Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048
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Abstract
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics organism description > plant |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab |
| Depositing User: | Matt Covey |
| Date: | 4 January 2018 |
| Date Deposited: | 01 Dec 2017 21:49 |
| Last Modified: | 20 Feb 2018 16:01 |
| PMCID: | PMC5753211 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/35682 |
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