Vercellini P, Viganò P, Somigliana E, Fedele L. Endometriosis: pathogenesis and treatment. Nat Rev Endocrinol. 2014;10:261–75. https://doi.org/10.1038/nrendo.2013.255.
Article CAS PubMed Google Scholar
Fung JN, Rogers PAW, Montgomery GW. Identifying the biological basis of GWAS hits for endometriosis1. Biol Reprod. 2015;92:1-12,87. https://doi.org/10.1095/biolreprod.114.126458.
Zhao L, Gu C, Ye M, Zhang Z, Han W, Fan W, et al. Identification of global transcriptome abnormalities and potential biomarkers in eutopic endometria of women with endometriosis: a preliminary study. Biomed Rep. 2017;6:654–62. https://doi.org/10.3892/br.2017.902.
Article CAS PubMed PubMed Central Google Scholar
Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes Dev. 2003;17:419–37. https://doi.org/10.1101/gad.1048803.
Article CAS PubMed Google Scholar
Garcia-Blanco MA, Baraniak AP, Lasda EL. Alternative splicing in disease and therapy. Nat Biotechnol. 2004;22:535–46. https://doi.org/10.1038/nbt964.
Article CAS PubMed Google Scholar
Fu R-H, Liu S-P, Huang S-J, Chen H-J, Chen P-R, Lin Y-H, et al. Aberrant alternative splicing events in Parkinson’s disease. Cell Transplant. 2013;22:653–61. https://doi.org/10.3727/096368912X655154.
Sun Y, Hu X. Aberrant alternative splicing in cancer: splicing events and their regulatory mechanisms (review). Int J Oncol. 2024;65:90. https://doi.org/10.3892/ijo.2024.5678.
Article CAS PubMed Google Scholar
Yang Q, Zhao J, Zhang W, Chen D, Wang Y. Aberrant alternative splicing in breast cancer. J Mol Cell Biol. 2019;11:920–9. https://doi.org/10.1093/jmcb/mjz033.
Article CAS PubMed PubMed Central Google Scholar
Fu X-D, Ares M. Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet. 2014;15:689–701. https://doi.org/10.1038/nrg3778.
Article CAS PubMed PubMed Central Google Scholar
Shilo A, Ben Hur V, Denichenko P, Stein I, Pikarsky E, Rauch J, et al. Splicing factor hnRNP A2 activates the Ras-MAPK-ERK pathway by controlling A-Raf splicing in hepatocellular carcinoma development. RNA. 2014;20:505–15. https://doi.org/10.1261/rna.042259.113.
Article CAS PubMed PubMed Central Google Scholar
Kono M, Kurita T, Yasuda S, Kono M, Fujieda Y, Bohgaki T, et al. Decreased expression of serine/arginine-rich splicing factor 1 in T cells from patients with active systemic lupus erythematosus accounts for reduced expression of RasGRP1 and DNA methyltransferase 1. Arthritis Rheumatol. 2018;70:2046–56. https://doi.org/10.1002/art.40585.
Article CAS PubMed Google Scholar
Su Y, Tian W, Cheng L, Yin L, He X, Wei X. Inhibition of IGF2BP1 attenuates the progression of endometriosis through PTBP1. Folia Histochem Cytobiol. 2024;62:25–36.
Article CAS PubMed Google Scholar
Abood A, Mesner LD, Jeffery ED, Murali M, Lehe MD, Saquing J, et al. Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. Am J Hum Genet. 2024;111:1914–31. https://doi.org/10.1016/j.ajhg.2024.07.003.
Article CAS PubMed PubMed Central Google Scholar
Tian C, Zhang Y, Tong Y, Kock KH, Sim DY, Liu F, et al. Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases. Nat Genet. 2024;56:2739–52. https://doi.org/10.1038/s41588-024-02019-8.
Article CAS PubMed PubMed Central Google Scholar
Bane K, Desouza J, Shetty D, Choudhary P, Kadam S, Katkam RR, et al. Endometrial DNA damage response is modulated in endometriosis. Hum Reprod. 2021;36:160–74. https://doi.org/10.1093/humrep/deaa255.
Article CAS PubMed Google Scholar
Sarsenova M, Boggavarapu NR, Kask K, Modhukur V, Samuel K, Karro H, et al. Hypoxic conditions affect transcriptome of endometrial stromal cells in endometriosis and promote TGFBI axis. Front Endocrinol (Lausanne). 2024;15. https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2024.1465393.
Frisendahl C, Tang Y, Boggavarapu NR, Peters M, Lalitkumar PG, Piltonen TT, et al. miR-193b-5p and miR-374b-5p are aberrantly expressed in endometriosis and suppress endometrial cell migration in vitro. Biomolecules. 2024;14:1400.
Article CAS PubMed PubMed Central Google Scholar
Zhang L, Feng Y, Zhang Y, Sun X, Ma Q, Ma F. The sweet relationship between the endometrium and protein glycosylation. Biomolecules. 2024;14:770.
Article CAS PubMed PubMed Central Google Scholar
Heldenbrand J, Ren Y, Asmann Y, Mainzer LS. Step-by-Step guide for downloading very large datasets to a supercomputer using the SRA Toolkit. 2017. https://doi.org/10.17504/protocols.io.kb6csre
Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta. 2023;2:e107. https://doi.org/10.1002/imt2.107.
Article CAS PubMed PubMed Central Google Scholar
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15. https://doi.org/10.1038/s41587-019-0201-4.
Article CAS PubMed PubMed Central Google Scholar
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10:giab008. https://doi.org/10.1093/gigascience/giab008.
Article CAS PubMed PubMed Central Google Scholar
Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30. https://doi.org/10.1093/bioinformatics/btt656.
Article CAS PubMed Google Scholar
Love M, Anders S, Huber M. Differential gene expression analysis based on the negative binomial distribution. Genome Biol. 2014;15:10–1186.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Article CAS PubMed PubMed Central Google Scholar
Pertea G, Pertea M. GFF utilities: GffRead and GffCompare. F1000Res. 2020;9:304.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. https://doi.org/10.1093/bioinformatics/bts635.
Article CAS PubMed Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323. https://doi.org/10.1186/1471-2105-12-323.
Article CAS PubMed PubMed Central Google Scholar
Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018;19:40. https://doi.org/10.1186/s13059-018-1417-1.
Article CAS PubMed PubMed Central Google Scholar
Schafer S, Miao K, Benson CC, Heinig M, Cook SA, Hubner N. Alternative splicing signatures in RNA-seq data: percent spliced in (PSI). Curr Protoc Hum Genet. 2015;87:11.16.1-11.16.14. https://doi.org/10.1002/0471142905.hg1116s87.
Comments (0)