ArticleBMC bioinformatics2009
AtPIN: Arabidopsis thaliana protein interaction network.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 117 citations in OpenAlex.
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- Genome-Wide Identification and Transcriptional Analysis of ArabidopsisInternational journal of molecular sciences · 2021Article
- Predictive Models of Genetic Redundancy in Arabidopsis thaliana.Molecular biology and evolution · 2021Article
- Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes.BMC genomics · 2021Article
- mPPI: a database extension to visualize structural interactome in a one-to-many manner.Database : the journal of biological databases and curation · 2021Article
- Co-expression Networks in Predicting Transcriptional Gene Regulation.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Interactomes: Experimental and In Silico Approaches.Advances in experimental medicine and biology · 2021Article
- Determinants of correlated expression of transcription factors and their target genes.Nucleic acids research · 2020Article
- Biased Gene Retention in the Face of Introgression Obscures Species Relationships.Genome biology and evolution · 2020Article
- Article
- PlaPPISite: a comprehensive resource for plant protein-protein interaction sites.BMC plant biology · 2020Article
- JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.BMC genomics · 2019Article
- Metatranscriptomic Analysis of Multiple Environmental Stresses Identifies RAP2.4 Gene Associated with Arabidopsis Immunity to Botrytis cinerea.Scientific reports · 2019Article
- TheFrontiers in plant science · 2019Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. DESCRIPTION: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C3) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening.
conclusionsAtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.