面向肿瘤精准医学的综合数据资源TCGA及其相关在线分析工具推荐
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摘要
癌症基因组图谱(TCGA)是一个公共资助的项目,旨在编目和发现引起癌变的主要人类基因组变化,目标是创建癌症基因组的全面"图谱"。TCGA数据库收录了多种癌症组学数据,包括转录组数据、表观遗传组学数据、基因突变数据和疾病样本临床数据等,为认识肿瘤发生的相关知识提供了丰富的资源,可以帮助科研人员更好地学习和认识癌症相关领域知识并促进肿瘤精准医学的实现。调查整理了TCGA数据在线分析工具并对其进行筛选推荐,可以帮助研究人员方便地进行TCGA数据分析。
TCGA,a public-funded project,is aimed at cataloguing and discovering the major human genome variations that induce canceration. Its goal is to establish a comprehensive cancer genome atlas. A variety of cancer genomics data are covered in TCGA database,including transcriptomics data,epigenomics data,gene mutation data,and disease sample clinical data,which provide a wealth of resources for understanding the knowledge in relation with tumorgenesis, and can thus help scientific researchers to effectively learn and understand cancer-related knowledge,and speed up the realization of oncology precision medicine. The online analysis tools of TCGA data were assessed in order to help scientific researchers to analyze the TCGA data.
TCGA,a public-funded project,is aimed at cataloguing and discovering the major human genome variations that induce canceration. Its goal is to establish a comprehensive cancer genome atlas. A variety of cancer genomics data are covered in TCGA database,including transcriptomics data,epigenomics data,gene mutation data,and disease sample clinical data,which provide a wealth of resources for understanding the knowledge in relation with tumorgenesis, and can thus help scientific researchers to effectively learn and understand cancer-related knowledge,and speed up the realization of oncology precision medicine. The online analysis tools of TCGA data were assessed in order to help scientific researchers to analyze the TCGA data.
引文
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[5]Samur M K,Yan Z,Wang X,et al.can Evolve:a web portal for integrative oncogenomics[J].PLo S One,2013,8(2):e56228.
[6]Madhavan S,Gusev Y,Natarajan TG,et al.Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse[J].Frontiers Genetics,2013,4:236.
[7]Li J,Lu Y,Akbani R,et al.TCPA:a resource for cancer functional proteomics data[J].Nature Methods,2013,10(11):1046-1047.
[8]Huang WY,Hsu SD,Huang HY,et al.Meth HC:a database of DNA methylation and gene expression in human cancer[J].Nucleic Acids Research,2015,43(Database issue):856-861.
[9]Yu KH,Fitzpatrick MR,Pappas L,et al.Omics Analy SIs System for PRecision Oncology(OASISPRO):a web-based omics analysis tool for clinical phenotype prediction[J].Bioinformatics,2017,34(2):319-320.
[10]Andreas S,Magali M,Rubayte R,et al.Onco Scape:exploring the cancer aberration landscape by genomic data fusion[J].Scientific Reports,2016,6(1):28103.
[11]Lee HJ,Palm J,Grimes SM,et al.The Cancer Genome Atlas Clinical Explorer:a web and mobile interface for identifying clinical-genomic driver associations[J].Genome Medicine,2015,7(1):1-14.
[12]Ryan M,Wong WC,Brown R,et al.TCGASplice Seq a compendium of alternative mRNA splicing in cancer[J].Nucleic Acids Research,2016,44(1):1018-1022.
[13]Porta-Pardo E,Hrabe T,Godzik A.Cancer3D:understanding cancer mutations through protein structures[J].Nucleic Acids Research,2015,43(1):968-973.
[14]Cerami E,Gao J,Dogrusoz U,et al.The c Bio cancer genomics portal:an open platform for exploring multidimensional cancer genomics data[J].Cancer Discovery,2012,2(5):401-404.
[15]Tang Z,Li C,Kang B,et al.GEPIA:a web server for cancer and normal gene expression profiling and interactive analyses[J].Nucleic Acids Research,2017,45(1):98-102.
[16]Gonzalez-Perez A,Perez-Llamas C,Deu-Pons J,et al.Int OGenmutations identifies cancer drivers across tumor types[J].Nature Methods,2013,10(11):1081-1082.
[17]Koch A,De TM,Jeschke J,et al.MEXPRESS:visualizing expression,DNA methylation and clinical TCGA data[J].BMC Genomics,2015,16(1):636.
[18]Goswami CP,Nakshatri H.PROGgene V2:enhancements on the existing database[J].BMC Cancer,2014,14:970.
[19]Li J,Han L,Roebuck P,et al.TANRIC:an interactive open platform to explore the function of lncRNAs in cancer[J].Cancer Research,2015,75(18):3728-3737.
[20]Huang ZZ,Duan HL,Li HM.Identification of gene expression pattern related to breast cancer survival using integrated TCGA datasets and genomic tools[J].Biomed Research International,2015(6):878546.
[21]Chandrashekar DS,Bashel B,Balasubramanya SAH,et al.UALCAN:a portal for facilitating tumor subgroup gene expression and survival analyses[J].Neoplasia,2017,19(8):649-658.
[22]Diez-Villanueva A,Mallona I,Peinado MA.Wanderer,an interactive viewer to explore DNA methylation and gene expression data in human cancer[J].Epigenetics Chromatin,2015,8(1):1-8.
[23]Zhu Y,Xu Y,Jr HD,et al.Zodiac:a comprehensive depiction of genetic interactions in cancer by integrating TCGA data[J].Journal of the National Cancer Insttitute,2015,107(8).
[24]Chang H,Han J,Borowsky A,et al.Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association[J].IEEE Transactions Medical Imaging,2013,32(4):670-682.
[25]Gutman DA,Cobb J,Somanna D,et al.Cancer Digital Slide Archive:an informatics resource to support integrated in silico analysis of TCGA pathology data[J].Journal of American Medical Informatics Association Jamia,2013,20(6):1091-1098.
[26]Ching KA,Wang K,Kan Z,et al.Cell Index Database(CELLX):a web tool for cancer precision medicine[J].Pacific Symposium on Biocomputing,2015:10-19.
[27]Spainhour J C G,Lim J,Qiu P.GDISC:a web portal for integrative analysis of gene-drug interaction for survival in cancer[J].Bioinformatics,2017,33(9):1426-1428.
[28]Bahceci I,Dogrusoz U,La KC,et al.Pathway Mapper:a collaborative visual web editor for cancer pathways and genomic data[J].Bioinformatics,2017,33(14):2238-2240.
[29]Clark K,Vendt B,Smith K,et al.The Cancer Imaging Archive(TCIA):maintaining and operating a public information repository[J].Journal of Digittal Imaging,2013,26(6):1045-1057.
[30]Huang PJ,Lee CC,Tan BC,et al.Vanno:a visualizationaided variant annotation tool[J].Human Mutation,2015,36(2):167-174.