GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.
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DOI：
10.1093/nar/gkac1066
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Song, Weihong
中科院分区：
文献类型：
--
作者：
Guo, Shipeng;Xu, Zhougeng;Dong, Xiangjun;Hu, Dongjie;Jiang, Yanshuang;Wang, Qunxian;Zhang, Jie;Zhou, Qian;Liu, Shengchun;Song, Weihong
Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.
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影响因子：
14.9
作者：
Kuleshov MV;Jones MR;Rouillard AD;Fernandez NF;Duan Q;Wang Z;Koplev S;Jenkins SL;Jagodnik KM;Lachmann A;McDermott MG;Monteiro CD;Gundersen GW;Ma'ayan A
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Ma'ayan A
影响因子：
14.9
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Gillespie M;Jassal B;Stephan R;Milacic M;Rothfels K;Senff-Ribeiro A;Griss J;Sevilla C;Matthews L;Gong C;Deng C;Varusai T;Ragueneau E;Haider Y;May B;Shamovsky V;Weiser J;Brunson T;Sanati N;Beckman L;Shao X;Fabregat A;Sidiropoulos K;Murillo J;Viteri G;Cook J;Shorser S;Bader G;Demir E;Sander C;Haw R;Wu G;Stein L;Hermjakob H;D'Eustachio P
通讯作者：
D'Eustachio P
影响因子：
14.9
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Martens M;Ammar A;Riutta A;Waagmeester A;Slenter DN;Hanspers K;A Miller R;Digles D;Lopes EN;Ehrhart F;Dupuis LJ;Winckers LA;Coort SL;Willighagen EL;Evelo CT;Pico AR;Kutmon M
通讯作者：
Kutmon M
影响因子：
14.9
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Kanehisa M;Sato Y;Kawashima M;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
Feng, Chenchen;Song, Chao;Li, Chunquan
通讯作者：
Li, Chunquan