{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:09:06Z","timestamp":1775873346055,"version":"3.50.1"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T00:00:00Z","timestamp":1720224000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82160389"],"award-info":[{"award-number":["82160389"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangxi Science and Technology Base and Talent Project","award":["2022AC19006"],"award-info":[{"award-number":["2022AC19006"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>As the most abundant messenger RNA (mRNA) modification, N6-methyladenosine (m6A) plays a crucial role in RNA fate, impacting cellular and physiological processes in various tumor types. However, our understanding of the role of the m6A methylome in tumor heterogeneity remains limited. Herein, we collected and analyzed m6A methylomes across nine human tissues from 97 m6A sequencing (m6A-seq) and RNA sequencing (RNA-seq) samples. Our findings demonstrate that m6A exhibits different heterogeneity in most tumor tissues compared to normal tissues, which contributes to the diverse clinical outcomes in different cancer types. We also found that the cancer type-specific m6A level regulated the expression of different cancer-related genes in distinct cancer types. Utilizing a novel and reliable method called \u201cm6A-express\u201d, we predicted m6A-regulated genes and revealed that cancer type-specific m6A-regulated genes contributed to the prognosis, tumor origin, and infiltration level of immune cells in diverse patient populations. Furthermore, we identified cell-specific m6A regulators that regulate cancer-specific m6A and constructed a regulatory network. Experimental validation was performed, confirming that the cell-specific m6A regulator CAPRIN1 controls the m6A level of TP53. Overall, our work reveals the clinical relevance of m6A in various tumor tissues and explains how such heterogeneity is established. These results further suggest the potential of m6A in cancer precision medicine for patients with different cancer types.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae052","type":"journal-article","created":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T04:07:36Z","timestamp":1720238856000},"source":"Crossref","is-referenced-by-count":21,"title":["Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1728-3791","authenticated-orcid":false,"given":"Yao","family":"Lin","sequence":"first","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6440-5106","authenticated-orcid":false,"given":"Jingyi","family":"Li","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]},{"name":"Department of Pathology, Guangdong Second Provincial General Hospital , Guangzhou 510317,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8099-6159","authenticated-orcid":false,"given":"Shuaiyi","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Anjin Biotechnology Co., Ltd. , Guangzhou 510000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5469-7080","authenticated-orcid":false,"given":"Yaxin","family":"Chen","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Research Center, West China Hospital, Department of Respiratory and Critical Care Medicine, Sichuan University , Chengdu 610041,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2640-4906","authenticated-orcid":false,"given":"Yueqi","family":"Li","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3951-942X","authenticated-orcid":false,"given":"Yixian","family":"Cun","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou 510080,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5268-5270","authenticated-orcid":false,"given":"Lei","family":"Tian","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8855-489X","authenticated-orcid":false,"given":"Yuanli","family":"Zhou","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2577-2897","authenticated-orcid":false,"given":"Yitong","family":"Chen","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2942-0490","authenticated-orcid":false,"given":"Jiemei","family":"Chu","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0216-7138","authenticated-orcid":false,"given":"Hubin","family":"Chen","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3753-7325","authenticated-orcid":false,"given":"Qiang","family":"Luo","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3246-0269","authenticated-orcid":false,"given":"Ruili","family":"Zheng","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7264-2457","authenticated-orcid":false,"given":"Gang","family":"Wang","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7534-5124","authenticated-orcid":false,"given":"Hao","family":"Liang","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7195-2832","authenticated-orcid":false,"given":"Ping","family":"Cui","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3177-213X","authenticated-orcid":false,"given":"Sanqi","family":"An","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Biosafety Level-3 Laboratory, Guangxi Medical University , Nanning 530021,","place":["China"]},{"name":"School of Basic Medical Sciences, Guangxi Medical University , Nanning 530021,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,7,5]]},"reference":[{"key":"2024102600012830900_qzae052-B1","doi-asserted-by":"crossref","first-page":"82\u2013","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","author":"ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium","year":"2020","journal-title":"Nature"},{"key":"2024102600012830900_qzae052-B2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.celrep.2018.03.064","article-title":"Pan-cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context","volume":"23","author":"Chiu","year":"2018","journal-title":"Cell