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To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp. Additionally, 20,887 transcripts were effectively identified and classified as known homologous genes. We also identified 787 HKGs, and the number of TSGs varied from 25 in the liver to 2073 in the brain. TSG functions were mainly enriched in certain signaling pathways involved in specific physiological processes, such as voltage-gated potassium channel activity, nervous system development, glial cell differentiation in the brain, and leukocyte transendothelial migration in the spleen and pronephros. Meanwhile, HKGs were highly enriched in some pathways involved in ribosome biogenesis, proteasome core complex, spliceosome activation, elongation factor activity, and translation initiation factor activity, which have been strongly implicated in fundamental biological tissue functions. We also predicted five modules, with eight hub genes in the brown module, most of which (such as rps3a, rps7, rps23, rpl11, rpl17, rpl27, and rpl28) were linked to ribosome biogenesis. Our results offer insights into ribosomal proteins that are indispensable in ribosome biogenesis and protein synthesis, which are crucial in various cell developmental processes and neural development of Chinese sturgeon. Overall, these findings will not only advance the understanding of fundamental biological functions in Chinese sturgeon but also supply a valuable genetic resource for characterizing this extremely important species.<\/jats:p>","DOI":"10.3390\/ani14233357","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T12:25:42Z","timestamp":1732191942000},"page":"3357","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Expression Profiles of Housekeeping Genes and Tissue-Specific Genes in Different Tissues of Chinese Sturgeon (Acipenser sinensis)"],"prefix":"10.3390","volume":"14","author":[{"given":"Yanping","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"},{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4941-268X","authenticated-orcid":false,"given":"Yunyun","family":"Lv","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peilin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Jiang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9823-9121","authenticated-orcid":false,"given":"Cao","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongming","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6198-5793","authenticated-orcid":false,"given":"Zhengyong","family":"Wen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiang","family":"Xie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jieming","family":"Chen","sequence":"additional","affiliation":[{"name":"Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6358-976X","authenticated-orcid":false,"given":"Qiong","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China"},{"name":"Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China"},{"name":"Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518057, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0018-1740","authenticated-orcid":false,"given":"Hao","family":"Du","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zhu, J., Guo, W., Li, Z., and Jiang, W. (2024). First Insights into the Migration Route and Spatial Distribution of the Endangered Chinese Sturgeon (Acipenser sinensis) in the Yangtze River Estuary. Fishes, 9.","DOI":"10.3390\/fishes9080321"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.18307\/2020.0509","article-title":"Conservation of Chinese sturgeon (Acipenser sinensis) based on its life history: Dilemma and breakthrough","volume":"32","author":"Wei","year":"2020","journal-title":"J. Lake Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s10641-016-0549-y","article-title":"Substrate color preference and feeding by juvenile Chinese sturgeon Acipenser sinensis: Exploration of a behavioral adaptation","volume":"100","author":"Gu","year":"2017","journal-title":"Environ. Biol. Fishes"},{"key":"ref_4","first-page":"150","article-title":"Skin mucus flora and habitat microbial composition of Chinese sturgeon (Acipenser sinensis) under different physiological states","volume":"45","author":"Zheng","year":"2024","journal-title":"Prog. Fish. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"9339","DOI":"10.1073\/pnas.0809434106","article-title":"Malformations of the endangered Chinese sturgeon, Acipenser sinensis, and its causal agent","volume":"106","author":"Hu","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1111\/j.1439-0426.2011.01716.x","article-title":"Conservation strategies for the Chinese sturgeon, Acipenser sinensis: An overview on 30 years of practices and future needs","volume":"27","author":"Wang","year":"2011","journal-title":"J. Appl. Ichthyol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1007\/s11033-011-1256-6","article-title":"EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, Acipenser sinensis","volume":"39","author":"Cao","year":"2012","journal-title":"Mol. Biol. