ArticleBioinformatics (Oxford, England)2020
BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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
3 citing papers in PubMed, 6 citations in OpenAlex.
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- HumanNet v3: an improved database of human gene networks for disease research.Nucleic acids research · 2022Article
- Bioinformatics services for analyzing massive genomic datasets.Genomics & informatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationOwing to advanced DNA sequencing and genome assembly technology, the number of species with sequenced genomes is rapidly increasing. The aim of the recently launched Earth BioGenome Project is to sequence genomes of all eukaryotic species on Earth over the next 10 years, making it feasible to obtain genomic blueprints of the majority of animal and plant species by this time. Genetic models of the sequenced species will later be subject to functional annotation, and a comprehensive molecular network should facilitate functional analysis of individual genes and pathways. However, network databases are lagging behind genome sequencing projects as even the largest network database provides gene networks for less than 10% of sequenced eukaryotic genomes, and the knowledge gap between genomes and interactomes continues to widen.
resultsWe present BiomeNet, a database of 95 scored networks comprising over 8 million co-functional links, which can build and analyze gene networks for any species with the sequenced genome. BiomeNet transfers functional interactions between orthologous proteins from source networks to the target species within minutes and automatically constructs gene networks with the quality comparable to that of existing networks. BiomeNet enables assembly of the first-in-species gene networks not available through other databases, which are highly predictive of diverse biological processes and can also provide network analysis by extracting subnetworks for individual biological processes and network-based gene prioritizations. These data indicate that BiomeNet could enhance the benefits of decoding the genomes of various species, thus improving our understanding of the Earth' biodiversity. AVAILABILITY AND IMPLEMENTATION: The BiomeNet is freely available at http://kobic.re.kr/biomenet/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.