{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T00:12:49Z","timestamp":1770336769430,"version":"3.49.0"},"reference-count":66,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T00:00:00Z","timestamp":1614816000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19H03427"],"award-info":[{"award-number":["19H03427"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["20K07315"],"award-info":[{"award-number":["20K07315"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005865","name":"Mochida Memorial Foundation for Medical and Pharmaceutical Research","doi-asserted-by":"publisher","award":["2019"],"award-info":[{"award-number":["2019"]}],"id":[{"id":"10.13039\/501100005865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Intramural Research Grants for Neurological and Psychiatric Disorders of NCNP","award":["29-4"],"award-info":[{"award-number":["29-4"]}]},{"name":"Intramural Research Grants for Neurological and Psychiatric Disorders of NCNP","award":["2-5"],"award-info":[{"award-number":["2-5"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The loss of skeletal muscle mass (muscle atrophy or wasting) caused by aging, diseases, and injury decreases quality of life, survival rates, and healthy life expectancy in humans. Although long non-coding RNAs (lncRNAs) have been implicated in skeletal muscle formation and differentiation, their precise roles in muscle atrophy remain unclear. In this study, we used RNA-sequencing (RNA-Seq) to examine changes in the expression of lncRNAs in four muscle atrophy conditions (denervation, casting, fasting, and cancer cachexia) in mice. We successfully identified 33 annotated lncRNAs and 18 novel lncRNAs with common expression changes in all four muscle atrophy conditions. Furthermore, an analysis of lncRNA\u2013mRNA correlations revealed that several lncRNAs affected small molecule biosynthetic processes during muscle atrophy. These results provide novel insights into the lncRNA-mediated regulatory mechanism underlying muscle atrophy and may be useful for the identification of promising therapeutic targets.<\/jats:p>","DOI":"10.3390\/ijms22052558","type":"journal-article","created":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T21:58:07Z","timestamp":1614895087000},"page":"2558","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["An Analysis of Differentially Expressed Coding and Long Non-Coding RNAs in Multiple Models of Skeletal Muscle Atrophy"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7300-5238","authenticated-orcid":false,"given":"Keisuke","family":"Hitachi","sequence":"first","affiliation":[{"name":"Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masashi","family":"Nakatani","sequence":"additional","affiliation":[{"name":"Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"},{"name":"Faculty of Rehabilitation and Care, Seijoh University, Tokai 476-0014, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuri","family":"Kiyofuji","sequence":"additional","affiliation":[{"name":"Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hidehito","family":"Inagaki","sequence":"additional","affiliation":[{"name":"Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake 470-1192, Japan"},{"name":"Division of Molecular Genetics, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroki","family":"Kurahashi","sequence":"additional","affiliation":[{"name":"Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake 470-1192, Japan"},{"name":"Division of Molecular Genetics, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3983-5756","authenticated-orcid":false,"given":"Kunihiro","family":"Tsuchida","sequence":"additional","affiliation":[{"name":"Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature21374","article-title":"An atlas of human long non-coding RNAs with accurate 5\u2032 ends","volume":"543","author":"Hon","year":"2017","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"D128","DOI":"10.1093\/nar\/gky960","article-title":"LncBook: A curated knowledgebase of human long non-coding RNAs","volume":"47","author":"Ma","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e60583","DOI":"10.7554\/eLife.60583","article-title":"Beyond the RNA-dependent function of LncRNA genes","volume":"9","author":"Ali","year":"2020","journal-title":"eLife"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: From microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"D1034","DOI":"10.1093\/nar\/gky905","article-title":"LncRNADisease 2.0: An updated database of long non-coding RNA-associated diseases","volume":"47","author":"Bao","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_6","first-page":"D118","article-title":"LncTarD: A manually-curated database of experimentally-supported functional lncRNA\u2013target regulations in human diseases","volume":"48","author":"Zhao","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"527484","DOI":"10.3389\/fgene.2020.527484","article-title":"Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci","volume":"11","author":"Aznaourova","year":"2020","journal-title":"Front. