Torre LA, Siegel RL, Ward EM, Jemal A (2015) Global cancer incidence and mortality rates and trends--an update. Cancer Epidemiol Biomark Prevent. 25:1–12. http://cebp.aacrjournals.org/cgi/doi/10.1158/1055-9965.EPI-15-0578
Blows FM, Driver KE, Schmidt MK, Broeks A, Van LFE, Wesseling J et al (2010) Subtyping of breast cancer by immunohistochemistry to investigate a relationship between subtype and short and long term survival: a collaborative analysis of data for 10, 159 cases from 12 studies. PLoS Med 7:e1000279
Article PubMed PubMed Central Google Scholar
Gellert P, Segal CV, Gao Q, López-Knowles E, Martin L, Dodson A et al (2016) Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation. Nat Commun. 7:13294. http://www.nature.com/articles/ncomms13294
Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW et al (2012) The life history of 21 breast cancers. Cell 149:994–1007
Article CAS PubMed PubMed Central Google Scholar
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X et al (2016) Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534:1–20. http://www.nature.com/doifinder/10.1038/nature17676
Pereira B, Chin S-F, Rueda OM, Vollan H-KM, Provenzano E, Bardwell HA et al (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun 7:11479. http://www.nature.com/doifinder/10.1038/ncomms11479
Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF et al (2012) Comprehensive molecular portraits of human breast tumours. Nature 490:61–70
Wang X, Fu L, Li X, Wu X, Zhu Z, Fu L et al (2011) Somatic mutations of the mixed-lineage leukemia 3 ( MLL3) gene in primary breast cancers. Pathol Oncol Res 3:429–433
Herz H, Mohan M, Garruss AS, Liang K, Takahashi Y, Mickey K et al (2012) Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev 2:2604–2620
Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD et al (2013) Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 51:310–25. https://linkinghub.elsevier.com/retrieve/pii/S1097276513005091
Hu D, Gao X, Morgan MA, Herz H, Smith ER, Shilatifard A (2013) The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. Mol Cell Biol 33:4745–4754
Article CAS PubMed PubMed Central Google Scholar
Cheng J, Blum R, Bowman C, Hu D, Shilatifard A, Shen S et al (2014) A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers. Mol Cell 53:979–992. http://www.ncbi.nlm.nih.gov/pubmed/24656132
Miller T, Krogan NJ, Dover J, Tempst P, Johnston M, Greenblatt JF et al (2001) COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci USA. https://doi.org/10.1073/pnas.231473398
Article PubMed PubMed Central Google Scholar
You JS, Jones PA (2012) Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22:9–20
Article CAS PubMed PubMed Central Google Scholar
Chen C, Liu Y, Rappaport AR, Kitzing T, Schultz N, Shroff AS et al (2014) MLL3 is a haploinsufficient 7q tumor suppressor in acute myeloid leukemia. Cancer Cell 25:652–665
Article PubMed PubMed Central Google Scholar
Jozwik KM, Chernukhin I, Serandour AA, Nagarajan S, Carroll JS (2016) FOXA1 directs H3K4 monomethylation at enhancers via recruitment of the methyltransferase MLL3. Cell Rep 17:2715–2723. https://doi.org/10.1016/j.celrep.2016.11.028
Article CAS PubMed PubMed Central Google Scholar
Gala K, Li Q, Sinha A, Razavi P, Dorso M, Sanchez-Vega F et al (2018) KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function. Oncogene 37:4692–4710. https://doi.org/10.1038/s41388-018-0273-5
Article CAS PubMed PubMed Central Google Scholar
Stauffer KM, Elion DL, Cook RS, Stricker T (2021) MLL3 is a de novo cause of endocrine therapy resistance. Cancer Med 1–20. https://onlinelibrary.wiley.com/doi/10.1002/cam4.4285
Ray Chaudhuri A, Callen E, Ding X, Gogola E, Duarte AA, Lee J et al (2016) Replication fork stability confers chemoresistance in BRCA-deficient cells. Nature 535:382–387. https://doi.org/10.1038/nature18325
Article CAS PubMed Google Scholar
Rampias T, Karagiannis D, Avgeris M, Polyzos A, Kokkalis A, Kanaki Z et al (2019) The lysine‐specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer. EMBO Reports 20:1–20. https://onlinelibrary.wiley.com/doi/10.15252/embr.201846821
Chang A, Liu L, Ashby JM, Wu D, Chen Y, O’Neill SS et al (2021) Recruitment of KMT2C/MLL3 to DNA damage sites mediates DNA Damage responses and regulates PARP inhibitor sensitivity in cancer. Cancer Res 81:3358–3373. http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-5472.CAN-21-0688
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21
Article CAS PubMed Google Scholar
