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Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server.
- Source :
-
Scientific reports [Sci Rep] 2016 Dec 06; Vol. 6, pp. 38178. Date of Electronic Publication: 2016 Dec 06. - Publication Year :
- 2016
-
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.
- Subjects :
- CD4-Positive T-Lymphocytes physiology
CD8-Positive T-Lymphocytes physiology
Host-Parasite Interactions immunology
Humans
Ionomycin pharmacology
Lymphocyte Activation drug effects
Malaria parasitology
Multivariate Analysis
Plasmodium falciparum pathogenicity
Proteome
Software
T-Lymphocytes physiology
User-Computer Interface
Data Mining methods
Gene Expression Regulation drug effects
Genomics methods
Malaria immunology
T-Lymphocytes immunology
Subjects
Details
- Language :
- English
- ISSN :
- 2045-2322
- Volume :
- 6
- Database :
- MEDLINE
- Journal :
- Scientific reports
- Publication Type :
- Academic Journal
- Accession number :
- 27922118
- Full Text :
- https://doi.org/10.1038/srep38178