ReviewBriefings in bioinformatics2014
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.
Review in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
15 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)Autophagy · 2021Guideline
- Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).Autophagy · 2016Guideline
- CGG toolkit: Software components for computational genomics.PLoS computational biology · 2023Article
- Prediction and Ranking of Biomarkers UsingInternational journal of molecular sciences · 2022Article
- Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase.Nature chemical biology · 2021Article
- UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.NAR genomics and bioinformatics · 2020Article
- Developing computational biology at meridian 23° E, and a little eastwards.Journal of biological research (Thessalonike, Greece) · 2018Article
- Article
- Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.BMC biology · 2018Review
- CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.Molecular biology and evolution · 2018Article
- Systematic identification and analysis of frequent gene fusion events in metabolic pathways.BMC genomics · 2016Article
- Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure.Standards in genomic sciences · 2015Article
- Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.BMC plant biology · 2014Article
- Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins.Scientific reports · 2014Article
- Application of Hybrid Functional Groups to Predict ATP Binding Proteins.ISRN computational biology · 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
More than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. This structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. Furthermore, this view has raised the real possibility to detect functional associations of genes and their corresponding proteins for any entire genome sequence. Yet, despite these exciting developments, there have been relatively few cases of real use of these methods outside the computational biology field, as reflected from citation analysis. These methods have the potential to be used in high-throughput experimental settings in functional genomics and proteomics to validate results with very high accuracy and good coverage. In this critical survey, we provide a comprehensive overview of 30 most prominent examples of single pairwise protein interaction cases in small-scale studies, where protein interactions have either been detected by gene fusion or yielded additional, corroborating evidence from biochemical observations. Our conclusion is that with the derivation of a validated gold-standard corpus and better data integration with big experiments, gene fusion detection can truly become a valuable tool for large-scale experimental biology.
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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.