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Identification of Hub Genes and Typing of Tuberculosis Infections Based on Autophagy-Related Genes

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Abdulgader SM, Okunola AO, Ndlangalavu G, Reeve BWP, Allwood BW, Koegelenberg CFN, Warren RM, Theron G. Diagnosing tuberculosis: What do new technologies allow us to (not) do? Respiration. 2022;101(9):797–813. https://doi.org/10.1159/000525142 AbdulgaderSM OkunolaAO NdlangalavuG ReeveBWP AllwoodBW KoegelenbergCFN WarrenRM TheronG Diagnosing tuberculosis: What do new technologies allow us to (not) do? Respiration 2022 101 9 797 813 https://doi.org/10.1159/000525142 Search in Google Scholar

Adikesavalu H, Gopalaswamy R, Kumar A, Ranganathan UD, Shanmugam S. Autophagy induction as a host-directed therapeutic strategy against Mycobacterium tuberculosis infection. Medicina (Kaunas). 2021 May;57(6):522. https://doi.org/10.3390/medicina57060522 AdikesavaluH GopalaswamyR KumarA RanganathanUD ShanmugamS Autophagy induction as a host-directed therapeutic strategy against Mycobacterium tuberculosis infection Medicina (Kaunas) 2021 May 57 6 522 https://doi.org/10.3390/medicina57060522 Search in Google Scholar

Alers S, Löffler AS, Wesselborg S, Stork B. Role of AMPK-mTOR-Ulk1/2 in the regulation of autophagy: cross talk, shortcuts, and feedbacks. Mol Cell Biol. 2012 Jan;32(1):2–11. https://doi.org/10.1128/MCB.06159-11 AlersS LöfflerAS WesselborgS StorkB Role of AMPK-mTOR-Ulk1/2 in the regulation of autophagy: cross talk, shortcuts, and feedbacks Mol Cell Biol 2012 Jan 32 1 2 11 https://doi.org/10.1128/MCB.06159-11 Search in Google Scholar

Cai Y, Yang Q, Tang Y, Zhang M, Liu H, Zhang G, Deng Q, Huang J, Gao Z, Zhou B, et al. Increased complement C1q level marks active disease in human tuberculosis. PLoS One. 2014 Mar;9(3): e92340. https://doi.org/10.1371/journal.pone.0092340 CaiY YangQ TangY ZhangM LiuH ZhangG DengQ HuangJ GaoZ ZhouB Increased complement C1q level marks active disease in human tuberculosis PLoS One 2014 Mar 9 3 e92340 https://doi.org/10.1371/journal.pone.0092340 Search in Google Scholar

Cardona PJ. [Pathogenesis of tuberculosis and other mycobacteriosis] (in Spanish). Enferm Infecc Microbiol Clin. 2018 Jan;36(1):38–46. https://doi.org/10.1016/j.eimc.2017.10.015 CardonaPJ [Pathogenesis of tuberculosis and other mycobacteriosis] (in Spanish) Enferm Infecc Microbiol Clin 2018 Jan 36 1 38 46 https://doi.org/10.1016/j.eimc.2017.10.015 Search in Google Scholar

Chandra P, He L, Zimmerman M, Yang G, Köster S, Ouimet M, Wang H, Moore KJ, Dartois V, Schilling JD, et al. Inhibition of fatty acid oxidation promotes macrophage control of Mycobacterium tuberculosis. mBio. 2020 Jul;11(4):e01139–20. https://doi.org/10.1128/mBio.01139-20 ChandraP HeL ZimmermanM YangG KösterS OuimetM WangH MooreKJ DartoisV SchillingJD Inhibition of fatty acid oxidation promotes macrophage control of Mycobacterium tuberculosis mBio 2020 Jul 11 4 e01139 20 https://doi.org/10.1128/mBio.01139-20 Search in Google Scholar

Chen G, Wu B, Wu M, Liu F, Qin C, Luo W. Autophagy-related genes affect drug resistance of mycobacteria by regulating autophagy. Int J Clin Exp Pathol. 2019 Jun;12(6):2001–2008. ChenG WuB WuM LiuF QinC LuoW Autophagy-related genes affect drug resistance of mycobacteria by regulating autophagy Int J Clin Exp Pathol 2019 Jun 12 6 2001 2008 Search in Google Scholar

Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11. https://doi.org/10.1186/1752-0509-8-S4-S11 ChinCH ChenSH WuHH HoCW KoMT LinCY cytoHubba: identifying hub objects and sub-networks from complex interactome BMC Syst Biol 2014 8 Suppl 4 S11 https://doi.org/10.1186/1752-0509-8-S4-S11 Search in Google Scholar

Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med. 2019 Jul;11(1):45. https://doi.org/10.1186/s13073-019-0660-8 CohenKA MansonAL DesjardinsCA AbeelT EarlAM Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges Genome Med 2019 Jul 11 1 45 https://doi.org/10.1186/s13073-019-0660-8 Search in Google Scholar

Donald P, Kaufmann S, Thee S, Mandalakas AM, Lange C. Pathogenesis of tuberculosis: the 1930 Lübeck disaster revisited. Eur Respir Rev. 2022 Jun;31(164):220046. https://doi.org/10.1183/16000617.0046-2022 DonaldP KaufmannS TheeS MandalakasAM LangeC Pathogenesis of tuberculosis: the 1930 Lübeck disaster revisited Eur Respir Rev 2022 Jun 31 164 220046 https://doi.org/10.1183/16000617.0046-2022 Search in Google Scholar

Ghafouri-Fard S, Shoorei H, Mohaqiq M, Majidpoor J, Moosavi MA, Taheri M. Exploring the role of non-coding RNAs in autophagy. Autophagy. 2022 May;18(5):949–970. https://doi.org/10.1080/15548627.2021.1883881 Ghafouri-FardS ShooreiH MohaqiqM MajidpoorJ MoosaviMA TaheriM Exploring the role of non-coding RNAs in autophagy Autophagy 2022 May 18 5 949 970 https://doi.org/10.1080/15548627.2021.1883881 Search in Google Scholar

Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013 Jan;14:7. https://doi.org/10.1186/1471-2105-14-7 HänzelmannS CasteloR GuinneyJ GSVA: gene set variation analysis for microarray and RNA-seq data BMC Bioinformatics 2013 Jan 14 7 https://doi.org/10.1186/1471-2105-14-7 Search in Google Scholar

Huang HY, Lin YC, Cui S, Huang Y, Tang Y, Xu J, Bao J, Li Y, Wen J, Zuo H, et al. miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 2022 Jan;50(D1):D222–D230. https://doi.org/10.1093/nar/gkab1079 HuangHY LinYC CuiS HuangY TangY XuJ BaoJ LiY WenJ ZuoH miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions Nucleic Acids Res 2022 Jan 50 D1 D222 D230 https://doi.org/10.1093/nar/gkab1079 Search in Google Scholar

Huang Z, Shi J, Gao Y, Cui C, Zhang S, Li J, Zhou Y, Cui Q. HMDD v3.0: a database for experimentally supported human microRNA-disease associations. Nucleic Acids Res. 2019 Jan;47(D1): D1013–D1017. https://doi.org/10.1093/nar/gky1010 HuangZ ShiJ GaoY CuiC ZhangS LiJ ZhouY CuiQ HMDD v3.0: a database for experimentally supported human microRNA-disease associations Nucleic Acids Res 2019 Jan 47 D1 D1013 D1017 https://doi.org/10.1093/nar/gky1010 Search in Google Scholar

Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst Pharmacol. 2013 Oct;2(10):e79. https://doi.org/10.1038/psp.2013.56 ItoK MurphyD Application of ggplot2 to pharmacometric graphics CPT Pharmacometrics Syst Pharmacol 2013 Oct 2 10 e79 https://doi.org/10.1038/psp.2013.56 Search in Google Scholar

Jia KG, Feng G, Tong YS, Tao GZ, Xu L. miR-206 regulates non-small-cell lung cancer cell aerobic glycolysis by targeting hexokinase 2. J Biochem. 2020 Apr;167(4):365–370. https://doi.org/10.1093/jb/mvz099 JiaKG FengG TongYS TaoGZ XuL miR-206 regulates non-small-cell lung cancer cell aerobic glycolysis by targeting hexokinase 2 J Biochem 2020 Apr 167 4 365 370 https://doi.org/10.1093/jb/mvz099 Search in Google Scholar

Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res. 2021 May; 246:126674. https://doi.org/10.1016/j.micres.2020.126674 KanabalanRD LeeLJ LeeTY ChongPP HassanL IsmailR ChinVK Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery Microbiol Res 2021 May 246 126674 https://doi.org/10.1016/j.micres.2020.126674 Search in Google Scholar

