMed
Google Scholar
Symonds ME, Pearce S, Bispham J, Gardner DS, Stephenson T. Timing of nutrient restriction and programming of fetal adipose tissue development. Proc Nutr Soc. 2004;63(3):397–403. https://doi.org/10.1079/PNS2004366.
Article
PubMed
Google Scholar
Symonds ME, Mostyn A, Pearce S, Budge H, Stephenson T. Endocrine and nutritional regulation of fetal adipose tissue development. J Endocrinol. 2003;179(3):293–9. https://doi.org/10.1677/joe.0.1790293.
Article
CAS
PubMed
Google Scholar
Bonnet M, Cassar-Malek I, Chilliard Y, Picard B. Ontogenesis of muscle and adipose tissues and their interactions in ruminants and other species. Animal. 2010;4(7):1093–109. https://doi.org/10.1017/S1751731110000601.
Article
CAS
PubMed
Google Scholar
Zheng M, Kim D-Y, Sung J-H. Ion channels and transporters in adipose-derived stem cells. J f Pharm Invest. 2019;49(3):287–94. https://doi.org/10.1007/s40005-018-00413-z.
Article
Google Scholar
Björklund M. Cell size homeostasis: metabolic control of growth and cell division. Biochimica et Biophysica Acta (BBA)-molecular. Cell Res. 2019;1866(3):409–17.
Google Scholar
Gadde S, Heald R. Mechanisms and molecules of the mitotic spindle. Curr Biol. 2004;14(18):R797–805. https://doi.org/10.1016/j.cub.2004.09.021.
Article
CAS
PubMed
Google Scholar
Vasconcelos LH, Souza IL, Pinheiro LS, Silva BA. Ion channels in obesity: pathophysiology and potential therapeutic targets. Front Pharmacol. 2016;7:58.
Article
PubMed
PubMed Central
Google Scholar
Kaverina I, Straube A. Regulation of cell migration by dynamic microtubules. Seminars in Cell & Developmental Biology: Elsevier; 2011.
Matis M. The mechanical role of microtubules in tissue remodeling. BioEssays. 2020;42(5):1900244. https://doi.org/10.1002/bies.201900244.
Article
Google Scholar
Gerriets VA, MacIver NJ. Role of T cells in malnutrition and obesity. Front Immunol. 2014;5:379.
Article
PubMed
PubMed Central
Google Scholar
Kim J, Choi A, Kwon YH. Maternal protein restriction altered insulin resistance and inflammation-associated gene expression in adipose tissue of young adult mouse offspring in response to a high-fat diet. Nutrients. 2020;12(4):1103. https://doi.org/10.3390/nu12041103.
Article
CAS
PubMed Central
Google Scholar
Aguilar D, Fernandez ML. Hypercholesterolemia induces adipose dysfunction in conditions of obesity and nonobesity. Adv Nutr. 2014;5(5):497–502. https://doi.org/10.3945/an.114.005934.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krause BR, Hartman AD. Adipose tissue and cholesterol metabolism. J Lipid Res. 1984;25(2):97–110. https://doi.org/10.1016/S0022-2275(20)37830-5.
Article
CAS
PubMed
Google Scholar
Zhang T, Chen J, Tang X, Luo Q, Xu D, Yu B. Interaction between adipocytes and high-density lipoprotein: new insights into the mechanism of obesity-induced dyslipidemia and atherosclerosis. Lipids Health Dis. 2019;18(1):223. https://doi.org/10.1186/s12944-019-1170-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huh JY, Park YJ, Ham M, Kim JB. Crosstalk between adipocytes and immune cells in adipose tissue inflammation and metabolic dysregulation in obesity. Mol Cells. 2014;37(5):365–71. https://doi.org/10.14348/molcells.2014.0074.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu J, Zhao J, Meng H, Zhang X. Adipose tissue-resident immune cells in obesity and type 2 diabetes. Front Immunol. 2019;10:1173. https://doi.org/10.3389/fimmu.2019.01173.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Wu H. T cells in adipose tissue: critical players in Immunometabolism. Front Immunol. 2018;9:2509. https://doi.org/10.3389/fimmu.2018.02509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ozanne SE, Hales CN. The long-term consequences of intra-uterine protein malnutrition for glucose metabolism. Proc Nutr Soc. 1999;58(3):615–9. https://doi.org/10.1017/S0029665199000804.
