title: PMD: A Resource for Archiving and Analyzing Protein Microarray data.
abstract: Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Zhaowei
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Likun
authors.initials: L
authors.lastname: Huang
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Hainan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Shujuan
authors.initials: S
authors.lastname: Guo
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.|School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.affiliation: School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Shi-Hua
authors.initials: SH
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Ziqing
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.|The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
authors.forename: Jingfang
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.|State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China.|Bio-ID center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Sheng-Ce
authors.initials: SC
authors.lastname: Tao
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D040081:Protein Array Analysis / Q000379:methods*; D012984:Software; D064878:Web Browser
references.citation: Proteomics. 2003 Jan;3(1):56-63
references.pmid: 12548634
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8
references.pmid: 15608197
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5
references.pmid: 15608260
references.citation: Chembiochem. 2005 Jun;6(6):985-9
references.pmid: 15798991
references.citation: Nat Methods. 2005 Nov;2(11):851-6
references.pmid: 16278656
references.citation: Comb Chem High Throughput Screen. 2007 Sep;10(8):706-18
references.pmid: 18045082
references.citation: Nat Protoc. 2009;4(1):44-57
references.pmid: 19131956
references.citation: Acta Biochim Biophys Sin (Shanghai). 2011 Mar;43(3):161-71
references.pmid: 21257623
references.citation: PLoS Pathog. 2012;8(10):e1002972
references.pmid: 23093938
references.citation: Chem Biol. 2013 May 23;20(5):685-99
references.pmid: 23706635
references.citation: Elife. 2013;2:e00726
references.pmid: 24015356
references.citation: Mol Cell Proteomics. 2013 Oct;12(10):2804-19
references.pmid: 23824909
references.citation: Cell Rep. 2014 Dec 24;9(6):2317-29
references.pmid: 25497094
references.citation: Breast Cancer Res. 2015;17:36
references.pmid: 25848723
references.citation: Science. 2001 Sep 14;293(5537):2101-5
references.pmid: 11474067
references.citation: Nat Genet. 2001 Dec;29(4):365-71
references.pmid: 11726920
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references.pmid: 11752295
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):258-61
references.pmid: 12519996
references.citation: Drug Discov Today. 2002 Aug 1;7(15):815-22
references.pmid: 12546969