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               REFERENCES
               1.       Lauby-Secretan B, Scoccianti C, Loomis D, Grosse Y, Bianchini F, Straif K. Body fatness and cancer - viewpoint of the IARC
                   working group. N Engl J Med 2016;375:794-8.  DOI  PubMed  PMC
               2.       Doerner SK, Reis ES, Leung ES, et al. High-fat diet-induced complement activation mediates intestinal inflammation and neoplasia,
                   independent of obesity. Mol Cancer Res 2016;14:953-65.  DOI  PubMed  PMC
               3.       Goncalves MD, Lu C, Tutnauer J, et al. High-fructose corn syrup enhances intestinal tumor growth in mice. Science 2019;363:1345-9.
                   DOI  PubMed  PMC
               4.       Berger NA, Scacheri PC. Targeting Epigenetics to prevent obesity promoted cancers. Cancer Prev Res 2018;11:125-8.  DOI  PubMed
               5.       Li R, Grimm SA, Chrysovergis K, et al. Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling
                   cancer progression. Cell Metab 2014;19:702-11.  DOI  PubMed  PMC
               6.       Li R, Grimm SA, Mav D, et al. Transcriptome and DNA methylome analysis in a mouse model of diet-induced obesity predicts
                   increased risk of colorectal cancer. Cell Rep 2018;22:624-37.  DOI  PubMed  PMC
               7.       Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science
                   2012;336:736-9.  DOI  PubMed  PMC
               8.       Cohen AJ, Saiakhova A, Corradin O, et al. Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome. Nat
                   Commun 2017;8:14400.  DOI  PubMed  PMC
               9.       Surwit R, Feinglos M, Rodin J, et al. Differential effects of fat and sucrose on the development of obesity and diabetes in C57BL/6J
                   and mice. Metabolism 1995;44:645-51.  DOI  PubMed
               10.      Morton AR, Dogan-Artun N, Faber ZJ, et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell
                   2019;179:1330-1341.e13.  DOI  PubMed  PMC
               11.      Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover
                   protein-DNA interactions. Methods 2009;48:240-8.  DOI  PubMed  PMC
               12.      Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human
                   genome. Genome Biol 2009;10:R25.  DOI  PubMed  PMC
               13.      Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078-9.  DOI
                   PubMed  PMC
               14.      Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9:R137.  DOI
               15.      Amemiya HM, Kundaje A, Boyle AP. The ENCODE blacklist: identification of problematic regions of the genome. Sci Rep
                   2019;9:9354.  DOI  PubMed  PMC
               16.      Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.  DOI
               17.      Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic
                   Acids Res 2014;42:W187-91.  DOI  PubMed  PMC
               18.      Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and
                   exploration. Brief Bioinform 2013;14:178-92.  DOI  PubMed  PMC
               19.      Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-2.  DOI
                   PubMed  PMC
               20.      Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol
                   2014;15:550.  DOI  PubMed  PMC
               21.      Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15-21.  DOI  PubMed
                   PMC
               22.      Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript
                   resolution with RNA-seq. Nat Biotechnol 2013;31:46-53.  DOI  PubMed  PMC
               23.      McLean CY, Bristor D, Hiller M, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol
                   2010;28:495-501.  DOI  PubMed  PMC
               24.      Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting
                   functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019;47:D607-13.  DOI  PubMed  PMC
               25.      Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements
                   required for macrophage and B cell identities. Mol Cell 2010;38:576-89.  DOI  PubMed  PMC
               26.      Sethi JK, Vidal-Puig A. Wnt signalling and the control of cellular metabolism. Biochem J 2010;427:1-17.  DOI  PubMed  PMC
               27.      Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.  DOI  PubMed  PMC
               28.      Traverso N, Ricciarelli R, Nitti M, et al. Role of glutathione in cancer progression and chemoresistance. Oxid Med Cell Longev
                   2013;2013:972913.  DOI  PubMed  PMC
               29.      Kennedy L, Sandhu JK, Harper ME, Cuperlovic-Culf M. Role of glutathione in cancer: from mechanisms to therapies. Biomolecules
                   2020;10:1429.  DOI  PubMed  PMC
               30.      Beyaz S, Chung C, Mou H, et al. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal
                   tumorigenesis. Cell Stem Cell 2021;28:1922-1935.e5.  DOI  PubMed  PMC
               31.      Cheng C, Geng F, Cheng X, Guo D. Lipid metabolism reprogramming and its potential targets in cancer. Cancer Commun 2018;38:27.
                   DOI  PubMed  PMC
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