Zobrazit více v PubMed
Jones FC, et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012;484:55–61. doi: 10.1038/nature10944.
PubMed
DOI
PMC
Bustamante CD, et al. Natural selection on protein-coding genes in the human genome. Nature. 2005;437:1153–1157. doi: 10.1038/nature04240.
PubMed
DOI
Wang T, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350:1096–1101. doi: 10.1126/science.aac7041.
PubMed
DOI
PMC
Lieben L. Evolution: Redefining gene essentiality. Nat. Rev. Genet. 2016;17:66. doi: 10.1038/nrg.2015.23.
PubMed
DOI
Manuylov NL, Manuylova E, Avdoshina V, Tevosian S. Serdin1/Lrrc10 is dispensable for mouse development. Genesis. 2008;46:441–446. doi: 10.1002/dvg.20422.
PubMed
DOI
Brody MJ, Lee Y. The Role of Leucine-Rich Repeat Containing Protein 10 (LRRC10) in Dilated Cardiomyopathy. Front Physiol. 2016;7:337. doi: 10.3389/fphys.2016.00337.
PubMed
DOI
PMC
Strasser B, et al. Evolutionary origin and diversification of epidermal barrier proteins in amniotes. Mol. Biol. Evol. 2014;31:3194–3205. doi: 10.1093/molbev/msu251.
PubMed
DOI
PMC
Kawasaki K, Lafont AG, Sire JY. The evolution of milk casein genes from tooth genes before the origin of mammals. Mol. Biol. Evol. 2011;28:2053–2061. doi: 10.1093/molbev/msr020.
PubMed
DOI
Meredith RW, Gatesy J, Springer MS. Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. BMC Evol. Biol. 2013;13:20. doi: 10.1186/1471-2148-13-20.
PubMed
DOI
PMC
Ellegren H. Comparative genomics and the study of evolution by natural selection. Mol. Ecol. 2008;17:4586–4596. doi: 10.1111/j.1365-294X.2008.03954.x.
PubMed
DOI
Zhang G, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346:1311–1320. doi: 10.1126/science.1251385.
PubMed
DOI
PMC
Jarvis ED, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346:1320–1331. doi: 10.1126/science.1253451.
PubMed
DOI
PMC
Seebacher F. The evolution of metabolic regulation in animals. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 2018;224:195–203. doi: 10.1016/j.cbpb.2017.11.002.
PubMed
DOI
Hedrick MS, Hillman SS. What drove the evolution of endothermy? J. Exp. Biol. 2016;219:300–301. doi: 10.1242/jeb.128009.
PubMed
DOI
Roberts RM, Green JA, Schulz LC. The evolution of the placenta. Reproduction. 2016;152:R179–R189. doi: 10.1530/REP-16-0325.
PubMed
DOI
PMC
Vize PD, Smith HW. A Homeric view of kidney evolution: A reprint of H.W. Smith’s classic essay with a new introduction. Evolution of the kidney. 1943. Anat. Rec. A Disco. Mol. Cell Evol. Biol. 2004;277:344–354. doi: 10.1002/ar.a.20017.
PubMed
DOI
Poulson TL, McNabb FM, Folk RL. Uric acid: the main nitrogenous excretory product of birds. Science. 1970;170:98–99. doi: 10.1126/science.170.3953.98.a.
PubMed
DOI
Galperin MY, Koonin EV. From complete genome sequence to ‘complete’ understanding? Trends Biotechnol. 2010;28:398–406. doi: 10.1016/j.tibtech.2010.05.006.
PubMed
DOI
PMC
Galperin MY, Koonin EV. ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res. 2004;32:5452–5463. doi: 10.1093/nar/gkh885.
PubMed
DOI
PMC
Pawlowski K. Uncharacterized/hypothetical proteins in biomedical ‘omics’ experiments: is novelty being swept under the carpet? Brief. Funct. Genom. Proteomic. 2008;7:283–290. doi: 10.1093/bfgp/eln033.
PubMed
DOI
Doridot L, et al. Nitroso-redox balance and mitochondrial homeostasis are regulated by STOX1, a pre-eclampsia-associated gene. Antioxid. Redox Signal. 2014;21:819–834. doi: 10.1089/ars.2013.5661.
PubMed
DOI
PMC
Bonavita R, et al. Cep126 is required for pericentriolar satellite localisation to the centrosome and for primary cilium formation. Biol. Cell. 2014;106:254–267. doi: 10.1111/boc.201300087.
