Bibliometric Analysis and Science Mapping on RNA-seq and Gene Expression in Sheep

Yıl 2024, Cilt: 21 Sayı: 2, 123 - 131, 02.08.2024

Esma Gamze Aksel

https://doi.org/10.32707/ercivet.1518359

Öz

This study aimed to determine the development of research articles on ‘RNA-sequencing and gene expres-sion’ in sheep between 2011-2023 in the Web of Science (WoS) database by scientific mapping method. In this regard, 205 articles were examined in the first search using the relevant keywords, and 124 articles suitable for analysis. They were analysed with the Shiny web application of the Bibliometrix R package, and VOSviewer. The results determined that the country with the most publications in the relevant field was China, the related institution with the most studies was “The University of Edinburgh”, and the journal with the most publications was “PLoS One”. According to the key-word analysis, the trend topics started from studies on granulosa cells and showed into research areas such as im-mune response, growth, pathway and meat quality. In the abstract analysis, the word ‘transcriptome’ and words such as mammary gland, muscle, fertility, Peripheral Blood Mononuclear Cells (PBMCs), lactation, fat storage were found together, while the words forming the parasitic agents, drug resistance, miRNA studies were clustered in different groups. The scarcity of the articles obtained in the analysed period reveals the openness of the study area. It can be suggested that the researchers who will plan to work on this subject can plan studies on the identification of variants belonging to different sheep breeds, resistance to antiparasitic drugs used in sheep, meat yield, disease resistance, reproductive tissues and organs, as well as designing all these studies as study subjects based on climate change and global warming factor.

Anahtar Kelimeler

Bibliometric analysis, gene expression, RNA-sequencing, sheep

Koyun Türünde RNA-Dizileme ve Gen İfadesi Üzerine Bibliyometrik Analiz ve Bilimsel Haritalama

Öz

Bu çalışmada, Web of Science (WoS) veri tabanında 2011-2023 yılları arasında koyunlarda 'RNA dizileme ve gen ifadesi' konulu araştırma makalelerinin gelişiminin bilimsel haritalama yöntemi ile belirlenmesi amaçlanmıştır. Bu kapsamda, ilgili anahtar kelimeler kullanılarak yapılan ilk taramada 205 makale incelenmiş ve 124 makale analize uy-gun bulunmuştur. Bu makaleler Bibliometrix R paketinin Shiny web uygulaması ve VOSviewer ile analiz edilmiştir. Sonuçlar, ilgili alanda en çok yayın yapılan ülkenin Çin, en çok çalışma yapılan ilgili kurumun "The University of Edin-burgh", en çok yayın yapılan derginin ise "PLoS One" olduğunu ortaya koymuştur. Anahtar kelime analizine göre trend konuları granüloza hücreleri üzerine yapılan çalışmalardan başlayarak bağışıklık tepkisi, büyüme, yolak ve et kalitesi gibi araştırma alanlarına doğru ilerlemiştir. Özet analizinde 'transkriptom' kelimesi ile meme bezi, kas, fertilite, PBMC, laktasyon, yağ depolama gibi kelimeler bir arada bulunurken, parazitik ajanlar, ilaç direnci, miRNA çalışmalarını oluşturan kelimeler farklı gruplarda kümelenmiştir. İncelenen dönemde elde edilen makalelerin azlığı çalışma alanının açıklığını ortaya koymaktadır. Bu konuda çalışma planlayacak araştırmacıların farklı koyun ırklarına ait varyantların belirlenmesi, koyunlarda kullanılan antiparaziter ilaçlara direnç, et verimi, hastalıklara direnç, üreme doku ve organları gibi konularda çalışmalar planlayabilecekleri gibi tüm bu çalışmaları iklim değişikliği ve küresel ısınma faktörüne dayalı çalışma konuları olarak tasarlamaları önerilebilir.