Rep"},{"key":"2024102600012830900_qzae052-B3","doi-asserted-by":"crossref","first-page":"386\u2013","DOI":"10.1016\/j.cell.2018.03.027","article-title":"A pan-cancer analysis of enhancer expression in nearly 9000 patient samples","volume":"173","author":"Chen","year":"2018","journal-title":"Cell"},{"key":"2024102600012830900_qzae052-B4","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/s41698-019-0087-0","article-title":"Pan-cancer analysis connects tumor matrisome to immune response","volume":"3","author":"Bin Lim","year":"2019","journal-title":"NPJ Precis Oncol"},{"key":"2024102600012830900_qzae052-B5","doi-asserted-by":"crossref","first-page":"3667","DOI":"10.1038\/s41388-019-0683-z","article-title":"The m6A methyltransferase METTL3 promotes bladder cancer progression via AFF4\/NF-\u03baB\/MYC signaling network","volume":"38","author":"Cheng","year":"2019","journal-title":"Oncogene"},{"key":"2024102600012830900_qzae052-B6","doi-asserted-by":"crossref","first-page":"87","DOI":"10.2217\/epi-2019-0182","article-title":"Xue D. m6A RNA modification modulates gene expression and cancer-related pathways in clear cell renal cell carcinoma","volume":"12","author":"Chen","year":"2020","journal-title":"Epigenomics"},{"key":"2024102600012830900_qzae052-B7","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.molcel.2016.04.024","article-title":"METTL3 gains R\/W access to the epitranscriptome","volume":"62","author":"Schumann","year":"2016","journal-title":"Mol Cell"},{"key":"2024102600012830900_qzae052-B8","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41556-018-0045-z","article-title":"Recognition of RNA\u00a0N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation","volume":"20","author":"Huang","year":"2018","journal-title":"Nat Cell Biol"},{"key":"2024102600012830900_qzae052-B9","doi-asserted-by":"crossref","first-page":"4507","DOI":"10.1038\/s41388-020-1303-7","article-title":"YTHDF2 promotes the liver cancer stem cell phenotype and cancer metastasis by regulating OCT4 expression via m6A RNA methylation","volume":"39","author":"Zhang","year":"2020","journal-title":"Oncogene"},{"key":"2024102600012830900_qzae052-B10","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA modifications in cancer","volume":"20","author":"Barbieri","year":"2020","journal-title":"Nat Rev Cancer"},{"key":"2024102600012830900_qzae052-B11","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s12943-020-01263-w","article-title":"The role of m6A, m5C and \u03a8 RNA modifications in cancer: novel therapeutic opportunities","volume":"20","author":"Nombela","year":"2021","journal-title":"Mol Cancer"},{"key":"2024102600012830900_qzae052-B12","doi-asserted-by":"crossref","first-page":"e116","DOI":"10.1093\/nar\/gkab714","article-title":"m6A-express: uncovering complex and condition-specific m6A regulation of gene expression","volume":"49","author":"Zhang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024102600012830900_qzae052-B13","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1093\/nar\/gkz1206","article-title":"Integrative network analysis identifies cell-specific trans regulators of m6A","volume":"48","author":"An","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024102600012830900_qzae052-B14","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s12943-021-01362-2","article-title":"Comprehensive analyses of m6A regulators and interactive coding and non-coding RNAs across 32 cancer types","volume":"20","author":"Shen","year":"2021","journal-title":"Mol Cancer"},{"key":"2024102600012830900_qzae052-B15","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s12943-019-1066-3","article-title":"Molecular characterization and clinical relevance of m6A regulators across 33 cancer types","volume":"18","author":"Li","year":"2019","journal-title":"Mol Cancer"},{"key":"2024102600012830900_qzae052-B16","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1016\/j.molcel.2022.04.012","article-title":"Domain confusion 2: m6A-independent role of YTHDC2","volume":"82","author":"Larivera","year":"2022","journal-title":"Mol Cell"},{"key":"2024102600012830900_qzae052-B17","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41556-021-00656-3","article-title":"m6A-independent genome-wide METTL3 and METTL14 redistribution drives the senescence-associated secretory phenotype","volume":"23","author":"Liu","year":"2021","journal-title":"Nat Cell Biol"},{"key":"2024102600012830900_qzae052-B18","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/s41556-021-00835-2","article-title":"METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis","volume":"24","author":"Su","year":"2022","journal-title":"Nat Cell Biol"},{"key":"2024102600012830900_qzae052-B19","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/nprot.2012.148","article-title":"Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing","volume":"8","author":"Dominissini","year":"2013","journal-title":"Nat Protoc"},{"key":"2024102600012830900_qzae052-B20","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.cell.2019.06.013","article-title":"Deciphering the \u201cm6A code\u201d via antibody-independent quantitative profiling","volume":"178","author":"Garcia-Campos","year":"2019","journal-title":"Cell"},{"key":"2024102600012830900_qzae052-B21","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41392-020-00450-x","article-title":"The