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1152\/physrev.00061.2017","article-title":"Sarcopenia: Aging-Related Loss of Muscle Mass and Function","volume":"99","author":"Larsson","year":"2019","journal-title":"Physiol. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"235","DOI":"10.3389\/fphys.2018.00235","article-title":"Muscle atrophy induced by mechanical unloading: Mechanisms and potential coun-termeasures","volume":"9","author":"Gao","year":"2018","journal-title":"Front. Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3310\/hta16190","article-title":"The effectiveness of interventions to treat severe acute malnutrition in young children: A systematic review","volume":"16","author":"Picot","year":"2012","journal-title":"Health Technol. Assess."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e47258","DOI":"10.15252\/embr.201847258","article-title":"Energy metabolism in cachexia","volume":"20","author":"Rohm","year":"2019","journal-title":"EMBO Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1002\/ehf2.12387","article-title":"Skeletal muscle wasting in chronic heart failure","volume":"5","author":"Suzuki","year":"2018","journal-title":"ESC Heart Fail."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"159","DOI":"10.3233\/BPL-140001","article-title":"Synaptic Failure: Focus in an Integrative View of ALS","volume":"1","author":"Casas","year":"2016","journal-title":"Brain Plast."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4294","DOI":"10.1111\/febs.12253","article-title":"Mechanisms regulating skeletal muscle growth and atrophy","volume":"280","author":"Schiaffino","year":"2013","journal-title":"FEBS J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4361","DOI":"10.1007\/s00018-014-1689-x","article-title":"Myostatin and the skeletal muscle atrophy and hypertrophy signaling pathways","volume":"71","author":"Rodriguez","year":"2014","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"12","DOI":"10.3389\/fphys.2015.00012","article-title":"The regulation of muscle mass by endogenous glucocorticoids","volume":"6","author":"Braun","year":"2015","journal-title":"Front. Physiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/s41467-020-20123-1","article-title":"Mechanisms of muscle atrophy and hypertrophy: Implications in health and disease","volume":"12","author":"Sartori","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"408","DOI":"10.3389\/fphys.2013.00408","article-title":"Role of microRNAs in skeletal muscle hypertrophy","volume":"4","author":"Hitachi","year":"2014","journal-title":"Front. Physiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1002\/jcsm.12321","article-title":"Long-noncoding RNA Atrolnc-1 promotes muscle wasting in mice with chronic kidney disease","volume":"9","author":"Sun","year":"2018","journal-title":"J. Cachex. Sarcopenia Muscle"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1093\/nar\/gkz007","article-title":"Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mi-tochondrial network","volume":"47","author":"Alessio","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e47468","DOI":"10.15252\/embr.201847468","article-title":"Myogenin promoter-associated lncRNA Myoparr is essential for myogenic differentiation","volume":"20","author":"Hitachi","year":"2019","journal-title":"EMBO Rep."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Hitachi, K., Nakatani, M., and Tsuchida, K. (2019). Long Non-Coding RNA Myoparr Regulates GDF5 Expression in Denervated Mouse Skeletal Muscle. Non-Coding RNA, 5.","DOI":"10.3390\/ncrna5020033"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hitachi, K., Nakatani, M., Funasaki, S., Hijikata, I., Maekawa, M., Honda, M., and Tsuchida, K. (2020). Expression Levels of Long Non-Coding RNAs Change in Models of Altered Muscle Activity and Muscle Mass. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21051628"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/978-3-030-44743-4_17","article-title":"The chemical biology of long noncoding RNAs","volume":"11","author":"Hitachi","year":"2020","journal-title":"RNA Technol."},{"key":"ref_25","first-page":"E245","article-title":"p53 and ATF4 mediate distinct and additive pathways to skeletal muscle atrophy during limb immobilization","volume":"307","author":"Fox","year":"2014","journal-title":"Am. J. Physiol. Metab."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1172\/JCI118398","article-title":"Interleukin 6 receptor antibody inhibits muscle atrophy and modulates proteolytic systems in interleukin 6 transgenic mice","volume":"97","author":"Tsujinaka","year":"1996","journal-title":"J. Clin. Investig."