ArticleNucleic acids research2015
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.
Article in Nucleic acids research, 2015. 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.
- Protein Self-Interaction in Cellular Function and Network Evolution: Molecular Mechanisms, AI-Driven Insights, and Therapeutic Potentials.International journal of molecular sciences · 2026Review
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- Systematic mapping of mitochondrial calcium uniporter channel (MCUC)-mediated calcium signaling networks.The EMBO journal · 2024Article
- PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.Microbiology spectrum · 2023Article
- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.BMC genomics · 2021Article
- CladeOScope: functional interactions through the prism of clade-wise co-evolution.NAR genomics and bioinformatics · 2021Article
- Impaired complex I repair causes recessive Leber's hereditary optic neuropathy.The Journal of clinical investigation · 2021Article
- Molecular machinery regulating mitochondrial calcium levels: The nuts and bolts of mitochondrial calcium dynamics.Mitochondrion · 2021Review
- HumDLoc: Human Protein Subcellular Localization Prediction Using Deep Neural Network.Current genomics · 2020Article
- Article
- Article
- Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study.Frontiers in plant science · 2017Article
- Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network.Functional & integrative genomics · 2016Article
- PTIR: Predicted Tomato Interactome Resource.Scientific reports · 2016Article
- SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.Bioinformatics (Oxford, England) · 2016Article
- PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.Database : the journal of biological databases and curation · 2016Article
- Review
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
ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein-protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.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.