Article
CAS
PubMed
Google Scholar
Ozanne S, Smith G, Tikerpae J, Hales C. Altered regulation of hepatic glucose output in the male offspring of protein-malnourished rat dams. Am J Physiol Endocrinol Metab. 1996;270(4):E559–E64. https://doi.org/10.1152/ajpendo.1996.270.4.E559.
Article
CAS
Google Scholar
Souza-Mello V, Mandarim-de-Lacerda CA, Aguila MB. Hepatic structural alteration in adult programmed offspring (severe maternal protein restriction) is aggravated by post-weaning high-fat diet. Br J Nutr. 2007;98(6):1159–69. https://doi.org/10.1017/S0007114507771878.
Article
CAS
PubMed
Google Scholar
Cordeiro AC, Qureshi AR, Lindholm B, Amparo FC, Tito-Paladino-Filho A, Perini M, et al. Visceral fat and coronary artery calcification in patients with chronic kidney disease. Nephrol Dial Transplant. 2013;28(suppl_4):iv152–iv9.
CAS
PubMed
Google Scholar
Declèves A-E, Sharma K. Obesity and kidney disease: differential effects of obesity on adipose tissue and kidney inflammation and fibrosis. Curr Opin Nephrol Hypertens. 2015;24(1):28–36. https://doi.org/10.1097/MNH.0000000000000087.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yun C-H, Lin T-Y, Wu Y-J, Liu C-C, Kuo J-Y, Yeh H-I, et al. Pericardial and thoracic peri-aortic adipose tissues contribute to systemic inflammation and calcified coronary atherosclerosis independent of body fat composition, anthropometric measures and traditional cardiovascular risks. Eur J Radiol. 2012;81(4):749–56. https://doi.org/10.1016/j.ejrad.2011.01.035.
Article
PubMed
Google Scholar
Hall JE, do Carmo JM, da Silva AA, Wang Z, Hall ME. Obesity-induced hypertension: interaction of neurohumoral and renal mechanisms. Circ Res. 2015;116(6):991–1006. https://doi.org/10.1161/CIRCRESAHA.116.305697.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu B-X, Sun W, Kong X-Q. Perirenal fat: a unique fat pad and potential target for cardiovascular disease. Angiology. 2019;70(7):584–93. https://doi.org/10.1177/0003319718799967.
Article
PubMed
Google Scholar
Khanal P, Axel AMD, Kongsted AH, Husted SV, Johnsen L, Pandey D, et al. Late gestation under-and overnutrition have differential impacts when combined with a post-natal obesogenic diet on glucose–lactate–insulin adaptations during metabolic challenges in adolescent sheep. Acta Physiol. 2015;213(2):519–36. https://doi.org/10.1111/apha.12391.
Article
CAS
Google Scholar
He X, Zhang J. Why do hubs tend to be essential in protein networks? PLoS Genet. 2006;2(6):e88. https://doi.org/10.1371/journal.pgen.0020088.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kogelman LJ, Cirera S, Zhernakova DV, Fredholm M, Franke L, Kadarmideen HN. Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA sequencing in a porcine model. BMC Med Genet. 2014;7(1):57. https://doi.org/10.1186/1755-8794-7-57.
Article
CAS
Google Scholar
Awaya T, Yokosaki Y, Yamane K, Usui H, Kohno N, Eboshida A. Gene-environment association of an ITGB2 sequence variant with obesity in ethnic Japanese. Obesity. 2008;16(6):1463–6. https://doi.org/10.1038/oby.2008.68.
Article
CAS
PubMed
Google Scholar
Xu X, Grijalva A, Skowronski A, van Eijk M, Serlie MJ, Ferrante AW Jr. Obesity activates a program of lysosomal-dependent lipid metabolism in adipose tissue macrophages independently of classic activation. Cell Metab. 2013;18(6):816–30. https://doi.org/10.1016/j.cmet.2013.11.001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cook NT. Bioinformatic analysis of adipose tissue Transcriptome of broiler chickens: Tennessee State University; 2016.
