The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challen...The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.展开更多
Dysregulated expression of microRNAs （miRNAs） in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and o...Dysregulated expression of microRNAs （miRNAs） in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. The levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same species. Employing Solexa, we sequenced all serum miRNAs of healthy Chinese subjects and found over 100 and 91 serum miRNAs in male and female subjects, respectively. We also identified specific expression patterns of serum miRNAs for lung cancer, colorectal cancer, and diabetes, providing evidence that serum miRNAs contain fingerprints for various diseases. Two non-small cell lung cancer-specific serum miRNAs obtained by Solexa were further validated in an independent trial of 75 healthy donors and 152 cancer patients, using quantitative reverse transcription polymerase chain reaction assays. Through these analyses, we conclude that serum miRNAs can serve as potential biomarkers for the detection of various cancers and other diseases.展开更多
自2006年9月在上海召开的全国慢性胃炎研讨会制订了《中国慢性胃炎共识意见》以来，国际上有关慢性胃炎的诊疗出现了某些新进展，包括慢性胃炎的分级分期评估系统（Operative Link for Gastritis Assessment，OLGA）、欧洲《胃癌癌前状...自2006年9月在上海召开的全国慢性胃炎研讨会制订了《中国慢性胃炎共识意见》以来，国际上有关慢性胃炎的诊疗出现了某些新进展，包括慢性胃炎的分级分期评估系统（Operative Link for Gastritis Assessment，OLGA）、欧洲《胃癌癌前状态处理共识意见》、Maastricht-4共识提出幽门螺杆菌（Hpylori）与慢性胃炎和胃癌的关系及根除Hpylori的作用、慢性胃炎内镜和病理诊断手段的进步等均要求我们更新共识意见。展开更多
基金This work was funded by the National Key Research and Developmental Program of China(2018YFD1000104)This work is also supported by awards to R.X.,Y.H.,and H.C.from the National Key Research and Developmental Program of China(2017YFD0101702,2018YFD1000500,2019YFD1000500)+4 种基金the National Science Foundation of China(#31872063)the Special Support Program of Guangdong Province(2019TX05N193)the Key-Area Research and Development Program of Guangdong Province(2018B020202011)the Guangzhou Science and Technology Key Project(201804020063)Support to M.H.F.comes from the NSF Faculty Early Career Development Program(IOS-1942437).
文摘The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
基金Acknowledgments We thank Drs Fengyong Liu and Sheng Luan at UC Berkeley, USA, for their discussion and help with the writing of the manuscript. This work was supported by grants from the National Natural Science Foundation of China （no. 30225037, 30471991, 30570731）, National Basic Research Program of China （973 Program） （no. 2006CB503909, 2004CB518603）, the ＂111＂ Project, and the Natural Science Foundation of Jiangsu Province （no. BK2004082, BK2006714）.
文摘Dysregulated expression of microRNAs （miRNAs） in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. The levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same species. Employing Solexa, we sequenced all serum miRNAs of healthy Chinese subjects and found over 100 and 91 serum miRNAs in male and female subjects, respectively. We also identified specific expression patterns of serum miRNAs for lung cancer, colorectal cancer, and diabetes, providing evidence that serum miRNAs contain fingerprints for various diseases. Two non-small cell lung cancer-specific serum miRNAs obtained by Solexa were further validated in an independent trial of 75 healthy donors and 152 cancer patients, using quantitative reverse transcription polymerase chain reaction assays. Through these analyses, we conclude that serum miRNAs can serve as potential biomarkers for the detection of various cancers and other diseases.
文摘自2006年9月在上海召开的全国慢性胃炎研讨会制订了《中国慢性胃炎共识意见》以来，国际上有关慢性胃炎的诊疗出现了某些新进展，包括慢性胃炎的分级分期评估系统（Operative Link for Gastritis Assessment，OLGA）、欧洲《胃癌癌前状态处理共识意见》、Maastricht-4共识提出幽门螺杆菌（Hpylori）与慢性胃炎和胃癌的关系及根除Hpylori的作用、慢性胃炎内镜和病理诊断手段的进步等均要求我们更新共识意见。