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.bcp.2014.06.023","article-title":"Dual response of the KATP channels to staurosporine: A novel role of SUR2B, SUR1 and Kir6.2 subunits in the regulation of the atrophy in different skeletal muscle phenotypes","volume":"91","author":"Mele","year":"2014","journal-title":"Biochem. Pharmacol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"C1312","DOI":"10.1152\/ajpcell.00117.2005","article-title":"Muscle LIM protein plays both structural and functional roles in skeletal muscle","volume":"289","author":"Barash","year":"2005","journal-title":"Am. J. Physiol. Physiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Cui, C., Han, S., Tang, S., He, H., Shen, X., Zhao, J., Chen, Y., Wei, Y., Wang, Y., and Zhu, Q. (2020). The Autophagy Regulatory Molecule CSRP3 Interacts with LC3 and Protects Against Muscular Dystrophy. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21030749"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e63726","DOI":"10.7554\/eLife.63726","article-title":"The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression","volume":"10","author":"Marchiano","year":"2021","journal-title":"eLife"},{"key":"ref_31","first-page":"4038","article-title":"Dach2-Hdac9 signaling regulates reinnervation of muscle endplates","volume":"142","author":"MacPherson","year":"2015","journal-title":"Development"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1002\/jnr.23619","article-title":"Glycoprotein nonmetastatic melanoma protein B ameliorates skeletal muscle lesions in a SOD1G93A mouse model of amyotrophic lateral sclerosis","volume":"93","author":"Nagahara","year":"2015","journal-title":"J. Neurosci. Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1002\/jcsm.12539","article-title":"Interleukin-4 administration improves muscle function, adult myogenesis, and lifespan of colon carcinoma-bearing mice","volume":"11","author":"Costamagna","year":"2020","journal-title":"J. Cachex. Sarcopenia Muscle"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1101\/gad.1318305","article-title":"Runx1 prevents wasting, myofibrillar dis-organization, and autophagy of skeletal muscle","volume":"19","author":"Wang","year":"2005","journal-title":"Gene Dev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1042\/bj3250793","article-title":"Neural regulation of the formation of skeletal muscle phosphorylase kinase holoenzyme in adult and developing rat muscle","volume":"325","author":"Ng","year":"1997","journal-title":"Biochem. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2152","DOI":"10.1210\/me.2007-0169","article-title":"Nur77 Coordinately Regulates Expression of Genes Linked to Glucose Metabolism in Skeletal Muscle","volume":"21","author":"Chao","year":"2007","journal-title":"Mol. Endocrinol."},{"key":"ref_37","first-page":"E144","article-title":"Spermine oxidase maintains basal skeletal muscle gene expression and fiber size and is strongly repressed by conditions that cause skeletal muscle atrophy","volume":"308","author":"Bongers","year":"2015","journal-title":"Am. J. Physiol. Metab."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Bonetto, A., Aydogdu, T., Kunzevitzky, N., Guttridge, D.C., Khuri, S., Koniaris, L.G., and Zimmers, T.A. (2011). STAT3 Activation in Skeletal Muscle Links Muscle Wasting and the Acute Phase Response in Cancer Cachexia. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0022538"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"11419","DOI":"10.1073\/pnas.1410854111","article-title":"Denervation protects limbs from inflammatory arthritis via an impact on the microvasculature","volume":"111","author":"Stangenberg","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1016\/j.cell.2011.11.055","article-title":"Conserved function of lincRNAs in vertebrate embryonic devel-opment despite rapid sequence evolution","volume":"147","author":"Ulitsky","year":"2011","journal-title":"Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e40815","DOI":"10.7554\/eLife.40815","article-title":"Individual long non-coding RNAs have no overt functions in zebrafish em-bryogenesis, viability and fertility","volume":"8","author":"Goudarzi","year":"2019","journal-title":"eLife"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"12943","DOI":"10.1093\/nar\/gkaa1151","article-title":"Interaction of OIP5-AS1 with MEF2C mRNA promotes myogenic gene expression","volume":"48","author":"Yang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"12397","DOI":"10.1038\/ncomms12397","article-title":"MRF4 negatively regulates adult skeletal muscle growth by repressing MEF2 activity","volume":"7","author":"Moretti","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Sakakibara, I., Santolini, M., Ferry, A., Hakim, V., and Maire, P. (2014). Six Homeoproteins and a linc-RNA at the Fast MYH Locus Lock Fast Myofiber Terminal Phenotype. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004386"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e105098","DOI":"10.15252\/embj.2020105098","article-title":"Linc-MYH configures INO 80 to regulate muscle stem cell numbers and skeletal muscle hypertrophy","volume":"39","author":"Schutt","year":"2020","journal-title":"EMBO J."