role of m6A modification in the biological functions and diseases","volume":"6","author":"Jiang","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2024102600012830900_qzae052-B22","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1038\/s41416-019-0429-2","article-title":"p53 expression status is associated with cancer-specific survival in stage III and high-risk stage II colorectal cancer patients treated with oxaliplatin-based adjuvant chemotherapy","volume":"120","author":"Oh","year":"2019","journal-title":"Br J Cancer"},{"key":"2024102600012830900_qzae052-B23","doi-asserted-by":"crossref","first-page":"2254","DOI":"10.1002\/hep.29683","article-title":"RNA\u00a0N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of\u00a0","volume":"67","author":"Chen","year":"2018","journal-title":"Hepatology"},{"key":"2024102600012830900_qzae052-B24","doi-asserted-by":"crossref","first-page":"e13168","DOI":"10.1111\/cpr.13168","article-title":"Insights into roles of METTL14 in tumors","volume":"55","author":"Liu","year":"2022","journal-title":"Cell Prolif"},{"key":"2024102600012830900_qzae052-B25","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41586-021-03536-w","article-title":"Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia","volume":"593","author":"Yankova","year":"2021","journal-title":"Nature"},{"key":"2024102600012830900_qzae052-B26","doi-asserted-by":"crossref","first-page":"1433323","DOI":"10.1155\/2022\/1433323","article-title":"29 m6A-RNA methylation (epitranscriptomic) regulators are regulated in 41 diseases including atherosclerosis and tumors potentially via ROS regulation \u2013 102 transcriptomic dataset analyses","volume":"2022","author":"Liu","year":"2022","journal-title":"J Immunol Res"},{"key":"2024102600012830900_qzae052-B27","doi-asserted-by":"crossref","first-page":"618374","DOI":"10.3389\/fonc.2020.618374","article-title":"Pan-cancer molecular characterization of m6A regulators and immunogenomic perspective on the tumor microenvironment","volume":"10","author":"Zhu","year":"2020","journal-title":"Front Oncol"},{"key":"2024102600012830900_qzae052-B28","doi-asserted-by":"crossref","first-page":"625797","DOI":"10.3389\/fgene.2021.625797","article-title":"Identification of m6A-associated RNA binding proteins using an integrative computational framework","volume":"12","author":"Zhang","year":"2021","journal-title":"Front Genet"},{"key":"2024102600012830900_qzae052-B29","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ccell.2020.04.017","article-title":"Targeting FTO suppresses cancer stem cell maintenance and immune evasion","volume":"38","author":"Su","year":"2020","journal-title":"Cancer Cell"},{"key":"2024102600012830900_qzae052-B30","doi-asserted-by":"crossref","first-page":"e2103628","DOI":"10.1002\/advs.202103628","article-title":"FIONA1-mediated m6A modification regulates the floral transition in\u00a0","volume":"9","author":"Xu","year":"2022","journal-title":"Adv Sci (Weinh)"},{"key":"2024102600012830900_qzae052-B31","doi-asserted-by":"crossref","first-page":"D1405\u2013","DOI":"10.1093\/nar\/gkaa811","article-title":"RMVar: an updated database of functional variants involved in RNA modifications","volume":"49","author":"Luo","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024102600012830900_qzae052-B32","doi-asserted-by":"crossref","first-page":"D1388\u2013","DOI":"10.1093\/nar\/gkac750","article-title":"RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication","volume":"51","author":"Song","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024102600012830900_qzae052-B33","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/j.gpb.2022.09.001","article-title":"m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues","volume":"21","author":"Song","year":"2023","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024102600012830900_qzae052-B34","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.7150\/thno.52717","article-title":"m6A regulator-based methylation modification patterns characterized by distinct tumor microenvironment immune profiles in colon cancer","volume":"11","author":"Chong","year":"2021","journal-title":"Theranostics"},{"key":"2024102600012830900_qzae052-B35","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/s41590-020-0650-4","article-title":"The RNA modification\u00a0N6-methyladenosine as a novel regulator of the immune system","volume":"21","author":"Shulman","year":"2020","journal-title":"Nat Immunol"},{"key":"2024102600012830900_qzae052-B36","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s12935-021-01868-1","article-title":"Role of m6A methyltransferase component VIRMA in multiple human cancers (Review)","volume":"21","author":"Zhu","year":"2021","journal-title":"Cancer Cell Int"},{"key":"2024102600012830900_qzae052-B37","doi-asserted-by":"crossref","first-page":"104019","DOI":"10.1016\/j.ebiom.2022.104019","article-title":"ALKBH5 regulates STAT3 activity to affect the proliferation and tumorigenicity of osteosarcoma via an m6A-YTHDF2-dependent manner","volume":"80","author":"Yang","year":"2022","journal-title":"EBioMedicine"},{"key":"2024102600012830900_qzae052-B38","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/s12943-019-1082-3","article-title":"YTHDF2 reduction fuels inflammation and vascular abnormalization in hepatocellular carcinoma","volume":"18","author":"Hou","year":"2019","journal-title":"Mol