Google Scholar
Ritter A, Louwen F, Yuan J. Deficient primary cilia in obese adipose-derived mesenchymal stem cells: obesity, a secondary ciliopathy? Obes Rev. 2018;19(10):1317–28. https://doi.org/10.1111/obr.12716.
Article
CAS
PubMed
Google Scholar
Ritter A, Friemel A, Kreis N-N, Hoock SC, Roth S, Kielland-Kaisen U, et al. Primary cilia are dysfunctional in obese adipose-derived mesenchymal stem cells. Stem Cell Rep. 2018;10(2):583–99. https://doi.org/10.1016/j.stemcr.2017.12.022.
Article
CAS
Google Scholar
Xu Z-P, Wawrousek EF, Piatigorsky J. Transketolase haploinsufficiency reduces adipose tissue and female fertility in mice. Mol Cell Biol. 2002;22(17):6142–7. https://doi.org/10.1128/MCB.22.17.6142-6147.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim DS, Lee MW, Yoo KH, Lee T-H, Kim HJ, Jang IK, et al. Gene expression profiles of human adipose tissue-derived mesenchymal stem cells are modified by cell culture density. PLoS One. 2014;9(1):e83363. https://doi.org/10.1371/journal.pone.0083363.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fowler KE, Pong-Wong R, Bauer J, Clemente EJ, Reitter CP, Affara NA, et al. Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds. BMC Genomics. 2013;14(1):784. https://doi.org/10.1186/1471-2164-14-784.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peng WX, Gao CH, Huang GB. High throughput analysis to identify key gene molecules that inhibit adipogenic differentiation and promote osteogenic differentiation of human mesenchymal stem cells. Exp Ther Med. 2019;17(4):3021–8. https://doi.org/10.3892/etm.2019.7287.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xing XK, Wu HY, Chen HL, Feng HG. NDC80 promotes proliferation and metastasis of colon cancer cells. Genet Mol Res. 2016;15(2).
Nair S, Lee Y, Rousseau E, Cam M, Tataranni P, Baier L, et al. Increased expression of inflammation-related genes in cultured preadipocytes/stromal vascular cells from obese compared with non-obese Pima Indians. Diabetologia. 2005;48(9):1784–8. https://doi.org/10.1007/s00125-005-1868-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Taleb S, Cancello R, Poitou C, Rouault C, Sellam P, Levy P, et al. Weight loss reduces adipose tissue cathepsin S and its circulating levels in morbidly obese women. J Clin Endocrinol Metab. 2006;91(3):1042–7. https://doi.org/10.1210/jc.2005-1601.
Article
CAS
PubMed
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. Babraham Institute, Cambridge, United Kingdom: Babraham Bioinformatics; 2010.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41(D1):D590–D6. https://doi.org/10.1093/nar/gks1219.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997; 2013.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2. https://doi.org/10.1093/bioinformatics/btq033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2012;41(D1):D48–55. https://doi.org/10.1093/nar/gks1236.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635.
Article
CAS
PubMed
Google Scholar
García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012;28(20):2678–9. https://doi.org/10.1093/bioinformatics/bts503.
Article
CAS
PubMed
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9. https://doi.org/10.1093/bioinformatics/btu638.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Team R. RStudio: Integrated Development for R (1.2. 5042) [Computer software]. RStudio. Inc; 2020.
Google Scholar
Yang L, He T, Xiong F, Chen X, Fan X, Jin S, et al. Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis. BMC Genomics. 2020;21:1–18.
Article
Google Scholar
Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: network analysis and visualization of proteomics data. J Proteome Res. 2018;18(2):623–32. https://doi.org/10.1021/acs.jproteome.8b00702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4(1):2. https://doi.org/10.1186/1471-2105-4-2.
Article
PubMed
PubMed Central
Google Scholar
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–3. https://doi.org/10.1093/bioinformatics/btp101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chin C-H, Chen S-H, Wu H-H, Ho C-W, Ko M-T, Lin C-Y. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(S4):S11.
Article
PubMed
PubMed Central
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504. https://doi.org/10.1101/gr.1239303.
Article
CAS
PubMed
PubMed Central
Google Scholar