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1111\/j.1095-8649.2012.12015.x","article-title":"Effects of age and size on critical swimming speed of juvenile Chinese sturgeon Acipenser sinensis at seasonal temperatures","volume":"82","author":"He","year":"2013","journal-title":"J. Fish Biol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Huang, Y., Li, Z., Li, M., Zhang, X., Shi, Q., and Xu, Z. (2024). Fish Genomics and Its Application in Disease-Resistance Breeding. Rev. Aquac., 1\u201324.","DOI":"10.1111\/raq.12973"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Wang, B., Wu, B., Liu, X., Hu, Y., Ming, Y., Bai, M., Liu, J., Xiao, K., Zeng, Q., and Yang, J. (2024). Whole-genome sequencing reveals autooctoploidy in chinese sturgeon and its evolutionary trajectories. Genom. Proteom. Bioinform., 22.","DOI":"10.1093\/gpbjnl\/qzad002"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41597-023-02014-4","article-title":"Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data","volume":"10","author":"Liao","year":"2023","journal-title":"Sci. Data"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ygcen.2018.10.001","article-title":"Tissue-specific gene regulation corresponds with seasonal plasticity in female testosterone","volume":"270","author":"Bentz","year":"2019","journal-title":"Gen. Comp. Endocrinol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Chikina, M.D., Huttenhower, C., Murphy, C.T., and Troyanskaya, O.G. (2009). Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000417"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Liu, X., Yu, X., Zack, D.J., Zhu, H., and Qian, J. (2008). TiGER: A database for tissue-specific gene expression and regulation. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-271"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Mohamed, A.R., King, H., Evans, B., Reverter, A., and Kijas, J.W. (2018). Multi-tissue transcriptome profiling of north American derived Atlantic salmon. Front. Genet., 9.","DOI":"10.3389\/fgene.2018.00369"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Liao, X., Cheng, L., Xu, P., Lu, G., Wachholtz, M., Sun, X., and Chen, S. (2013). Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0062308"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Thorstensen, M.J., Weinrauch, A.M., Bugg, W.S., Jeffries, K.M., and Anderson, W.G. (2023). Tissue-specific transcriptomes reveal mechanisms of microbiome regulation in an ancient fish. Database, baad055.","DOI":"10.1093\/database\/baad055"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Salem, M., Paneru, B., Al-Tobasei, R., Abdouni, F., Thorgaard, G.H., Rexroad, C.E., and Yao, J. (2015). Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0121778"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Matsubara, S., Osugi, T., Shiraishi, A., Wada, A., and Satake, H. (2021). Comparative analysis of transcriptomic profiles among ascidians, zebrafish, and mice: Insights from tissue-specific gene expression. PLoS ONE, 16.","DOI":"10.1101\/2021.07.23.453541"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1152\/physiolgenomics.2001.7.2.95","article-title":"Further defining housekeeping, or \u201cmaintenance\u201d, genes Focus on \u201cA compendium of gene expression in normal human tissues\u201d","volume":"7","author":"Butte","year":"2001","journal-title":"Physiol. Genom."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.gep.2011.01.003","article-title":"Identification of housekeeping genes suitable for gene expression analysis in the zebrafish","volume":"11","author":"Casadei","year":"2011","journal-title":"Gene Expr. Patterns"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Nguinkal, J.A., Verleih, M., De Los Rios-Perez, L., Brunner, R.M., Sahm, A., Bej, S., Rebl, A., and Goldammer, T. (2021). Comprehensive characterization of multitissue expression landscape, co-expression networks and positive selection in pikeperch. Cells, 10.","DOI":"10.3390\/cells10092289"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"Accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/j.infsof.2005.09.005","article-title":"Engineering a software tool for gene structure prediction in higher organisms","volume":"47","author":"Gremme","year":"2005","journal-title":"Inf. Softw. Technol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat. Protoc."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: Tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D277","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resource for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/bioinformatics\/18.1.77","article-title":"Tolerating some redundancy significantly speeds up clustering of large protein databases","volume":"18","author":"Li","year":"2002","journal-title":"Bioinformatics"},{"key":"ref_32","first-page":"205","article-title":"A benchmark of gene expression tissue-specificity metrics","volume":"18","year":"2017","journal-title":"Brief. Bioinform."