Kang L, Guo N, Liu X, Wang X, Guo W, Xie SM, Liu C, Lv P, Xing L, Zhang X, et al. High mobility group box-1 protects against Aflatoxin G1-induced pulmonary epithelial cell damage in the lung inflammatory environment. Toxicol Lett. 2020 Oct;331:92–101. https://doi.org/10.1016/j.toxlet.2020.05.013 KangL GuoN LiuX WangX GuoW XieSM LiuC LvP XingL ZhangX High mobility group box-1 protects against Aflatoxin G1-induced pulmonary epithelial cell damage in the lung inflammatory environment Toxicol Lett 2020 Oct 331 92 101 https://doi.org/10.1016/j.toxlet.2020.05.013 Search in Google Scholar

Kaur T, Kapila S, Kapila R, Kumar S, Upadhyay D, Kaur M, Sharma C. Tmprss2 specific miRNAs as promising regulators for SARS-CoV-2 entry checkpoint. Virus Res. 2021 Mar;294:198275. https://doi.org/10.1016/j.virusres.2020.198275 KaurT KapilaS KapilaR KumarS UpadhyayD KaurM SharmaC Tmprss2 specific miRNAs as promising regulators for SARS-CoV-2 entry checkpoint Virus Res 2021 Mar 294 198275 https://doi.org/10.1016/j.virusres.2020.198275 Search in Google Scholar

Khan A, Jagannath C. Analysis of host-pathogen modulators of autophagy during Mycobacterium tuberculosis infection and therapeutic repercussions. Int Rev Immunol. 2017 Sep;36(5):271–286. https://doi.org/10.1080/08830185.2017.1356924 KhanA JagannathC Analysis of host-pathogen modulators of autophagy during Mycobacterium tuberculosis infection and therapeutic repercussions Int Rev Immunol 2017 Sep 36 5 271 286 https://doi.org/10.1080/08830185.2017.1356924 Search in Google Scholar

Khan MK, Islam MN, Ferdous J, Alam MM. An overview on epidemiology of tuberculosis. Mymensingh Med J. 2019 Jan;28(1): 259–266. KhanMK IslamMN FerdousJ AlamMM An overview on epidemiology of tuberculosis Mymensingh Med J 2019 Jan 28 1 259 266 Search in Google Scholar

Kim JK, Kim YS, Lee HM, Jin HS, Neupane C, Kim S, Lee SH, Min JJ, Sasai M, Jeong JH, et al. GABAergic signaling linked to autophagy enhances host protection against intracellular bacterial infections. Nat Commun. 2018 Oct;9(1):4184. https://doi.org/10.1038/s41467-018-06487-5 KimJK KimYS LeeHM JinHS NeupaneC KimS LeeSH MinJJ SasaiM JeongJH GABAergic signaling linked to autophagy enhances host protection against intracellular bacterial infections Nat Commun 2018 Oct 9 1 4184 https://doi.org/10.1038/s41467-018-06487-5 Search in Google Scholar

Kocak M, Ezazi Erdi S, Jorba G, Maestro I, Farrés J, Kirkin V, Martinez A, Pless O. Targeting autophagy in disease: established and new strategies. Autophagy. 2022 Mar;18(3):473–495. https://doi.org/10.1080/15548627.2021.1936359 KocakM Ezazi ErdiS JorbaG MaestroI FarrésJ KirkinV MartinezA PlessO Targeting autophagy in disease: established and new strategies Autophagy 2022 Mar 18 3 473 495 https://doi.org/10.1080/15548627.2021.1936359 Search in Google Scholar

Kumar S, Jain A, Choi SW, Peixoto Duarte da Silva G, Allers L, Mudd MH, Peters RS, Anonsen JH, Rusten TE, Lazarou M, et al. Mammalian Atg8-family proteins are upstream regulators of the lysosomalsystem by controlling MTOR and TFEB. Autophagy. 2020 Dec; 16(12):2305–2306. https://doi.org/10.1080/15548627.2020.1837423 KumarS JainA ChoiSW Peixoto Duarte da SilvaG AllersL MuddMH PetersRS AnonsenJH RustenTE LazarouM Mammalian Atg8-family proteins are upstream regulators of the lysosomalsystem by controlling MTOR and TFEB Autophagy 2020 Dec 16 12 2305 2306 https://doi.org/10.1080/15548627.2020.1837423 Search in Google Scholar

Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T, Cui Q. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 2014 Jan;42(D1):D1070–D1704. https://doi.org/10.1093/nar/gkt1023 LiY QiuC TuJ GengB YangJ JiangT CuiQ HMDD v2.0: a database for experimentally supported human microRNA and disease associations Nucleic Acids Res 2014 Jan 42 D1 D1070 D1704 https://doi.org/10.1093/nar/gkt1023 Search in Google Scholar

Lin Y, Duan Z, Xu F, Zhang J, Shulgina MV, Li F. Construction and analysis of the transcription factor-microRNA co-regulatory network response to Mycobacterium tuberculosis: a view from the blood. Am J Transl Res. 2017 Apr;9(4):1962–1976. LinY DuanZ XuF ZhangJ ShulginaMV LiF Construction and analysis of the transcription factor-microRNA co-regulatory network response to Mycobacterium tuberculosis: a view from the blood Am J Transl Res 2017 Apr 9 4 1962 1976 Search in Google Scholar

Liu C, Wu Z, Wang L, Yang Q, Huang J, Huang J. A mitophagy-related gene signature for subtype identification and prognosis prediction of hepatocellular carcinoma. Int J Mol Sci. 2022 Oct;23(20): 12123. https://doi.org/10.3390/ijms232012123 LiuC WuZ WangL YangQ HuangJ HuangJ A mitophagy-related gene signature for subtype identification and prognosis prediction of hepatocellular carcinoma Int J Mol Sci 2022 Oct 23 20 12123 https://doi.org/10.3390/ijms232012123 Search in Google Scholar

Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q. An analysis of human microRNA and disease associations. PLoS One. 2008;3(10):e3420. https://doi.org/10.1371/journal.pone.0003420 LuM ZhangQ DengM MiaoJ GuoY GaoW CuiQ An analysis of human microRNA and disease associations PLoS One 2008 3 10 e3420 https://doi.org/10.1371/journal.pone.0003420 Search in Google Scholar

Lu Y, Wang X, Dong H, Wang X, Yang P, Han L, Wang Y, Zheng Z, Zhang W, Zhang L. Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections. Exp Ther Med. 2019 May;17(5):3977–3988. https://doi.org/10.3892/etm.2019.7424 LuY WangX DongH WangX YangP HanL WangY ZhengZ ZhangW ZhangL Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections Exp Ther Med 2019 May 17 5 3977 3988 https://doi.org/10.3892/etm.2019.7424 Search in Google Scholar

Lukassen S, Chua RL, Trefzer T, Kahn NC, Schneider MA, Muley T, Winter H, Meister M, Veith C, Boots AW, et al. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J. 2020 May 18;39(10):e105114. https://doi.org/10.15252/embj.20105114 LukassenS ChuaRL TrefzerT KahnNC SchneiderMA MuleyT WinterH MeisterM VeithC BootsAW SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells EMBO J 2020 May 18 39 10 e105114 https://doi.org/10.15252/embj.20105114 Search in Google Scholar

Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003 Jul;34(3):267–273. https://doi.org/10.1038/ng1180 MoothaVK LindgrenCM ErikssonKF SubramanianA SihagS LeharJ PuigserverP CarlssonE RidderstråleM LaurilaE PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes Nat Genet 2003 Jul 34 3 267 273 https://doi.org/10.1038/ng1180 Search in Google Scholar

Muhammad JS, Nanjo S, Ando T, Yamashita S, Maekita T, Ushijima T, Tabuchi Y, Sugiyama T. Autophagy impairment by Helicobacter pylori-induced methylation silencing of MAP1LC3Av1 promotes gastric carcinogenesis. Int J Cancer. 2017 May;140(10): 2272–2283. https://doi.org/10.1002/ijc.30657 MuhammadJS NanjoS AndoT YamashitaS MaekitaT UshijimaT TabuchiY SugiyamaT Autophagy impairment by Helicobacter pylori-induced methylation silencing of MAP1LC3Av1 promotes gastric carcinogenesis Int J Cancer 2017 May 140 10 2272 2283 https://doi.org/10.1002/ijc.30657 Search in Google Scholar

Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019 Jul;37(7):773–782. https://doi.org/10.1038/s41587-019-0114-2 NewmanAM SteenCB LiuCL GentlesAJ ChaudhuriAA SchererF KhodadoustMS EsfahaniMS LucaBA SteinerD Determining cell type abundance and expression from bulk tissues with digital cytometry Nat Biotechnol 2019 Jul 37 7 773 782 https://doi.org/10.1038/s41587-019-0114-2 Search in Google Scholar

Ní Cheallaigh C, Keane J, Lavelle EC, Hope JC, Harris J. Autophagy in the immune response to tuberculosis: clinical perspectives. Clin Exp Immunol. 2011 Jun;164(3):291–300. https://doi.org/10.1111/j.1365-2249.2011.04381.x Ní CheallaighC KeaneJ LavelleEC HopeJC HarrisJ Autophagy in the immune response to tuberculosis: clinical perspectives Clin Exp Immunol 2011 Jun 164 3 291 300 https://doi.org/10.1111/j.1365-2249.2011.04381.x Search in Google Scholar

Ouimet M, Koster S, Sakowski E, Ramkhelawon B, van Solingen C, Oldebeken S, Karunakaran D, Portal-Celhay C, Sheedy FJ, Ray TD, et al. Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism. Nat Immunol. 2016 Jun;17(6):677–686. https://doi.org/10.1038/ni.3434 OuimetM KosterS SakowskiE RamkhelawonB van SolingenC OldebekenS KarunakaranD Portal-CelhayC SheedyFJ RayTD Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism Nat Immunol 2016 Jun 17 6 677 686 https://doi.org/10.1038/ni.3434 Search in Google Scholar

Pahari S, Negi S, Aqdas M, Arnett E, Schlesinger LS, Agrewala JN. Induction of autophagy through CLEC4E in combination with TLR4: an innovative strategy to restrict the survival of Mycobacterium tuberculosis. Autophagy. 2020 Jun;16(6):1021–1043. https://doi.org/10.1080/15548627.2019.1658436 PahariS NegiS AqdasM ArnettE SchlesingerLS AgrewalaJN Induction of autophagy through CLEC4E in combination with TLR4: an innovative strategy to restrict the survival of Mycobacterium tuberculosis Autophagy 2020 Jun 16 6 1021 1043 https://doi.org/10.1080/15548627.2019.1658436 Search in Google Scholar

Paik S, Kim JK, Chung C, Jo EK. Autophagy: A new strategy for host-directed therapy of tuberculosis. Virulence. 2019 Dec;10(1): 448–459. https://doi.org/10.1080/21505594.2018.1536598 PaikS KimJK ChungC JoEK Autophagy: A new strategy for host-directed therapy of tuberculosis Virulence 2019 Dec 10 1 448 459 https://doi.org/10.1080/21505594.2018.1536598 Search in Google Scholar

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr;43(7):e47. https://doi.org/10.1093/nar/gkv007 RitchieME PhipsonB WuD HuY LawCW ShiW SmythGK limma powers differential expression analyses for RNA-sequencing and microarray studies Nucleic Acids Res 2015 Apr 43 7 e47 https://doi.org/10.1093/nar/gkv007 Search in Google Scholar

Sampath P, Periyasamy KM, Ranganathan UD, Bethunaickan R. Monocyte and macrophage miRNA: Potent biomarker and target for host-directed therapy for tuberculosis. Front Immunol. 2021 Jun;12:667206. https://doi.org/10.3389/fimmu.2021.667206 SampathP PeriyasamyKM RanganathanUD BethunaickanR Monocyte and macrophage miRNA: Potent biomarker and target for host-directed therapy for tuberculosis Front Immunol 2021 Jun 12 667206 https://doi.org/10.3389/fimmu.2021.667206 Search in Google Scholar

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genom Res. 2003 Nov;13(11):2498–2504. https://doi.org/10.1101/gr.1239303 ShannonP MarkielA OzierO BaligaNS WangJT RamageD AminN SchwikowskiB IdekerT Cytoscape: A software environment for integrated models of biomolecular interaction networks Genom Res 2003 Nov 13 11 2498 2504 https://doi.org/10.1101/gr.1239303 Search in Google Scholar

Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, et al. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy. 2023 Jan;19(1):3–23. https://doi.org/10.1080/15548627.2021.2021495 ShariqM QuadirN AlamA ZarinS SheikhJA SharmaN SamalJ AhmadU KumariI HasnainSE The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection Autophagy 2023 Jan 19 1 3 23 https://doi.org/10.1080/15548627.2021.2021495 Search in Google Scholar