PubMed
DOI
PMC
Chen L, Wolf AB, Fu W, Li L, Akey JM. Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals. Cell. 2020;180:677–687.e616. doi: 10.1016/j.cell.2020.01.012.
PubMed
DOI
Posth C, et al. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe. Curr. Biol. 2016;26:827–833. doi: 10.1016/j.cub.2016.01.037.
PubMed
DOI
Rito T, et al. A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration. Sci. Rep. 2019;9:4728. doi: 10.1038/s41598-019-41176-3.
PubMed
DOI
PMC
Genomes Project, C. et al. A global reference for human genetic variation. Nature. 2015;526:68–74. doi: 10.1038/nature15393.
PubMed
DOI
PMC
Mafessoni F, et al. A high-coverage Neandertal genome from Chagyrskaya Cave. Proc. Natl Acad. Sci. USA. 2020;117:15132–15136. doi: 10.1073/pnas.2004944117.
PubMed
DOI
PMC
Prufer K, et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science. 2017;358:655–658. doi: 10.1126/science.aao1887.
PubMed
DOI
PMC
Prufer K, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014;505:43–49. doi: 10.1038/nature12886.
PubMed
DOI
PMC
Mafessoni F, Prufer K. Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans. Proc. Natl Acad. Sci. USA. 2017;114:E10256–E10257. doi: 10.1073/pnas.1716918114.
PubMed
DOI
PMC
Green RE, et al. A draft sequence of the Neandertal genome. Science. 2010;328:710–722. doi: 10.1126/science.1188021.
PubMed
DOI
PMC
Huerta-Sanchez E, et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 2014;512:194–197. doi: 10.1038/nature13408.
PubMed
DOI
PMC
Kong A, et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature. 2010;467:1099–1103. doi: 10.1038/nature09525.
PubMed
DOI
Tabula Muris C, et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature. 2018;562:367–372. doi: 10.1038/s41586-018-0590-4.
PubMed
DOI
PMC
Park J, et al. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science. 2018;360:758–763. doi: 10.1126/science.aar2131.
PubMed
DOI
PMC
Deutsch EW. The PeptideAtlas Project. Methods Mol. Biol. 2010;604:285–296. doi: 10.1007/978-1-60761-444-9_19.
PubMed
DOI
PMC
Huttlin EL, et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell. 2010;143:1174–1189. doi: 10.1016/j.cell.2010.12.001.
PubMed
DOI
PMC
Schmidt T, et al. ProteomicsDB. Nucleic Acids Res. 2018;46:D1271–D1281. doi: 10.1093/nar/gkx1029.
PubMed
DOI
PMC
Wang D, et al. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Mol. Syst. Biol. 2019;15:e8503. doi: 10.15252/msb.20188503.
PubMed
DOI
PMC
Li S, et al. Digging More Missing Proteins Using an Enrichment Approach with ProteoMiner. J. Proteome Res. 2017;16:4330–4339. doi: 10.1021/acs.jproteome.7b00353.
PubMed
DOI
Rinschen MM, et al. Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells. Proc. Natl Acad. Sci. USA. 2010;107:3882–3887. doi: 10.1073/pnas.0910646107.
PubMed
DOI
PMC
MacKenzie EL, Iwasaki K, Tsuji Y. Intracellular iron transport and storage: from molecular mechanisms to health implications. Antioxid. Redox Signal. 2008;10:997–1030. doi: 10.1089/ars.2007.1893.
PubMed
DOI
PMC
Ho HY, et al. Toca-1 mediates Cdc42-dependent actin nucleation by activating the N-WASP-WIP complex. Cell. 2004;118:203–216. doi: 10.1016/j.cell.2004.06.027.
PubMed
DOI
Kakimoto T, Katoh H, Negishi M. Regulation of neuronal morphology by Toca-1, an F-BAR/EFC protein that induces plasma membrane invagination. J. Biol. Chem. 2006;281:29042–29053. doi: 10.1074/jbc.M604025200.
PubMed
DOI
Lee J, Kim MS, Park SH, Jang YK. Tousled-like kinase 1 is a negative regulator of core transcription factors in murine embryonic stem cells. Sci. Rep. 2018;8:334. doi: 10.1038/s41598-017-18628-9.
PubMed
DOI
PMC
Zhang R, Thamm DH, Misra V. The effect of Zhangfei/CREBZF on cell growth, differentiation, apoptosis, migration, and the unfolded protein response in several canine osteosarcoma cell lines. BMC Vet. Res. 2015;11:22. doi: 10.1186/s12917-015-0331-y.
