ArticleNucleic acids research2001
Chloroplast transit peptide prediction: a peek inside the black box.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 92 citations in OpenAlex.
- Chlamy_ChloroPred: a deep learning-based, highly accurate binary classifier for chloroplast protein prediction in the model microalga,Frontiers in microbiology · 2026Article
- Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing.PLoS computational biology · 2024Article
- Maize β-amylase7 encodes 2 proteins using alternative transcriptional start sites: Nuclear BAM7 and plastidic BAM2.Plant physiology · 2023Article
- Genome-wide identification, expression profile and evolutionary relationships of TPS genes in the neotropical fruit tree species Psidium cattleyanum.Scientific reports · 2023Article
- Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants.Advances in experimental medicine and biology · 2021Article
- Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants.Scientific reports · 2020Article
- Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions.Scientific reports · 2018Article
- Molecular characterization of XopAG effector AvrGf2 from Xanthomonas fuscans ssp. aurantifolii in grapefruit.Molecular plant pathology · 2017Article
- Chloroplast DNA Copy Number Changes during Plant Development in Organelle DNA Polymerase Mutants.Frontiers in plant science · 2016Article
- Broad 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicide tolerance in soybean with an optimized enzyme and expression cassette.Plant physiology · 2014Article
- Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model.PloS one · 2014Article
- Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.PloS one · 2014Article
- Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer.Plant physiology · 2013Article
- SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis.Nucleic acids research · 2013Article
- Article
- The rice ASR5 protein: a putative role in the response to aluminum photosynthesis disturbance.Plant signaling & behavior · 2012Article
- Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora.Theory in biosciences = Theorie in den Biowissenschaften · 2012Article
- Agrobacterium-mediated transient expression in citrus leaves: a rapid tool for gene expression and functional gene assay.Plant cell reports · 2011Article
- Critical role of 7,8-didemethyl-8-hydroxy-5-deazariboflavin for photoreactivation in Chlamydomonas reinhardtii.The Journal of biological chemistry · 2010Article
- Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana.The Journal of biological chemistry · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criteria that are used in making predictions. We address this concern with several new prediction methods that base predictions explicitly on the abundance of different amino acid types in the N-terminal region of the protein. Our successful prediction accuracy suggests that ChloroP uses little positional information in its decision-making; an unexpected result given the elaborate ChloroP input scheme. By removing positional information, our simpler methods allow us to identify those amino acids that are useful for successful prediction. The identification of important sequence features, such as amino acid content, is advantageous if one of the goals of localization predictors is to gain an understanding of the biological process of chloroplast localization. Our most accurate predictor combines principal component analysis and logistic regression. Web-based prediction using this method is available online at http://apicoplast.cis.upenn.edu/pclr/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.