ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics

Computational and Structural Biotechnology Journal - Tập 18 - Trang 1695-1703 - 2020
George Minadakis1,2, Kleitos Sokratous1,3, George M. Spyrou1,2
1Department of Bioinformatics, The Cyprus Institute of Neurology & Genetics, 6 International Airport Avenue, 2370 Nicosia, P.O. Box 23462, 1683 Nicosia, Cyprus
2The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, 6 International Airport Avenue, 2370 Nicosia, P.O. Box 23462, 1683 Nicosia, Cyprus
3OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, UK

Tài liệu tham khảo

Efstathiou, 2017, ProteoSign: an end-user online differential proteomics statistical analysis platform, Nucleic Acids Res, 45, W300, 10.1093/nar/gkx444

Nolte, 2018, Instant Clue: a software suite for interactive data visualization and analysis, Sci Rep, 8, 12648, 10.1038/s41598-018-31154-6

Misra, 2018, Updates on resources, software tools, and databases for plant proteomics in 2016–2017, Electrophoresis, 39, 1543, 10.1002/elps.201700401

Qu, 2016, Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace, Nat Methods, 13, 245, 10.1038/nmeth.3732

Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, 13, 2498, 10.1101/gr.1239303

Ritchie, 2015, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, 43, 10.1093/nar/gkv007

Sales, 2011, parmigene—a parallel R package for mutual information estimation and gene network reconstruction, Bioinformatics, 27, 1876, 10.1093/bioinformatics/btr274

Kuleshov, 2016, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Res, 44, W90, 10.1093/nar/gkw377

Hastie, 1999, Botstein D: Imputing missing data for gene expression arrays, Stanford University Statistics Department Technical report

Troyanskaya, 2001, Missing value estimation methods for DNA microarrays, Bioinformatics, 17, 520, 10.1093/bioinformatics/17.6.520

Smyth, 2004, Linear models and empirical bayes methods for assessing differential expression in microarray experiments, Stat Appl Genet Mol Biol, 3, 1, 10.2202/1544-6115.1027

Faith, 2007, Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles, PLoS Biol, 5, 10.1371/journal.pbio.0050008

Altay, 2010, Inferring the conservative causal core of gene regulatory networks, BMC Syst Biol, 4, 132, 10.1186/1752-0509-4-132

Peng, 2005, Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy, IEEE Trans Pattern Anal Mach Intell, 1226, 10.1109/TPAMI.2005.159

Pons, 2005, Computing communities in large networks using random walks, 284

Clauset, 2004, Finding community structure in very large networks, Phys Rev E, 70, 10.1103/PhysRevE.70.066111

Newman, 2006, Finding community structure in networks using the eigenvectors of matrices, Phys Rev E, 74, 10.1103/PhysRevE.74.036104

Brandes, 2008, On modularity clustering, IEEE Trans Knowl Data Eng, 20, 172, 10.1109/TKDE.2007.190689

Tyanova, 2016, The Perseus computational platform for comprehensive analysis of (prote) omics data, Nat Methods, 13, 731, 10.1038/nmeth.3901

Weiner, 2018, Graphical interpretation and analysis of proteins and their ontologies (GiaPronto): A one-click graph visualization software for proteomics data sets, Mol Cell Proteomics, 17, 1426, 10.1074/mcp.TIR117.000438

Shi, 2013, NetGestalt: integrating multidimensional omics data over biological networks, Nat Methods, 10, 597, 10.1038/nmeth.2517

Kanehisa, 2002, The KEGG database, Silico Simul Biol Process, 247, 91, 10.1002/0470857897.ch8

Croft, 2010, Reactome: a database of reactions, pathways and biological processes, Nucleic Acids Res, 39, D691, 10.1093/nar/gkq1018

Emmert-Streib, 2011, Networks for systems biology: conceptual connection of data and function, IET Syst Biol, 5, 185, 10.1049/iet-syb.2010.0025

Najafi, 2014, Genome scale modeling in systems biology: algorithms and resources, Curr Genomics, 15, 130, 10.2174/1389202915666140319002221

Serin, 2016, Learning from co-expression networks: possibilities and challenges, Front Plant Sci, 7, 444, 10.3389/fpls.2016.00444