PubMed
DOI
PMC
Pardo M, et al. Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells. Sci. Rep. 2017;7:8157. doi: 10.1038/s41598-017-08456-2.
PubMed
DOI
PMC
Nilsson R, et al. Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis. Cell Metab. 2009;10:119–130. doi: 10.1016/j.cmet.2009.06.012.
PubMed
DOI
PMC
Tschop MH, et al. A guide to analysis of mouse energy metabolism. Nat. Methods. 2011;9:57–63. doi: 10.1038/nmeth.1806.
PubMed
DOI
PMC
West DB, Boozer CN, Moody DL, Atkinson RL. Dietary obesity in nine inbred mouse strains. Am. J. Physiol. 1992;262:R1025–R1032.
PubMed
Dunaief JL. Iron induced oxidative damage as a potential factor in age-related macular degeneration: the Cogan Lecture. Invest Ophthalmol. Vis. Sci. 2006;47:4660–4664. doi: 10.1167/iovs.06-0568.
PubMed
DOI
Sypes EE, et al. Higher Body Mass Index Is Associated with Iron Deficiency in Children 1 to 3 Years of Age. J. Pediatr. 2019;207:198–204 e191. doi: 10.1016/j.jpeds.2018.11.035.
PubMed
DOI
Kamat MA, et al. PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. Bioinformatics. 2019;35:4851–4853. doi: 10.1093/bioinformatics/btz469.
PubMed
DOI
PMC
Prins BP, et al. Genome-wide analysis of health-related biomarkers in the UK Household Longitudinal Study reveals novel associations. Sci. Rep. 2017;7:11008. doi: 10.1038/s41598-017-10812-1.
PubMed
DOI
PMC
Gopal SK, et al. YBX1/YB-1 induces partial EMT and tumourigenicity through secretion of angiogenic factors into the extracellular microenvironment. Oncotarget. 2015;6:13718–13730. doi: 10.18632/oncotarget.3764.
PubMed
DOI
PMC
Tang J, et al. Knockdown of TPT1-AS1 inhibits cell proliferation, cell cycle G1/S transition, and epithelial-mesenchymal transition in gastric cancer. Bosn. J. Basic Med. Sci. 2021;21:39–46.
PubMed
PMC
Ye Z, et al. ODC1 promotes proliferation and mobility via the AKT/GSK3beta/beta-catenin pathway and modulation of acidotic microenvironment in human hepatocellular carcinoma. Onco Targets Ther. 2019;12:4081–4092. doi: 10.2147/OTT.S198341.
PubMed
DOI
PMC
Meng Q, et al. Abrogation of glutathione peroxidase-1 drives EMT and chemoresistance in pancreatic cancer by activating ROS-mediated Akt/GSK3beta/Snail signaling. Oncogene. 2018;37:5843–5857. doi: 10.1038/s41388-018-0392-z.
PubMed
DOI
Xu C, et al. SPP1, analyzed by bioinformatics methods, promotes the metastasis in colorectal cancer by activating EMT pathway. Biomed. Pharmacother. 2017;91:1167–1177. doi: 10.1016/j.biopha.2017.05.056.
PubMed
DOI
Soldatov R, et al. Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 2019;364:eaas9536. doi: 10.1126/science.aas9536.
PubMed
DOI
Guan C, Ye C, Yang X, Gao J. A review of current large-scale mouse knockout efforts. Genesis. 2010;48:73–85.
PubMed
Wenger MJ, DellaValle DM, Murray-Kolb LE, Haas JD. Effect of iron deficiency on simultaneous measures of behavior, brain activity, and energy expenditure in the performance of a cognitive task. Nutr. Neurosci. 2019;22:196–206. doi: 10.1080/1028415X.2017.1360559.
PubMed
DOI
PMC
Blankenhaus B, et al. Ferritin regulates organismal energy balance and thermogenesis. Mol. Metab. 2019;24:64–79. doi: 10.1016/j.molmet.2019.03.008.
PubMed
DOI
PMC
Bogdan AR, Miyazawa M, Hashimoto K, Tsuji Y. Regulators of Iron Homeostasis: New Players in Metabolism, Cell Death, and Disease. Trends Biochem Sci. 2016;41:274–286. doi: 10.1016/j.tibs.2015.11.012.
PubMed
DOI
PMC
Wasserman DH, O’Doherty RM, Zinker BA. Role of the endocrine pancreas in control of fuel metabolism by the liver during exercise. Int J. Obes. Relat. Metab. Disord. 1995;19:S22–S30.
