Liu X, Zhang J, Xie W (2022) The role of ferroptosis in acute lung injury. Mol Cell Biochem 477:1453–1461. https://doi.org/10.1007/s11010-021-04327-7
Gonçalves-de-Albuquerque CF, Silva AR, Burth P, et al (2015) Acute Respiratory Distress Syndrome: Role of Oleic Acid-Triggered Lung Injury and Inflammation. Mediators Inflamm 2015:260465. https://doi.org/10.1155/2015/260465
He Y-Q, Zhou C-C, Yu L-Y, et al (2021) Natural product derived phytochemicals in managing acute lung injury by multiple mechanisms. Pharmacol Res 163:105224. https://doi.org/10.1016/j.phrs.2020.105224
Mokra D, Mikolka P, Kosutova P, Mokry J (2019) Corticosteroids in Acute Lung Injury: The Dilemma Continues. Int J Mol Sci 20:4765. https://doi.org/10.3390/ijms20194765
Mowery NT, Terzian WTH, Nelson AC (2020) Acute lung injury. Curr Probl Surg 57:100777. https://doi.org/10.1016/j.cpsurg.2020.100777
Matthay MA, Zemans RL, Zimmerman GA, et al (2019) Acute respiratory distress syndrome. Nat Rev Dis Primers 5:18. https://doi.org/10.1038/s41572-019-0069-0.
Zhang H, Wang Z, Liu R, et al (2018) Reactive oxygen species stimulated pulmonary epithelial cells mediate the alveolar recruitment of FasL+ killer B cells in LPS-induced acute lung injuries. J Leukoc Biol 104:1187–1198. https://doi.org/10.1002/JLB.3A0218-075R
Nadeem A, Al-Harbi NO, Ahmad SF, Ibrahim KE, Siddiqui N, Al-Harbi MM (2018) Glucose-6-phosphate dehydrogenase inhibition attenuates acute lung injury through reduction in NADPH oxidase-derived reactive oxygen species. Clin Exp Immunol 191:279–287. https://doi.org/10.1111/cei.13097
Fan K, Lin L, Ai Q, et al (2018) Lipopolysaccharide-Induced Dephosphorylation of AMPK-Activated Protein Kinase Potentiates Inflammatory Injury via Repression of ULK1-Dependent Autophagy. Front Immunol 9:1464. https://doi.org/10.3389/fimmu.2018.01464
Zhang D, Zhou J, Ye LC, et al (2018) Autophagy maintains the integrity of endothelial barrier in LPS-induced lung injury. J Cell Physiol 233:688–698. https://doi.org/10.1002/jcp.25928
Lee S, Piao C, Kim G, Kim JY, Choi E, Lee M (2018) Production and application of HMGB1 derived recombinant RAGE-antagonist peptide for anti-inflammatory therapy in acute lung injury. Eur J Pharm Sci. 114:275-284. https://doi.org/10.1016/j.ejps.2017.12.019
Shi L, Dong N, Ji D, Huang X, Ying Z, Wang X, Chen C (2018) Lipopolysaccharide-induced CCN1 production enhances interleukin-6 secretion in bronchial epithelial cells. Cell Biol Toxicol. 34(1):39-49. https://doi.org/10.1007/s10565-017-9401-1
Patel VJ, Biswas Roy S, Mehta HJ, Joo M, Sadikot RT (2018) Alternative and Natural Therapies for Acute Lung Injury and Acute Respiratory Distress Syndrome. Biomed Res Int 2018:2476824. https://doi.org/10.1155/2018/2476824.
Artham S, Verma A, Newsome AS, Somanath PR (2020) Patients with acute respiratory distress syndrome exhibit increased stromelysin1 activity in the blood samples. Cytokine 131:155086. https://doi.org/10.1016/j.cyto.2020.155086
Mao K, Geng W, Liao Y, et al (2020) Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets. Aging (Albany NY) 12:18716–18740. https://doi.org/10.18632/aging.104042
Sciuto AM, Phillips CS, Orzolek LD, Hege AI, Moran TS, Dillman JF 3rd (2005) Genomic analysis of murine pulmonary tissue following carbonyl chloride inhalation. Chem Res Toxicol 18:1654–60. https://doi.org/10.1021/tx050126f.