Anahtar Kelimeler

Bibliyometrik analiz, gen ifadesi, koyun, RNA-dizileme

Kaynakça

• Alonso-García M, Suárez-Vega A, Fonseca PAS, Marina H, Pelayo R, Mateo J, Arranz JJ, Gutiérrez-Gil B. Transcriptome analysis of perirenal fat from Spanish Assaf suckling lamb carcasses showing different levels of kidney knob and channel fat. Front Vet Sci 2023; 10: 1150996.
• Aria M, Cuccurullo C. Bibliometrix: An R-tool for comprehensive science mapping analysis. J Informetr 2017; 11: 959-75.
• Armstrong E, Iriarte A, Nicolini P, De Los Santos J, Ithurralde J, Bielli A, Bianchi G, Peñagaricano F. Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq. PLoS One 2018; 13(7): e0200732.
• Bakhtiarizadeh MR, Salehi A, Alamouti AA, Abdollahi-Arpanahi R, Salami SA. Deep transcriptome analy-sis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep. Sci Rep 2019; 9(1): 9203.
• Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. Front Genet 2022; 13: 1067350.
• Bush SJ, McCulloch MEB, Summers KM, Hume DA, Clark EL. Integration of quantitated expression esti-mates from polyA-selected and rRNA-depleted RNA-seq libraries. BMC Bioinformatics 2017; 18: 301.
• Bush SJ, Muriuki C, McCulloch MEB, Farquhar IL, Clark EL, Hume DA. Cross-species inference of long non-coding RNAs greatly expands the rumi-nant transcriptome. Genet Sel 2018; 50(1): 20.
• Bush SJ, McCulloch MEB, Muriuki C, Salavati M, Davis GM, Farquhar IL, Lisowski ZM, Archibald AL, Hume DA, Clark EL. Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmen-tal stage specific gene expression. G3 (Bethesda) 2019; 9(2): 359-73.
• Bush SJ, McCulloch MEB, Lisowski ZM, Muriuki C, Clark EL, Young R, Pridans C, Prendergast JGD, Summers KM, Hume DA. Species-specificity of transcriptional regulation and the response to lipo-polysaccharide in mammalian macrophages. Front Cell Dev Biol 2020; 8: 661.
• Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid transcriptomic profiling reveals the follic-ular phase differential regulation of lncRNA and mRNA related to prolificacy in Small Tail Han sheep with two FecB genotypes. Genes 2022; 13(5): 849.
• Chen Y, Liu Y, Chu M. miRNA-mRNA analysis of sheep adrenal glands reveals the network regulating reproduction. BMC Genom Data 2022; 23(1): 44.
• Czech B, Wang Y, Wang K, Luo H, Hu L, Szyda J. Host transcriptome and microbiome interactions in Holstein cattle under heat stress condition. Front Microbiol 2022; 13: 998093.
• Chitneedi PK, Arranz JJ, Suárez-Vega A, Martínez-Valladares M, Gutiérrez-Gil B. Identification of potential functional variants underlying ovine re-sistance to gastrointestinal nematode infection by using RNA-Seq. Anim Genet 2020; 51(2): 266-77.
• Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA. A high res-olution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet 2017; 13(9): e1006997.
• Dou J F, Puttabyatappa M, Padmanabhan V, Bakul-ski KM. Developmental programming: Transcrip-tional regulation of visceral and subcutaneous adi-pose by prenatal bisphenol-A in female sheep. Chemosphere 2020; 255: 127000.
• Farhadi S, Hasanpur K, Ghias JS, Palangi V, Maggi-olino A, Landi V. Comprehensive gene expression profiling analysis of adipose tissue in male ındividu-als from fat- and thin-tailed sheep breeds. Animals 2023; 13(22): 3475.
• Farhadian M, Rafat SA, Panahi B, Ebrahimie E. Tran-scriptome signature of two lactation stages in Ghezel sheep identifies using RNA-Sequencing. Anim Biotecnol 2022; 33(2): 223-33.
• Gauvin MC, Pillai SM, Reed SA, Stevens JR, Hoff-man ML, Jones AK, Zinn SA, Govoni KE. Poor ma-ternal nutrition during gestation in sheep alters pre-natal muscle growth and development in offspring. J Anim Sci 2020; 98(1): skz388.
• Jäger M, Ott CE, Grünhagen J, Hecht J, Schell H, Mundlos S, Duda GN, Robinson PN, Lienau J. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. BMC Genom 2011; 12: 158.
• Ji P, Liu Y, Yan L, Jia Y, Zhao M, Lv D, Yao Y, Ma W, Yin D, Liu F, Gao S, Wusiman A, Yang K, Zhang L, Liu G. Melatonin improves the vitrification of sheep morulae by modulating transcriptome. Front Vet Sci 2023; 10: 1212047.
• Khan A, Dou J, Wang Y, Jiang X, Khan MZ, Luo H, Usman T, Zhu H. Evaluation of heat stress effects on cellular and transcriptional adaptation of bovine granulosa cells. JABS 2020; 11: 25.
