ArticleBMC genomics2007
Quantitative assessment of relationship between sequence similarity and function similarity.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed.
- Benchmarking protein sequence and structure search methods for remote homology detection.Genome biology · 2026Article
- Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution.Genome biology and evolution · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- ToxIR: an accurate RNA-seq pipeline for high-precision toxin transcriptome profiling, validated in odontobuthus doriae venom glands.Scientific reports · 2025Article
- Genetic Variation and Gene Expression of the Antimicrobial Peptide Macins in Asian Buffalo Leech (Biology · 2025Article
- TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.Nature communications · 2025Article
- Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.Frontiers in microbiology · 2025Article
- Integrated multi-omics analysis and experimental investigation of mitochondrial dynamics-related genes: molecular subtypes, immune landscape, and prognostic implications in lung adenocarcinoma.Frontiers in immunology · 2025Article
- Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.Cellular and molecular neurobiology · 2024Article
- Comparative proteomic profiling of the ovine and human PBMC inflammatory response.Scientific reports · 2024Article
- Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes.Animals : an open access journal from MDPI · 2024Article
- Comparative genomics reveals insight into the phylogeny and habitat adaptation of novelFrontiers in plant science · 2024Article
- Multi-omics profiling and experimental verification of tertiary lymphoid structure-related genes: molecular subgroups, immune infiltration, and prognostic implications in lung adenocarcinoma.Frontiers in immunology · 2024Article
- Genome mining ofFrontiers in microbiology · 2024Article
- SLC7A11, a potential immunotherapeutic target in lung adenocarcinoma.Scientific reports · 2023Article
- Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview.Computational and structural biotechnology journal · 2023Review
- Conserved coronavirus proteins as targets of broad-spectrum antivirals.Antiviral research · 2022Article
- Article
- ISM1 protects lung homeostasis via cell-surface GRP78-mediated alveolar macrophage apoptosis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level.BioMed research international · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative sequence analysis is considered as the first step towards annotating new proteins in genome annotation. However, sequence comparison may lead to creation and propagation of function assignment errors. Thus, it is important to perform a thorough analysis for the quality of sequence-based function assignment using large-scale data in a systematic way.
resultsWe present an analysis of the relationship between sequence similarity and function similarity for the proteins in four model organisms, i.e., Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorrhabditis elegans, and Drosophila melanogaster. Using a measure of functional similarity based on the three categories of Gene Ontology (GO) classifications (biological process, molecular function, and cellular component), we quantified the correlation between functional similarity and sequence similarity measured by sequence identity or statistical significance of the alignment and compared such a correlation against randomly chosen protein pairs.
conclusionVarious sequence-function relationships were identified from BLAST versus PSI-BLAST, sequence identity versus Expectation Value, GO indices versus semantic similarity approaches, and within genome versus between genome comparisons, for the three GO categories. Our study provides a benchmark to estimate the confidence in assignment of functions purely based on sequence similarity.
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.