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1093\/molbev\/msj119","article-title":"Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution","volume":"23","author":"Liao","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Camargo, A.P., Vasconcelos, A.A., Fiamenghi, M.B., Pereira, G.A., and Carazzolle, M.F. (2020). Tspex: A tissue-specificity calculator for gene expression data. Res. Sq.","DOI":"10.21203\/rs.3.rs-51998\/v1"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: An R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Kerseviciute, I., and Gordevicius, J. (2023). aPEAR: An R package for autonomous visualization of pathway enrichment networks. Bioinformatics, 39.","DOI":"10.1093\/bioinformatics\/btad672"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Kassambara, A., and Mundt, F. (2024, November 02). Factoextra: Extract and Visualize the Results of Multivariate Data Analyses. 2017. R Package Version 1.0.7. Available online: https:\/\/CRAN.R-project.org\/package=factoextra.","DOI":"10.32614\/CRAN.package.factoextra"},{"key":"ref_38","first-page":"1","article-title":"ggplot2-elegant graphics for data analysis","volume":"77","year":"2017","journal-title":"J. Stat. Softw."},{"key":"ref_39","first-page":"1","article-title":"FactoMineR: An R package for multivariate analysis","volume":"25","author":"Josse","year":"2008","journal-title":"J. Stat. Softw."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1039\/C0MB00190B","article-title":"Systems biology of ovine intestinal parasite resistance: Disease gene modules and biomarkers","volume":"7","author":"Kadarmideen","year":"2011","journal-title":"Mol. Biosyst."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"17","DOI":"10.2202\/1544-6115.1128","article-title":"A general framework for weighted gene co-expression network analysis","volume":"4","author":"Zhang","year":"2005","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1126\/science.1073374","article-title":"Hierarchical organization of modularity in metabolic networks","volume":"297","author":"Ravasz","year":"2002","journal-title":"Science"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1093\/bioinformatics\/btm563","article-title":"Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R","volume":"24","author":"Langfelder","year":"2008","journal-title":"Bioinformatics"},{"key":"ref_46","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"Complex Syst."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., Stein, T.I., Nudel, R., Lieder, I., and Mazor, Y. (2016). The GeneCards suite: From gene data mining to disease genome sequence analyses. Curr. Protoc. Bioinform., 54.","DOI":"10.1002\/cpbi.5"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1101\/gr.250704.119","article-title":"Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle","volume":"30","author":"Fang","year":"2020","journal-title":"Genome Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"715","DOI":"10.4067\/S0717-95022014000200055","article-title":"Morphology and histochemistry of the liver of carnivorous fish Hemisorubim platyrhynchos","volume":"32","author":"Faccioli","year":"2014","journal-title":"Int. J. Morphol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1007\/s10126-010-9279-x","article-title":"Immunological control of fish diseases","volume":"12","author":"Magnadottir","year":"2010","journal-title":"Mar. Biotechnol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.fsi.2004.09.005","article-title":"Ontogeny of the immune system of fish","volume":"20","author":"Zapata","year":"2006","journal-title":"Fish Shellfish Immunol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3987","DOI":"10.1007\/s12649-023-02107-6","article-title":"Structural properties and biological activities of collagens from four main processing by-products (skin, fin, cartilage, notochord) of sturgeon (Acipenser gueldenstaedti)","volume":"14","author":"Meng","year":"2023","journal-title":"Waste Biomass Valorization"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Qin, C., Wang, D., Han, H., Cao, Y., Wang, X., Xuan, Z., Wei, M., Li, Z., and Liu, Q. (2024). Expression patterns of housekeeping genes and tissue-specific genes in black goats across multiple tissues. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-72844-8"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Zhang, T., Wang, T., Niu, Q., Xu, L., Chen, Y., Gao, X., Gao, H., Zhang, L., Liu, G.E., and Li, J. (2022). Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biol., 20.","DOI":"10.1186\/s12915-022-01269-4"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Laine, V.N., Verhagen, I., Mateman, A.C., Pijl, A., Williams, T.D., Gienapp, P., van Oers, K., and Visser, M.E. (2019). Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird. BMC Genom., 20.","DOI":"10.1186\/s12864-019-6043-0"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Li, B., Qing, T., Zhu, J., Wen, Z., Yu, Y., Fukumura, R., Zheng, Y., Gondo, Y., and Shi, L. (2017). A comprehensive mouse transcriptomic BodyMap across 17 tissues by RNA-seq. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-04520-z"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"3230","DOI":"10.1038\/ncomms4230","article-title":"A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages","volume":"5","author":"Yu","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"Fagerberg","year":"2015","journal-title":"Science"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Zhu, J., Chen, G., Zhu, S., Li, S., Wen, Z., Li, B., Zheng, Y., and Shi, L. (2016). Identification of tissue-specific protein-coding and noncoding transcripts across 14 human tissues using RNA-seq. Sci. Rep., 6.","DOI":"10.1038\/srep28400"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1016\/j.tig.2013.05.010","article-title":"Human housekeeping genes, revisited","volume":"29","author":"Eisenberg","year":"2013","journal-title":"Trends Genet."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Jonge, H.J.M.D., Fehrmann, R.S.N., Bont, E.S.J.M.D., Hofstra, R.M.W., and Elst, A.T. (2007). Evidence Based Selection of Housekeeping Genes. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0000898"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Pan, X., Cai, J., Wang, Y., Xu, D., Jiang, Y., Gong, W., Tian, Y., Shen, Q., and Zhang, Z. (2022). Expression profile of housekeeping genes and tissue-specific genes in multiple tissues of pigs. Animals, 12.","DOI":"10.3390\/ani12243539"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1007\/s00109-003-0461-8","article-title":"Not just for housekeeping: Protein initiation and elongation factors in cell growth and tumorigenesis","volume":"81","author":"Thornton","year":"2003","journal-title":"J. Mol. Med."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/nature14427","article-title":"Structure of the human 80S ribosome","volume":"520","author":"Khatter","year":"2015","journal-title":"Nature"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Mathavan, S., Lee, S.G.P., Mak, A., Miller, L.D., Murthy, K.R.K., Govindarajan, K.R., Tong, Y., Wu, Y.L., Lam, S.H., and Yang, H. (2005). Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet., 1.","DOI":"10.1371\/journal.pgen.0010029"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1074\/jbc.RA118.004928","article-title":"The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3\u2013uS5 interaction","volume":"294","author":"Dionne","year":"2019","journal-title":"J. Biol. Chem."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Kuang, G., Tao, W., Zheng, S., Wang, X., and Wang, D. (2020). Genome-wide identification, evolution and expression of the complete set of cytoplasmic ribosomal protein genes in Nile Tilapia. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21041230"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Robson, A., Owens, N.D., Baserga, S.J., Khokha, M.K., and Griffin, J.N. (2016). Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Dev. Biol., 16.","DOI":"10.1186\/s12861-016-0138-5"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1007\/s10126-008-9104-y","article-title":"Translational machinery of senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.): Comparative sequence analysis of the complete set of 60s ribosomal proteins and their expression","volume":"10","author":"Matsuoka","year":"2008","journal-title":"Mar. Biotechnol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0378-1119(02)01183-6","article-title":"Translational machinery of channel catfish: II. Complementary DNA and expression of the complete set of 47 60S ribosomal proteins","volume":"305","author":"Patterson","year":"2003","journal-title":"Gene"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1016\/j.febslet.2014.03.024","article-title":"Diverse diseases from a ubiquitous process: The ribosomopathy paradox","volume":"588","author":"Armistead","year":"2014","journal-title":"FEBS Lett."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1002\/ajh.23807","article-title":"Exploiting pre-rRNA processing in D iamond B lackfan anemia gene discovery and diagnosis","volume":"89","author":"Farrar","year":"2014","journal-title":"Am. J. Hematol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Uechi, T., Nakajima, Y., Nakao, A., Torihara, H., Chakraborty, A., Inoue, K., and Kenmochi, N. (2006). Ribosomal protein gene knockdown causes developmental defects in zebrafish. 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