Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable o...

The Phenoscape Knowledgebase: Tools and APIs for Computing Across Phenotypes from Evolutionary Diversity and Model Organisms

The Phenoscape Knowledgebase (KB) is an ontologydriven database that combines existing phenotype annotations from model organism databases with new phenotype annotations from the evolutionary literature. Phenoscape curators have created phenotype annotations for more than 5,000 species and higher taxa, by defining computable phenotype concepts for more than 20,000 character states from over 160...

Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes

The Genetics of Reading Disabilities: From Phenotypes to Candidate Genes

This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationshi...

Evolutionary Distance of Amino Acid Sequence Orthologs across Macaque Subspecies: Identifying Candidate Genes for SIV Resistance in Chinese Rhesus Macaques

We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list ...