Sharma A, Machado E, Lima KVB, Suffys PN, Conceição EC. Tuberculosis drug resistance profiling based on machine learning: A literature review. Braz J Infect Dis. 2022 Jan–Feb;26(1):102332. https://doi.org/10.1016/j.bjid.2022.102332 SharmaA MachadoE LimaKVB SuffysPN ConceiçãoEC Tuberculosis drug resistance profiling based on machine learning: A literature review Braz J Infect Dis 2022 Jan–Feb 26 1 102332 https://doi.org/10.1016/j.bjid.2022.102332 Search in Google Scholar

Shen Y, Gao Y, Shi J, Huang Z, Dai R, Fu Y, Zhou Y, Kong W, Cui Q. MicroRNA-Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice. Genomics Proteomics Bioinf. 2022. https://doi.org/10.1016/j.gpb.2022.08.002 ShenY GaoY ShiJ HuangZ DaiR FuY ZhouY KongW CuiQ MicroRNA-Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice Genomics Proteomics Bioinf 2022 https://doi.org/10.1016/j.gpb.2022.08.002 Search in Google Scholar

Sinigaglia A, Peta E, Riccetti S, Venkateswaran S, Manganelli R, Barzon L. Tuberculosis-associated microRNAs: From pathogenesis to disease biomarkers. Cells. 2020 Sep;9(10):2160. https://doi.org/10.3390/cells9102160 SinigagliaA PetaE RiccettiS VenkateswaranS ManganelliR BarzonL Tuberculosis-associated microRNAs: From pathogenesis to disease biomarkers Cells 2020 Sep 9 10 2160 https://doi.org/10.3390/cells9102160 Search in Google Scholar

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005 Oct;102(43):15545–15550. https://doi.org/10.1073/pnas.0506580102 SubramanianA TamayoP MoothaVK MukherjeeS EbertBL GilletteMA PaulovichA PomeroySL GolubTR LanderES Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005 Oct 102 43 15545 15550 https://doi.org/10.1073/pnas.0506580102 Search in Google Scholar

Sun S, Shen Y, Wang J, Li J, Cao J, Zhang J. Identification and validation of autophagy-related genes in chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2021 Jan; 16:67–78. https://doi.org/10.2147/COPD.S288428 SunS ShenY WangJ LiJ CaoJ ZhangJ Identification and validation of autophagy-related genes in chronic obstructive pulmonary disease Int J Chron Obstruct Pulmon Dis 2021 Jan 16 67 78 https://doi.org/10.2147/COPD.S288428 Search in Google Scholar

Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023 Jan;51(D1):D638–D646. https://doi.org/10.1093/nar/gkac1000 SzklarczykD KirschR KoutrouliM NastouK MehryaryF HachilifR GableAL FangT DonchevaNT PyysaloS The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest Nucleic Acids Res 2023 Jan 51 D1 D638 D646 https://doi.org/10.1093/nar/gkac1000 Search in Google Scholar

Wang H, Sun HQ, Zhu X, Zhang L, Albanesi J, Levine B, Yin H. GABARAPs regulate PI4P-dependent autophagosome:lysosome fusion. Proc Natl Acad Sci USA. 2015 Jun;112(22):7015–7020. https://doi.org/10.1073/pnas.1507263112 WangH SunHQ ZhuX ZhangL AlbanesiJ LevineB YinH GABARAPs regulate PI4P-dependent autophagosome:lysosome fusion Proc Natl Acad Sci USA 2015 Jun 112 22 7015 7020 https://doi.org/10.1073/pnas.1507263112 Search in Google Scholar

Wei T, Simko V. R package ‘corrplot’: Visualization of a correlation matrix. (Version 0.92); 2021 [cited 2022 Dec 1]. Available from https://github.com/taiyun/corrplot WeiT SimkoV R package ‘corrplot’: Visualization of a correlation matrix. (Version 0.92) 2021 [cited 2022 Dec 1]. Available from https://github.com/taiyun/corrplot Search in Google Scholar

Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010 Jun;26(12):1572–1573. https://doi.org/10.1093/bioinformatics/btq170 WilkersonMD HayesDN ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking Bioinformatics 2010 Jun 26 12 1572 1573 https://doi.org/10.1093/bioinformatics/btq170 Search in Google Scholar

