ArticleNucleic acids research2013
JiffyNet: a web-based instant protein network modeler for newly sequenced species.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.BMC genomics · 2020Article
- BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome.Bioinformatics (Oxford, England) · 2020Article
- BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley,Frontiers in plant science · 2020Article
- A predicted protein functional network aids in novel gene mining for characteristic secondary metabolites in tea plantJournal of biosciences · 2020Article
- Article
- Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera.BMC genomics · 2019Article
- A Genome-Scale Co-Functional Network ofMolecules and cells · 2019Article
- Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus.Scientific reports · 2018Article
- SoyNet: a database of co-functional networks for soybean Glycine max.Nucleic acids research · 2017Article
- From sequencing data to gene functions: co-functional network approaches.Animal cells and systems · 2017Review
- Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource.Nucleic acids research · 2016Article
- PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants.Scientific reports · 2016Article
- Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa.Scientific reports · 2016Article
- MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.Nucleic acids research · 2016Article
- Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans.Scientific reports · 2015Article
- AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species.Nucleic acids research · 2015Article
- EcoliNet: a database of cofunctional gene network for Escherichia coli.Database : the journal of biological databases and curation · 2015Article
- WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans.Nucleic acids research · 2014Article
- YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae.Nucleic acids research · 2014Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Revolutionary DNA sequencing technology has enabled affordable genome sequencing for numerous species. Thousands of species already have completely decoded genomes, and tens of thousands more are in progress. Naturally, parallel expansion of the functional parts list library is anticipated, yet genome-level understanding of function also requires maps of functional relationships, such as functional protein networks. Such networks have been constructed for many sequenced species including common model organisms. Nevertheless, the majority of species with sequenced genomes still have no protein network models available. Moreover, biologists might want to obtain protein networks for their species of interest on completion of the genome projects. Therefore, there is high demand for accessible means to automatically construct genome-scale protein networks based on sequence information from genome projects only. Here, we present a public web server, JiffyNet, specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided. Assessment of the networks by JiffyNet demonstrated generally high predictive ability for pathway annotations. Furthermore, JiffyNet provides network visualization and analysis pages for wide variety of molecular concepts to facilitate network-guided hypothesis generation. JiffyNet is freely accessible at http://www.jiffynet.org.
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.