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. 2016 Jan 4;44(D1):D1189-94.
doi: 10.1093/nar/gkv1237. Epub 2015 Nov 17.

LegumeIP 2.0--a Platform for the Study of Gene Function and Genome Evolution in Legumes

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Free PMC article

LegumeIP 2.0--a Platform for the Study of Gene Function and Genome Evolution in Legumes

Jun Li et al. Nucleic Acids Res. .
Free PMC article

Abstract

The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea) and two outgroup reference species: Arabidopsis thaliana and Poplar trichocarpa. Moreover, the LegumeIP 2.0 features the following new data resources and bioinformatics tools: (i) an integrative gene expression atlas for four model legumes that include 550 array hybridizations from M. truncatula, 962 gene expression profiles of G. max, 276 array hybridizations from L. japonicas and 56 RNA-Seq-based gene expression profiles for C. arietinum. These datasets were manually curated and hierarchically organized based on Experimental Ontology and Plant Ontology so that users can browse, search, and retrieve data for their selected experiments. (ii) New functions/analytical tools to query, mine and visualize large-scale gene sequences, annotations and transcriptome profiles. Users may select a subset of expression experiments and visualize and compare expression profiles for multiple genes. The LegumeIP 2.0 database is freely available to the public at http://plantgrn.noble.org/LegumeIP/.

Figures

Figure 1.
Figure 1.
The Experimental Ontology and Plant Ontology treeview browser for selecting a subset of microarray or RNA-Seq experiments.
Figure 2.
Figure 2.
The comprehensive keyword search interface for retrieving genes’ expression in the user-selected experiments.
Figure 3.
Figure 3.
A table of retrieved gene expression profiles (A) and a plot of a gene's expression (B) in the user selected experiments.

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