悟空云平台交流第28期---(O)PLS-DA模块
相比较于非监督的主成分分析，有牛人开发出了监督的PLS-DA和OPLS-DA模型，因此当你的数据结构比较复杂时，可以试试这类方法，来看看最后样本的分类效果。在这里，我们给大家介绍了如何在悟空云平台上实现操作这些模型，感兴趣的伙伴们可以来试试。往期的视频也可以参见悟空云平台的首页链接以及我们的微信公众号推文和视频号。最后也祝大家：阳历新年快乐，元旦快乐，新的一年实验顺利，投稿顺利，项目顺利！！！本系列视频会收录在我们公众号菜单：技术动态->悟空云系列讲座
使用悟空云平台，可在文章中如下描述：
1) 比如在正文Methods部分：We use 'Wu Kong' platform (https://www.omicsolution.com/wkomics/main/) for relative xxx analysis.
2) 比如在致谢(Acknowledgements)部分：Thank Dr. Shisheng Wang (West China Hospital, Sichuan University) and Dr. Chengpin Shen (Omicsolution Co., Ltd) for giving some advices about data analysis and 'Wu Kong' platform (https://www.omicsolution.com/wkomics/main/) for relative xxx analysis.
目前基于悟空平台开发的分析工具已发表以下文章：
1. (2020) Shisheng Wang , Wenxue Li, Liqiang Hu, Jingqiu Cheng, Hao Yang, Yansheng Liu, NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses, Nucleic Acids Research, gkaa498. (2021 IF: 19.16).
2. (2022) Huilin Yu, Haiyu Luo, Luping Chang, Shisheng Wang （共一作） , ..., Hao Yang, Wenying Fan & Bing-Qiao Zhao, The NEDD8-activating enzyme inhibitor MLN4924 reduces ischemic brain injury in mice. Proceedings of the National Academy of Sciences, 119(6). (2021 IF: 12.779).
3. (2021) Shisheng Wang , et al. StatsPro: Systematic integration and evaluation of statistical approaches for detecting differential expression in label-free quantitative proteomics, Journal of Proteomics, 10.1016/j.jprot.2021.104386. (2020 IF: 4.04).
4. (2021) Shisheng Wang , Yi Zhong, Jingqiu Cheng, Hao Yang, EnrichVisBox: A Versatile and Powerful Web Toolbox for Visualizing Complex Functional Enrichment Results of Omics Data, Journal of computational biology, 10.1089/cmb.2020.0564. (2020 IF: 1.479).
5. (2020) Shisheng Wang , Hongwen Zhu, Hu Zhou, Jingqiu Cheng and Hao Yang. MSpectraAI: a powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks. BMC Bioinformatics 21, 439 (2020). (2019 IF: 3.242).
6. (2019) Shisheng Wang , Yue Cai, Jingqiu Cheng, Wenxue Li, Yansheng Liu and Hao Yang. motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs. Proteomics: 201900245. (2018 IF: 3.106).
7. (2019) Shisheng Wang and Hao Yang. pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets. Proteomics: 1900264. (2018 IF: 3.106).
8. (2018) Shisheng Wang , ..., and Meng Gong. MetaboGroupS: A Group Entropy-Based Web Platform for Evaluating Normalization Methods in Blood Metabolomics Data from Maintenance Hemodialysis Patients. Anal Chem 90, 11124-11130. (2017 IF: 6.042).
9. (2018) Shisheng Wang , ..., and Hao Yang. MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data. Journal of computational biology : a journal of computational molecular cell biology 25, 1123-1127. (2017 IF: 1.191).
10. (2018) Qing-Run Li, Shi-Sheng Wang(共一作) , Hong-Wen Zhu, Fang-Ying Xia, Peter Roepstorff, Jia-Rui Wu, and Rong Zeng. Data-Independent Acquisition Mass Spectrometry to Localize Phosphosites. bioRxiv: 464545.
同时悟空平台整合上百个分析模块，包括且远不止以下功能
Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture
Yueting Xiong, ...,Hebin Liu,...,Xiaohui Liu EMBO Mol Med, IF12.3,2022
High-throughput site-specific N-glycoproteomics reveals glyco-signatures for liver disease diagnosis
Zhenyu Sun, et al. National Science Review , IF19,2022 Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer
Runqiu Yi, Liying Xie, Xiaoqing Wang, Chengpin Shen, Xiaojun Chen*, Liang Qiao*，Frontiers in Oncology，IF6.3,2022
Mesoporous Silica as Sorbents and Enzymatic Nanoreactors for Microbial Membrane Proteomics
J. Zhao, R. Jian, Y. Wang, B. Yang, D. Zhao, C. Shen, L. Qiao*, B. Liu*, ACS Applied Materials & Interfaces, IF9,2021
Direct MALDI-TOF Profiling of Gingival Crevicular Fluid Sediments for Periodontitis Diagnosis,
J. Yi, Y. Shen, Y. Yang, C. Shen, B. Liu, L. Qiao*, Y. Wang*, Talanta, IF5,2021
Proteomic and Metabolic Elucidation of Solar-Powered Biomanufacturing by Bio-Abiotic Hybrid System.
Rutan Zhang, ..., Chengpin Shen, ..., Liang Qiao Chem IF18,2020
In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics.
Yi Yang, ...,Chengpin Shen,... and Liang Qiao Nature Communications IF13,2020
Metaproteomics characterizes human gut microbiome function in colorectal cancer.
Shuping Long, ..., Chengpin Shen,.. and Liang Qiao npj Biofilms and Microbiomes IF5,2020