• Kyselová J, Tichý L, Sztankóová Z, Marková J, Ka-vanová K, Beinhauerová M, Mušková M. Comparative characterization of imune response in sheep with caseous lymphadenitis through analysis of the whole blood transcriptome. Animals (Basel) 2023; 13(13): 2144.
• Kukurba KR, Montgomery SB. RNA squencing and analysis. Cold Spring Harb Protoc 2015; 11: 951-69.
• Li W, Zeng W, Jin X, Xu H, Fang X, Ma Z, Cao G, Li R, Ma L. High-Altitude stress orchestrates mrna expression and alternative splicing of ovarian follicle development genes in Tibetan sheep. Animals (Basel) 2022; 12(20): 2812.
• Li Z, Du Z, Sun Y, Wang J, Liu H, Yang Y, Zhao N. Comprehensive RNA-Seq profiling of the lung tran-scriptome of Argali hybrid sheep in response to experimental Mycoplasma ovipneumoniae infec-tion. Res Vet Sci 2020; 132: 57-68.
• Lins JGG, Albuquerque ACA, Almeida FA, Britton C, Malossi C, Araújo-Júnior JP, Louvandini H, Ama-rante AFT. Abomasal RNA-seq reveals a strong local cellular response in suckling lambs with re-sistance against Haemonchus contortus. Int J Par-asitol 2023; 53(13): 739-49.
• Liu Z, Fu S, He X, Dai L, Liu X, Narisu Shi C, Gu M, Wang Y, Manda Guo L, Bao Y, Baiyinbatu Chang C, Liu Y, Zhang W. Integrated multi-tissue transcriptome profiling characterizes the genetic basis and biomarkers affecting reproduction in sheep (Ovis Aries). Genes 2023; 14(10): 1881.
• Lv X, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo JM, Haile A, Sun W. ıntegrated hair folli-cle profiles of micrornas and mrnas to reveal the pattern formation of Hu sheep lambskin. Genes 2022; 13(2): 342.
• Miao X, Luo Q, Qin X, Guo Y, Zhao H. Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep. Bio-chem Biophysic Res Commun 2015; 467(2): 413-20.
• Miao X, Luo Q, Qin X. Guo Y. Genome-wide analysis of microRNAs identifies the lipid metabolism path-way to be a defining factor in adipose tissue from different sheep. Sci Rep 2016; 5: 18470
• Quttainah M, Raveendran VV, Saleh S, Parhar R, Aljoufan M, Moorjani N, Al-Halees ZY, AlShahid M, Collison KS, Westaby S, Al-Mohanna F. Tran-scriptomal insights of heart failure from normality to recovery. Biomolecules 2022; 12(5): 731.
• Sadeghi M, Bahrami A, Hasankhani A, Kioumarsi H, Nouralizadeh R, Abdulkareem SA, Ghafouri F, Barkema HW. lncRNA-miRNA-mRNA ceRNA net-work ınvolved in sheep prolificacy: An integrated approach. Genes 2022; 13(8): 1295.
• Salavati M, Bush SJ, Palma-Vera S, McCulloch MEB, Hume DA, Clark EL. Elimination of reference map-ping bias reveals robust immune related allele-specific expression in crossbred sheep. Front Genet 2019; 10: 863.
• Salinas-Ríos K, López A. Bibliometrics, a useful tool within the field of research. Journal of Basic and Applied Psychology 2022; 3: 9-16.
• Shi R, Li S, Liu P, Zhang S, Wu Z, Wu T, Gong S, Wan Y. Identification of key genes and signaling pathways related to Hetian sheep wool density by RNA-seq technology. PLoS One 2022; 17(5): e0265989.
• Sinha N, Roy S, Huang B, Wang J, Padmanabhan V, Sen A. Developmental programming: prenatal tes-tosterone-induced epigenetic modulation and its effect on gene expression in sheep ovary. Biol Re-prod 2020; 102(5): 1045-54.
• Suárez-Vega A, Arranz JJ, Pérez V, de la Fuente LF, Mateo J, Gutiérrez-Gil B. Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs. Anim Genet 2018; 49(6): 605-17.
• Suárez-Vega A, Frutos P, Gutiérrez-Gil B, Esteban-Blanco C, Toral PG, Arranz JJ, Hervás G. Feed efficiency in dairy sheep: An insight from the milk transcriptome. Front Vet Sci 2023; 10: 1122953.
• Tsang HG, Clark EL, Markby GR, Bush SJ, Hume DA, Corcoran BM, MacRae VE, Summers KM. Expression of calcification and extracellular matrix genes in the cardiovascular system of the healthy domestic sheep (Ovis Aries). Front Genet 2020; 11: 919.
• van Eck NJ, Waltman L. Software Survey: VOSview-er, a computer program for bibliometric mapping. Scientometrics 2010; 84: 523-38.
• Wang W, Li C, Li F, Wang X, Zhang X, Liu T, Nian F, Yue X, Li F, Pan X, La Y, Mo F, Wang F, Li B. Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs. Sci Rep 2016; 6: 32479.
• Wang J, Zhou H, Hickford J GH, Hao Z, Shen J, Luo Y, Hu J, Liu X, Li S. Comparison of the transcriptome of the ovine mammary gland in lactating and non-lactating Small-Tailed Han sheep. Front Genet 2020; 11: 472.