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4050","DOI":"10.1038\/s41598-020-61059-2","article-title":"Deletion of metal transporter Zip14 (Slc39a14) produces skeletal muscle wasting, endotoxemia, Mef2c activation and induction of miR-675 and Hspb","volume":"10","author":"Kim","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e00305","DOI":"10.1128\/MCB.00305-16","article-title":"Blockade of Metallothioneins 1 and 2 Increases Skeletal Muscle Mass and Strength","volume":"37","author":"Summermatter","year":"2017","journal-title":"Mol. Cell. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1016\/j.biocel.2013.05.016","article-title":"Muscle type and fiber type specificity in muscle wasting","volume":"45","author":"Ciciliot","year":"2013","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1002\/mus.24322","article-title":"Electrical stimulation influences satellite cell differentiation after sciatic nerve crush injury in rats","volume":"51","author":"Xing","year":"2015","journal-title":"Muscle Nerve"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"4821","DOI":"10.1172\/JCI68523","article-title":"NF-\u039aB-mediated Pax7 dysregulation in the muscle microenvironment promotes cancer cachexia","volume":"123","author":"He","year":"2013","journal-title":"J. Clin. Investig."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"4360","DOI":"10.1002\/jcp.26282","article-title":"Muscle regeneration potential and satellite cell activation profile during recovery following hindlimb immobilization in mice","volume":"233","author":"Guitart","year":"2018","journal-title":"J. Cell. Physiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1007\/s004419900168","article-title":"Effect of fasting and refeeding on in vitro muscle cell proliferation in rainbow trout (Oncorhynchus mykiss)","volume":"301","author":"Fauconneau","year":"2000","journal-title":"Cell Tissue Res."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Li, R., Li, B., Jiang, A., Cao, Y., Hou, L., Zhang, Z., Zhang, X., Liu, H., Kim, K.-H., and Wu, W. (2020). Exploring the lncRNAs Related to Skeletal Muscle Fiber Types and Meat Quality Traits in Pigs. Genes, 11.","DOI":"10.3390\/genes11080883"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"32464","DOI":"10.1073\/pnas.2005868117","article-title":"A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression","volume":"117","author":"Dong","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1038\/s41467-020-16553-6","article-title":"Long noncoding RNA SAM promotes myoblast proliferation through stabilizing Sugt1 and facilitating kinetochore assembly","volume":"11","author":"Li","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Li, J., Zhao, W., Li, Q., Huang, Z., Shi, G., and Li, C. (2020). Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43. Genes, 11.","DOI":"10.3390\/genes11030259"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"843","DOI":"10.3389\/fgene.2020.00843","article-title":"Long Noncoding RNA (lncRNA) CTTN-IT1 Elevates Skeletal Muscle Satellite Cell Proliferation and Differentiation by Acting as ceRNA for YAP1 Through Absorbing miR-29a in Hu Sheep","volume":"11","author":"Wu","year":"2020","journal-title":"Front. Genet."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"djv274","DOI":"10.1093\/jnci\/djv274","article-title":"Preclinical Investigation of the Novel Histone Deacetylase Inhibitor AR-42 in the Treatment of Cancer-Induced Cachexia","volume":"107","author":"Tseng","year":"2015","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"1000 Genome Project Data Processing Subgroup. The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nmeth.4078","article-title":"TACO produces robust multisample transcriptome assem-blies from RNA-Seq","volume":"14","author":"Niknafs","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e74","DOI":"10.1093\/nar\/gkt006","article-title":"CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Li, T., Chen, B., Yang, P., Wang, D., Du, B., and Kang, L. (2020). Long non-coding RNA derived from lncRNA\u2013mRNA co-expression net-works modulates the locust phase change. Genom. Proteom. Bioinform., in press.","DOI":"10.1101\/2020.04.11.036848"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/s41596-018-0103-9","article-title":"Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap","volume":"14","author":"Reimand","year":"2019","journal-title":"Nat. Protoc."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/5\/2558\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:32:33Z","timestamp":1760160753000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/5\/2558"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3,4]]},"references-count":66,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021,3]]}},"alternative-id":["ijms22052558"],"URL":"https:\/\/doi.org\/10.3390\/ijms22052558","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,3,4]]}}}