18 papers · ranked by Valyu relevance
Xiaoshu Chen, Jianzhi Zhang, Christos A. Ouzounis
The ortholog conjecture posits that orthologous genes are functionally more similar than paralogous genes. This conjecture is a cornerstone of phylogenomics and is used daily by both computational and experimental biologists in predicting, interpreting, and understanding gene functions. A recent study, however…
Casey W. Dunn, Felipe Zapata, Catriona Munro, Stefan Siebert + 1 more
There is now considerable interest in comparing functional genomics data across species. One goal of this work is to provide an integrated understanding of genome and phenotype evolution. Most studies of this type have relied on multiple pairwise comparisons of functional genomic data between species, an approach that…
Yuyao Song, Detlev Arendt, Irene Papatheodorou, Alvis Brazma
The cross-species comparison of expression profiles uncovers functional similarities and differences between cell types and helps refining their evolutionary relationships. Current analysis strategies typically follow the ortholog conjecture, which posits that the expression of orthologous genes is most similar between…
Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac
The computational prediction of gene function is a key step in making full use of newly sequenced genomes. Function is generally predicted by transferring annotations from homologous genes or proteins for which experimental evidence exists. The “ortholog conjecture” proposes that orthologous genes should be preferred…
Marc Robinson‐Rechavi
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which allows comparisons which are both large scale and evolutionarily relevant. The…
Kyle T. David, Jamie R. Oaks, Kenneth M. Halanych, David Ferrier
Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event…
Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi, Christos A. Ouzounis
'Christos A. Ouzounis'] The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on…
Igor B. Rogozin
Ongoing debates about functional importance of gene duplications have been recently intensified by a heated discussion of the “ortholog conjecture” (OC). Under the OC, which is central to functional annotation of genomes, orthologous genes are functionally more similar than paralogous genes at the same level of…
Tina Begum, Marc Robinson-Rechavi, Yoko Satta
How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as…
Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide…
David Schaller, Manuela Geiß, Peter F. Stadler, Marc Hellmuth
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss…
Kun Gao, Jonathan Miller
Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Debra L Fulton, Yvonne Y Li, Matthew R Laird, Benjamin GS Horsman + 2 more
'Fiona M Roche' 'Fiona SL Brinkman'] Background Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available…
Kun Gao, Jonathan Miller
Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context—as short as single maximal matches—also provides an effective means to identify orthologs within whole genomes. On pristine (un-repeatmasked) mammalian…
Jean-David Aguilar, Safa Jammali, Esaie Kuitche, Aïda Ouangraoua
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in genomes. Here, we re-visit it for the purpose of identifying CDS ortholog…
Soheil Jahangiri-Tazehkand, Limsoon Wong, Changiz Eslahchi
Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…