Wu Z, Hai E, Di Z, et al (2020) Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat. PLoS One 15:e0243507. https://doi.org/10.1371/journal.pone.0243507
Liang J-W, Fang Z-Y, Huang Y, et al (2018) Application of Weighted Gene Co-Expression Network Analysis to Explore the Key Genes in Alzheimer’s Disease. J Alzheimers Dis 65:1353–1364. https://doi.org/10.3233/JAD-180400
Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559. https://doi.org/10.1186/1471-2105-9-559
Conesa A, Nueda MJ, Ferrer A, Talón M (2006) maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22:1096–102. https://doi.org/10.1093/bioinformatics/btl056
Yin L, Wang Y, Guo X, Xu C, Yu G (2018) Comparison of gene expression in liver regeneration and hepatocellular carcinoma formation. Cancer Manag Res 10:5691–708. https://doi.org/10.2147/CMAR.S172945.
Tong Y, Song Y, Xia C, Deng S (2020) Theoretical and in silico Analyses Reveal MYC as a Dynamic Network Biomarker in Colon and Rectal Cancer. Front Genet 11:555540. https://doi.org/10.3389/fgene.2020.555540
Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD (2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 28(6):882-883.https://doi.org/10.1093/bioinformatics/bts034.
Peng X-Y, Wang Y, Hu H, Zhang X-J, Li Q (2019) Identification of the molecular subgroups in coronary artery disease by gene expression profiles. J Cell Physiol 10.1002/jcp.28324. https://doi.org/10.1002/jcp.28324.
David CC, Jacobs DJ (2014) Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol 1084:193–226. https://doi.org/10.1007/978-1-62703-658-0_11
Zhou Y, Zhou B, Pache L, et al (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10:1523. https://doi.org/10.1038/s41467-019-09234-6
Al-Mansour MR, Wu J, Gagnon G, Knee A, Romanelli JR, Seymour NE (2021) Linear versus volumetric CT analysis in predicting tension-free fascial closure in abdominal wall reconstruction. Hernia 25:91–8. https://doi.org/10.1007/s10029-020-02349-6
Li J, Zhou D, Qiu W, et al (2018) Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design. Sci Rep 8:622. https://doi.org/10.1038/s41598-017-18705-z
Cao F, Wang C, Long D, Deng Y, Mao K, Zhong H (2021) Network-Based Integrated Analysis of Transcriptomic Studies in Dissecting Gene Signatures for LPS-Induced Acute Lung Injury. Inflammation 44(6):2486-2498. doi:10.1007/s10753-021-01518-8
Ganesh SK, Joo J, Skelding K, et al (2011) Time course analysis of gene expression identifies multiple genes with differential expression in patients with in-stent restenosis. BMC Med Genomics 4:20. https://doi.org/10.1186/1755-8794-4-2
Haspel JA, Chettimada S, Shaik RS, et al (2014) Circadian rhythm reprogramming during lung inflammation. Nat Commun 5:4753. https://doi.org/10.1038/ncomms5753
Yu D, Fang X, Xu Y, et al (2019) Rev-erbα can regulate the NF-κB/NALP3 pathway to modulate lipopolysaccharide-induced acute lung injury and inflammation. Int Immunopharmacol 73:312–320. https://doi.org/10.1016/j.intimp.2019.04.035
Huang S, Jiao X, Lu D, et al (2020) Recent advances in modulators of circadian rhythms: an update and perspective. J Enzyme Inhib Med Chem 35:1267–1286. https://doi.org/10.1080/14756366.2020.1772249
