title: Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server.
abstract: Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
authors.forename: Carla
authors.initials: C
authors.lastname: Proietti
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
authors.forename: Martha
authors.initials: M
authors.lastname: Zakrzewski
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Watkins
authors.affiliation: Nestlé Research Centre, Vers-chez-les-Blanc, Lausanne, Switzerland.
authors.forename: Bernard
authors.initials: B
authors.lastname: Berger
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
authors.forename: Shihab
authors.initials: S
authors.lastname: Hasan
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
authors.forename: Champa N
authors.initials: CN
authors.lastname: Ratnatunga
authors.affiliation: The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
authors.forename: Marie-Jo
authors.initials: MJ
authors.lastname: Brion
authors.affiliation: Malaria Infection Biology and Immunity Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Crompton
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia.
authors.forename: John J
authors.initials: JJ
authors.lastname: Miles
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia.
authors.forename: Denise L
authors.initials: DL
authors.lastname: Doolan
authors.affiliation: QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
mesh_terms: D015496:CD4-Positive T-Lymphocytes / Q000502:physiology; D018414:CD8-Positive T-Lymphocytes / Q000502:physiology; D057225:Data Mining / Q000379:methods*; D005786:Gene Expression Regulation / Q000187:drug effects; D023281:Genomics / Q000379:methods*; D006790:Host-Parasite Interactions / Q000276:immunology; D006801:Humans; D015759:Ionomycin / Q000494:pharmacology; D008213:Lymphocyte Activation / Q000187:drug effects; D008288:Malaria / Q000276:immunology* / Q000469:parasitology; D015999:Multivariate Analysis; D010963:Plasmodium falciparum / Q000472:pathogenicity; D020543:Proteome; D012984:Software; D013601:T-Lymphocytes / Q000276:immunology* / Q000502:physiology; D014584:User-Computer Interface
chemical_list: D020543:Proteome; D015759:Ionomycin