Yang L, Hu X, Chai X, Ye Q, Pang J, Li D, Hou T. Opportunities for overcoming tuberculosis: Emerging targets and their inhibitors. Drug Discov Today. 2022 Jan;27(1):326–336. https://doi.org/10.1016/j.drudis.2021.09.003 YangL HuX ChaiX YeQ PangJ LiD HouT Opportunities for overcoming tuberculosis: Emerging targets and their inhibitors Drug Discov Today 2022 Jan 27 1 326 336 https://doi.org/10.1016/j.drudis.2021.09.003 Search in Google Scholar

Yang T, Ge B. miRNAs in immune responses to Mycobacterium tuberculosis infection. Cancer Lett. 2018 Sep;431:22–30. https://doi.org/10.1016/j.canlet.2018.05.028 YangT GeB miRNAs in immune responses to Mycobacterium tuberculosis infection Cancer Lett 2018 Sep 431 22 30 https://doi.org/10.1016/j.canlet.2018.05.028 Search in Google Scholar

Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612. https://doi.org/10.1038/ncomms3612 YoshiharaK ShahmoradgoliM MartínezE VegesnaR KimH Torres-GarciaW TreviñoV ShenH LairdPW LevineDA Inferring tumour purity and stromal and immune cell admixture from expression data Nat Commun 2013 4 2612 https://doi.org/10.1038/ncomms3612 Search in Google Scholar

Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012 May;16(5):284–287. https://doi.org/10.1089/omi.2011.0118 YuG WangLG HanY HeQY clusterProfiler: an R package for comparing biological themes among gene clusters OMICS 2012 May 16 5 284 287 https://doi.org/10.1089/omi.2011.0118 Search in Google Scholar

Zhang MY, Huo C, Liu JY, Shi ZE, Zhang WD, Qu JJ, Yue YL, Qu YQ. Identification of a five autophagy subtype-related gene expression pattern for improving the prognosis of lung adenocarcinoma. Front Cell Dev Biol. 2021 Nov;9:756911. https://doi.org/10.3389/fcell.2021.756911 ZhangMY HuoC LiuJY ShiZE ZhangWD QuJJ YueYL QuYQ Identification of a five autophagy subtype-related gene expression pattern for improving the prognosis of lung adenocarcinoma Front Cell Dev Biol 2021 Nov 9 756911 https://doi.org/10.3389/fcell.2021.756911 Search in Google Scholar

Zhao S, Guo Y, Sheng Q, Shyr Y. Advanced heat map and clustering analysis using heatmap3. Biomed Res Int. 2014;2014:986048. https://doi.org/10.1155/2014/986048 ZhaoS GuoY ShengQ ShyrY Advanced heat map and clustering analysis using heatmap3 Biomed Res Int 2014 2014 986048 https://doi.org/10.1155/2014/986048 Search in Google Scholar

Zhou J, Lv J, Carlson C, Liu H, Wang H, Xu T, Wu F, Song C, Wang X, Wang T, et al. Trained immunity contributes to the prevention of Mycobacterium tuberculosis infection, a novel role of autophagy. Emerg Microbes Infect. 2021 Dec;10(1):578–588. https://doi.org/10.1080/22221751.2021.1899771 ZhouJ LvJ CarlsonC LiuH WangH XuT WuF SongC WangX WangT Trained immunity contributes to the prevention of Mycobacterium tuberculosis infection, a novel role of autophagy Emerg Microbes Infect 2021 Dec 10 1 578 588 https://doi.org/10.1080/22221751.2021.1899771 Search in Google Scholar

Zhu Q, Zhang Q, Gu M, Zhang K, Xia T, Zhang S, Chen W, Yin H, Yao H, Fan Y, et al. MIR106A-5p upregulation suppresses autophagy and accelerates malignant phenotype in nasopharyngeal carcinoma. Autophagy. 2021 Jul;17(7):1667–1683. https://doi.org/10.1080/15548627.2020.1781368 ZhuQ ZhangQ GuM ZhangK XiaT ZhangS ChenW YinH YaoH FanY MIR106A-5p upregulation suppresses autophagy and accelerates malignant phenotype in nasopharyngeal carcinoma Autophagy 2021 Jul 17 7 1667 1683 https://doi.org/10.1080/15548627.2020.1781368 Search in Google Scholar

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