ArticleBioinformatics and biology insights2009
Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case.
Article in Bioinformatics and biology insights, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins.International journal of molecular sciences · 2022Review
- Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives.International journal of molecular sciences · 2022Review
- Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response toPlants (Basel, Switzerland) · 2022Article
- Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review.Life (Basel, Switzerland) · 2021Review
- Conserved co-functional network between maize and Arabidopsis aid in the identification of seed defective genes in maize.Genes & genomics · 2021Article
- Physiological and Biochemical Traits of Two MajorFrontiers in plant science · 2021Article
- The Cell Wall Proteome ofFrontiers in plant science · 2021Article
- An integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations ofCells · 2020Article
- Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development.International journal of molecular sciences · 2019Article
- Transcriptomic and cell wall proteomic datasets of rosettes and floral stems from fiveData in brief · 2019Article
- Cell Wall Proteins Play Critical Roles in Plant Adaptation to Phosphorus Deficiency.International journal of molecular sciences · 2019Review
- Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes.BMC plant biology · 2016Article
- Article
- WallProtDB, a database resource for plant cell wall proteomics.Plant methods · 2015Article
- Review
- Proteomic analysis of tomato (Solanum lycopersicum) secretome.Journal of plant research · 2013Article
- Plant cell wall proteomics: the leadership of Arabidopsis thaliana.Frontiers in plant science · 2013Article
- PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.The Plant cell · 2011Article
- Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).
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