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930
Article CAS PubMed Google Scholar
Ewels P, Magnusson M, Lundin S, Kaeller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048
Article CAS PubMed PubMed Central Google Scholar
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–21
Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J et al (2003) PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267–273. http://www.nature.com/articles/ng1180
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550
Article CAS PubMed PubMed Central Google Scholar
Zhou Y, Zhou B, Pache L, Chang M, Benner C, Chanda SK et al (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10:1–10. https://doi.org/10.1038/s41467-019-09234-6
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (San Diego, Calif) [cited 2014 Mar 26];48:240–248. http://www.ncbi.nlm.nih.gov/pubmed/19275939
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Article CAS PubMed PubMed Central Google Scholar
Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P (2015) Sambamba: fast processing of NGS alignment formats. Bioinformatics 31:2032–2034
Article CAS PubMed PubMed Central Google Scholar
Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T (2014) DeepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res 42:187–191
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO et al (2021) Twelve years of SAMtools and BCFtools. GigaScience 10:1–4
Stovner EB, Sætrom P (2019) Epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics 35:4392–4393
Article CAS PubMed Google Scholar
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) [cited 2014 Jul 9];26:841–842. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2832824&tool=pmcentrez&rendertype=abstract
Khan A, Mathelier A (2017) Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics 18:1–8
Hahne F, Ivanek R (2016) Visualizing Genomic Data Using Gviz and Bioconductor. pp 335–351. http://link.springer.com/10.1007/978-1-4939-3578-9_16
Yu G, Wang LG, He QY (2015) ChIP seeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31:2382–2383
Article CAS PubMed Google Scholar
Ye T, Krebs AR, Choukrallah M-A, Keime C, Plewniak F, Davidson I et al (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39:e35–e35. https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq1287
Yu G, Wang LG, Han Y, He QY (2012) ClusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16:284–287
Article CAS PubMed PubMed Central Google Scholar
Herrmann C, Van De Sande B, Potier D, Aerts S (2012) i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res 40:1–17
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P et al (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589
Article CAS PubMed PubMed Central Google Scholar
Győrffy B (2021) Survival analysis across the entire transcriptome identifies biomarkers with the highest prognostic power in breast cancer. Comput Struct Biotechnol J 19:4101–4109
Article PubMed PubMed Central Google Scholar
Tsakiri EN, Gumeni S, Iliaki KK, Benaki D, Vougas K, Sykiotis GP et al (2019) Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation. Aging Cell. https://doi.org/10.1111/acel.12845
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA et al (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data: figure 1. Cancer Discov 2:401–404. http://cancerdiscovery.aacrjournals.org/lookup/doi/10.1158/2159-8290.CD-12-0095
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO et al (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6:1–20. http://www.ncbi.nlm.nih.gov/pubmed/23550210%0A. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4160307
Van Keymeulen A, Rocha AS, Ousset M, Beck B, Bouvencourt G, Rock J et al (2011) Distinct stem cells contribute to mammary gland development and maintenance. Nature 479:189–193. http://www.ncbi.nlm.nih.gov/pubmed/21983963
Hollern DP, Swiatnicki MR, Andrechek ER (2018) Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers. PLoS Genet. https://doi.org/10.1371/journal.pgen.1007135
Article PubMed PubMed Central Google Scholar
Dankort D, Maslikowski B, Warner N, Kanno N, Kim H, Wang Z et al (2001) Grb2 and Shc adapter proteins play distinct roles in Neu (ErbB-2)-induced mammary tumorigenesis: implications for human breast cancer. Mol Cell Biol 21:1540–1551. http://mcb.asm.org/cgi/doi/10.1128/MCB.21.5.1540-1551.2001
Stewart TA, Pattengale PK, Leder P (1984) Spontaneous mammary adenocarcinomas transgenic mice that carry and express MTV/myc fusion genes. Cell 38:627–637
留言 (0)