Authors: Murillo, J.; Krsticevic, F.; Spetale, F.; Tapia, E.; Bulacio, Pilar.
Title: Predicting Cellular Component of Ommochrome Pathway eye genes in D. melanogaster based on Machine Learning.
Resumen: The prediction of protein subcellular location (SCL) describes locations, at the levelsof subcellular structures contributing to strong experimental designs. In this context,a step further towards the complete annotation of genomes, machine learning (ML)methods can be useful. In this work, we focus on SCL of proteins involved in fly eyepigment due to its relation with a memory loss, synaptic pathology, and a brainplasticity. Two different pigments are in fly compound eyes: brown ommochromesand red drosopterin. With this regard, we predict SCLs of 6 genes involved inommochrome biosynthetic in D. melanogaster. We consider ML predictions on GeneOntology -Cellular Component (GO-CC) where SCLs, relationships, and constraintsare plainly defined; and in multi-label form, several SCL per protein, allowing aubiquitous character. Our ML proposal is a hierarchical ensemble method made intwo steps: in the first, a set of binary classifiers is built to predict GO-CC SCL; in thesecond, the consistency of former SCL predictions is checked by a Factor Graphstrategy. Our results are as expected. The conversion of tryptophan to xanthommatinstarts with the amino acid passage from the plasmatic membrane to the cytoplasmvia white/scarlet permease complex, GO:1902495. There, vermilion catalyzestryptophan to formylkynurenine; despite no location is available we predict severalGO terms, GO:0031967, organelle envelope; GO:0071011, spliceosome;GO:0005856 cytoskeleton. Cinnabar catalyzes kynurenine to 3-hydroxykynurenineand is part of the plasma membrane, GO:0005886 and intracellular organelle,GO:0043229. Finally, 3-hydroxykynurenine leaves the mitochondria and is catalyzedby cardinal (GO:0016021, integral component of membrane and GO:0043226,organelle) to xanthommatin and is kept by permease karmoisin into pigment granule(GO:0016021). Our GO-SCL predictions confirm existing annotations and alsospecify more SCLs describing better the pathway.
Meeting type: Simposio.
Type of job: Resumen.
Production: Predicting Cellular Component of Ommochrome Pathway eye genes in D. melanogaster based on Machine Learning.
Scientific meeting: X Simpósio de Ecologia, Genética e Evolução de Drosophila.
Meeting place: Ouro Preto.
Organizing Institution: Universidade Federal de Minas Gerais.
It's published?: Yes
Publication place: Ouro Preto
Meeting month: 11