PubMed
Bhattacharya D, Azambuja AP, Simoes-Costa M. Metabolic Reprogramming Promotes Neural Crest Migration via Yap/Tead Signaling. Dev. Cell. 2020;53:199–211.e196. doi: 10.1016/j.devcel.2020.03.005.
PubMed
DOI
PMC
Manz DH, Blanchette NL, Paul BT, Torti FM, Torti SV. Iron and cancer: recent insights. Ann. N. Y Acad. Sci. 2016;1368:149–161. doi: 10.1111/nyas.13008.
PubMed
DOI
PMC
Yuan M, et al. N-myristoylation: from cell biology to translational medicine. Acta Pharm. Sin. 2020;41:1005–1015. doi: 10.1038/s41401-020-0388-4.
PubMed
DOI
PMC
Lin CY, et al. Membrane protein-regulated networks across human cancers. Nat. Commun. 2019;10:3131. doi: 10.1038/s41467-019-10920-8.
PubMed
DOI
PMC
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340.
PubMed
DOI
PMC
Carithers LJ, et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015;13:311–319. doi: 10.1089/bio.2015.0032.
PubMed
DOI
PMC
Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 2018;36:411–420. doi: 10.1038/nbt.4096.
PubMed
DOI
PMC
Formstecher E, et al. Protein interaction mapping: a Drosophila case study. Genome Res. 2005;15:376–384. doi: 10.1101/gr.2659105.
PubMed
DOI
PMC
Rain JC, et al. The protein-protein interaction map of Helicobacter pylori. Nature. 2001;409:211–215. doi: 10.1038/35051615.
PubMed
DOI
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008;26:1367–1372. doi: 10.1038/nbt.1511.
PubMed
DOI
Zhang X, et al. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat. Protoc. 2018;13:530–550. doi: 10.1038/nprot.2017.147.
PubMed
DOI
Go CD, et al. A proximity-dependent biotinylation map of a human cell. Nature. 2021;595:120–124. doi: 10.1038/s41586-021-03592-2.
PubMed
DOI
Ransick A, et al. Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Dev. Cell. 2019;51:399–413 e397. doi: 10.1016/j.devcel.2019.10.005.
PubMed
DOI
PMC
Stuart T, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177:1888–1902.e1821. doi: 10.1016/j.cell.2019.05.031.
PubMed
DOI
PMC
Wolock SL, Lopez R, Klein AM. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. Cell Syst. 2019;8:281–291.e289. doi: 10.1016/j.cels.2018.11.005.
PubMed
DOI
PMC
Wilson PC, et al. The single-cell transcriptomic landscape of early human diabetic nephropathy. Proc. Natl Acad. Sci. USA. 2019;116:19619–19625. doi: 10.1073/pnas.1908706116.
PubMed
DOI
PMC
Chung JJ, et al. Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury. J. Am. Soc. Nephrol. 2020;31:2341–2354. doi: 10.1681/ASN.2020020220.
PubMed
DOI
PMC
Schroeder AW, et al. NOVEL HUMAN KIDNEY CELL SUBSETS IDENTIFIED BY MUX-SEQ. Transplantation. 2020;104:S85. doi: 10.1097/01.tp.0000698680.69665.ce.
DOI
Weir JB. New methods for calculating metabolic rate with special reference to protein metabolism. J. Physiol. 1949;109:1–9. doi: 10.1113/jphysiol.1949.sp004363.
PubMed
DOI
PMC
Even PC, Mokhtarian A, Pele A. Practical aspects of indirect calorimetry in laboratory animals. Neurosci. Biobehav Rev. 1994;18:435–447. doi: 10.1016/0149-7634(94)90056-6.
PubMed
DOI
Concordet JP, Haeussler M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 2018;46:W242–W245. doi: 10.1093/nar/gky354.
PubMed
DOI
PMC
Shalem O, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–87. doi: 10.1126/science.1247005.
PubMed
DOI
PMC
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25:402–408. doi: 10.1006/meth.2001.1262.
PubMed
DOI
Beck T, Rowlands T, Shorter T, Brookes AJ. GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies. Nucleic Acids Res. 2023;51:D986–D993. doi: 10.1093/nar/gkac1017.
PubMed
DOI
PMC
Howe KL, et al. Ensembl 2021. Nucleic Acids Res. 2021;49:D884–D891. doi: 10.1093/nar/gkaa942.
PubMed
DOI
PMC