Lutkewitte AJ, Finck BN (2020) Regulation of Signaling and Metabolism by Lipin-mediated Phosphatidic Acid Phosphohydrolase Activity. Biomolecules 10:1386. https://doi.org/10.3390/biom10101386
Zeng C, Wen B, Hou G, et al (2017) Lipidomics profiling reveals the role of glycerophospholipid metabolism in psoriasis. Gigascience 6:1–11. https://doi.org/10.1093/gigascience/gix087
Wang K, Chen Y, Zhang P, Lin P, Xie N, Wu M (2019) Protective Features of Autophagy in Pulmonary Infection and Inflammatory Diseases. Cells 8:123. https://doi.org/10.3390/cells8020123
Vishnupriya S, Priya Dharshini LC, Sakthivel KM, Rasmi RR (2020) Autophagy markers as mediators of lung injury-implication for therapeutic intervention. Life Sci 260:118308. https://doi.org/10.1016/j.lfs.2020.118308
Liu KE, Frazier WA (2015) Phosphorylation of the BNIP3 C-Terminus Inhibits Mitochondrial Damage and Cell Death without Blocking Autophagy. PLoS One 10:e0129667. https://doi.org/10.1371/journal.pone.0129667
Zhang W, Zhang J (2017) Dexmedetomidine preconditioning protects against lung injury induced by ischemia-reperfusion through inhibition of autophagy. Exp Ther Med 14:973–980. https://doi.org/10.3892/etm.2017.4623
Chang SK, Noss EH, Chen M, et al (2011) Cadherin-11 regulates fibroblast inflammation. Proc Natl Acad Sci USA 108:8402–8407. https://doi.org/10.1073/pnas.1019437108
Schroer AK, Bersi MR, Clark CR, et al (2019) Cadherin-11 blockade reduces inflammation-driven fibrotic remodeling and improves outcomes after myocardial infarction. JCI Insight 4:e131545. https://doi.org/10.1172/jci.insight.131545
iang X, Wang X, Ding X, et al (2020) FAM134B oligomerization drives endoplasmic reticulum membrane scission for ER-phagy. EMBO J 39:e102608. https://doi.org/10.15252/embj.2019102608
Mo J, Chen J, Zhang B (2020) Critical roles of FAM134B in ER-phagy and diseases. Cell Death Dis 11:983. https://doi.org/10.1038/s41419-020-03195-1
Melchiotti R, Puan KJ, Andiappan AK, et al (2014) Genetic analysis of an allergic rhinitis cohort reveals an intercellular epistasis between FAM134B and CD39. BMC Med Genet 15:73. https://doi.org/10.1186/1471-2350-15-73
James MO, Ambadapadi S (2013) Interactions of cytosolic sulfotransferases with xenobiotics. Drug Metab Rev 45:401–14. https://doi.org/10.3109/03602532.2013.835613
Guo L, Yu F, Zhang T, Wu B (2018) The Clock Protein Bmal1 Regulates Circadian Expression and Activity of Sulfotransferase 1a1 in Mice. Drug Metab Dispos 46:1403–1410. https://doi.org/10.1124/dmd.118.082503
Sukumaran S, Almon RR, DuBois DC, Jusko WJ (2010) Circadian rhythms in gene expression: Relationship to physiology, disease, drug disposition and drug action. Adv Drug Deliv Rev 62:904–17. https://doi.org/10.1016/j.addr.2010.05.009
Kim JH, Rasaei R, Park S, Kim JY, Na S, Hong SH (2020) Altered Gene Expression Profiles in the Lungs of Streptozotocin-induced Diabetic Mice. Dev Reprod. 24(3):197-205. https://doi:10.12717/DR.2020.24.3.197.
Sadler AJ, Rossello FJ, Yu L, et al (2015) BTB-ZF transcriptional regulator PLZF modifies chromatin to restrain inflammatory signaling programs. Proc Natl Acad Sci U S A 112:1535–40. https://doi.org/10.1073/pnas.1409728112
Mokra D, Mikolka P, Kosutova P, Mokry J (2019) Corticosteroids in Acute Lung Injury: The Dilemma Continues. Int J Mol Sci 20:4765. https://doi.org/10.3390/ijms20194765