Bio-TDS: bioscience query tool discovery system
Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, b...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Gnimpieba, E. Z., VanDiermen, M. S., Gustafson, S. M., Conn, B., Lushbough, C. M. Tags: Database Issue Source Type: research
Proteome-pI: proteome isoelectric point database
Proteome-pI is an online database containing information about predicted isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography–mass spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kozlowski, L. P. Tags: Database Issue Source Type: research
jPOSTrepo: an international standard data repository for proteomes
Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researche...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S., Ishihama, Y. Tags: Database Issue Source Type: research
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data re...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Deutsch, E. W., Csordas, A., Sun, Z., Jarnuczak, A., Perez-Riverol, Y., Ternent, T., Campbell, D. S., Bernal-Llinares, M., Okuda, S., Kawano, S., Moritz, R. L., Carver, J. J., Wang, M., Ishihama, Y., Bandeira, N., Hermjakob, H., Vizcaino, J. A. Tags: Database Issue Source Type: research
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network. We further provided network comparison analysis for orthologous genes across the diploid...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: You, Q., Xu, W., Zhang, K., Zhang, L., Yi, X., Yao, D., Wang, C., Zhang, X., Zhao, X., Provart, N. J., Li, F., Su, Z. Tags: Database Issue Source Type: research
SoyNet: a database of co-functional networks for soybean Glycine max
Soybean (Glycine max) is a legume crop with substantial economic value, providing a source of oil and protein for humans and livestock. More than 50% of edible oils consumed globally are derived from this crop. Soybean plants are also important for soil fertility, as they fix atmospheric nitrogen by symbiosis with microorganisms. The latest soybean genome annotation (version 2.0) lists 56 044 coding genes, yet their functional contributions to crop traits remain mostly unknown. Co-functional networks have proven useful for identifying genes that are involved in a particular pathway or phenotype with various network algorit...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kim, E., Hwang, S., Lee, I. Tags: Database Issue Source Type: research
Rice SNP-seek database update: new SNPs, indels, and queries
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of H...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Mansueto, L., Fuentes, R. R., Borja, F. N., Detras, J., Abriol-Santos, J. M., Chebotarov, D., Sanciangco, M., Palis, K., Copetti, D., Poliakov, A., Dubchak, I., Solovyev, V., Wing, R. A., Hamilton, R. S., Mauleon, R., McNally, K. L., Alexandrov, N. Tags: Database Issue Source Type: research
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent vi...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N., Millar, A. H. Tags: Database Issue Source Type: research
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype–phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel h...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lv, Q., Lan, Y., Shi, Y., Wang, H., Pan, X., Li, P., Shi, T. Tags: Database Issue Source Type: research
AraPheno: a public database for Arabidopsis thaliana phenotypes
Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for mo...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Seren, U., Grimm, D., Fitz, J., Weigel, D., Nordborg, M., Borgwardt, K., Korte, A. Tags: Database Issue Source Type: research
PMDBase: a database for studying microsatellite DNA and marker development in plants
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying microsatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMDBase, which integrates large amounts of microsatellite DNAs from genome sequenced plant species and includes a web service for mic...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yu, J., Dossa, K., Wang, L., Zhang, Y., Wei, X., Liao, B., Zhang, X. Tags: Database Issue Source Type: research
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Jin, J., Tian, F., Yang, D.-C., Meng, Y.-Q., Kong, L., Luo, J., Gao, G. Tags: Database Issue Source Type: research
Plant Reactome: a resource for plant pathways and comparative analysis
Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (ric...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Naithani, S., Preece, J., D'Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., Wu, G., Fabregat, A., Elser, J. L., Weiser, J., Keays, M., Fuentes, A. M.-P., Petryszak, R., Stein, L. D., Ware, D., Jaiswal, P. Tags: Database Issue Source Type: research
PlaMoM: a comprehensive database compiles plant mobile macromolecules
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Guan, D., Yan, B., Thieme, C., Hua, J., Zhu, H., Boheler, K. R., Zhao, Z., Kragler, F., Xia, Y., Zhang, S. Tags: Database Issue Source Type: research
PIECE 2.0: an update for the plant gene structure comparison and evolution database
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wang, Y., Xu, L., Thilmony, R., You, F. M., Gu, Y. Q., Coleman-Derr, D. Tags: Database Issue Source Type: research