Cancer"},{"key":"2024102600012830900_qzae052-B39","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1016\/j.gendis.2021.12.005","article-title":"Systematic analysis of clinical relevance and molecular characterization of m6A in COVID-19 patients","volume":"9","author":"An","year":"2022","journal-title":"Genes Dis"},{"key":"2024102600012830900_qzae052-B40","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1186\/s13059-019-1915-9","article-title":"RADAR: differential analysis of MeRIP-seq data with a random effect model","volume":"20","author":"Zhang","year":"2019","journal-title":"Genome Biol"},{"key":"2024102600012830900_qzae052-B41","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/s41586-018-0538-8","article-title":"mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis","volume":"561","author":"Choe","year":"2018","journal-title":"Nature"},{"key":"2024102600012830900_qzae052-B42","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1038\/s41556-018-0174-4","article-title":"m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer","volume":"20","author":"Liu","year":"2018","journal-title":"Nat Cell Biol"},{"key":"2024102600012830900_qzae052-B43","doi-asserted-by":"crossref","first-page":"556497","DOI":"10.3389\/fonc.2020.556497","article-title":"Landscape of N6-methyladenosine modification patterns in human ameloblastoma","volume":"10","author":"Niu","year":"2020","journal-title":"Front Oncol"},{"key":"2024102600012830900_qzae052-B44","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.molcel.2019.09.032","article-title":"Landscape and regulation of m6A and m6Am methylome across human and mouse tissues","volume":"77","author":"Liu","year":"2020","journal-title":"Mol Cell"},{"key":"2024102600012830900_qzae052-B45","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12967-021-03204-7","article-title":"Integrated weighted gene coexpression network analysis identifies Frizzled 2 (FZD2) as a key gene in invasive malignant pleomorphic adenoma","volume":"20","author":"Han","year":"2022","journal-title":"J Transl Med"},{"key":"2024102600012830900_qzae052-B46","doi-asserted-by":"crossref","first-page":"127\u2013","DOI":"10.1016\/j.ccell.2016.11.017","article-title":"FTO plays an oncogenic role in acute myeloid leukemia as a\u00a0N6-methyladenosine RNA demethylase","volume":"31","author":"Li","year":"2017","journal-title":"Cancer Cell"},{"key":"2024102600012830900_qzae052-B47","doi-asserted-by":"crossref","first-page":"715674","DOI":"10.3389\/fcell.2021.715674","article-title":"Decreased m6A modification of CD34\/CD276(B7-H3) leads to immune escape in colon cancer","volume":"9","author":"Zhou","year":"2021","journal-title":"Front Cell Dev Biol"},{"key":"2024102600012830900_qzae052-B48","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/s12935-021-01839-6","article-title":"Comprehensive analysis of the transcriptome-wide m6A methylome in invasive malignant pleomorphic adenoma","volume":"21","author":"Han","year":"2021","journal-title":"Cancer Cell Int"},{"key":"2024102600012830900_qzae052-B49","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat Methods"},{"key":"2024102600012830900_qzae052-B50","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2024102600012830900_qzae052-B51","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.stem.2014.09.019","article-title":"m6A RNA modification controls cell fate transition in mammalian embryonic stem cells","volume":"15","author":"Batista","year":"2014","journal-title":"Cell Stem Cell"},{"key":"2024102600012830900_qzae052-B52","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature11112","article-title":"Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq","volume":"485","author":"Dominissini","year":"2012","journal-title":"Nature"},{"key":"2024102600012830900_qzae052-B53","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime\u00a0cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"2024102600012830900_qzae052-B54","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform"},{"key":"2024102600012830900_qzae052-B55","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"Hanzelmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2024102600012830900_qzae052-B56","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btq170","article-title":"ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking","volume":"26","author":"Wilkerson","year":"2010","journal-title":"Bioinformatics"},{"key":"2024102600012830900_qzae052-B57","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkm415","article-title":"DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists","volume":"35","author":"Huang","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2024102600012830900_qzae052-B58","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzae052\/58459010\/qzae052.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/4\/qzae052\/60094560\/qzae052.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/4\/qzae052\/60094560\/qzae052.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T20:02:45Z","timestamp":1729886565000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzae052\/7708393"}},"subtitle":[],"editor":[{"given":"Jianhua","family":"Yang","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,7,5]]},"references-count":58,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzae052","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.12.11.571179","asserted-by":"object"}]},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,8]]},"published":{"date-parts":[[2024,7,5]]},"article-number":"qzae052"}}