title: Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.
abstract: Proteogenomic re-annotation and mRNA splicing information can lead to the discovery of various protein forms for eukaryotic model organisms like rat. However, detection of novel proteoforms using mass spectrometry proteomics data remains a formidable challenge. We developed EuGenoSuite, an open source multiple algorithmic proteomic search tool and utilized it in our in-house integrated transcriptomic-proteomic pipeline to facilitate automated proteogenomic analysis. Using four proteogenomic pipelines (integrated transcriptomic-proteomic, Peppy, Enosi, and ProteoAnnotator) on publicly available RNA-sequence and MS proteomics data, we discovered 363 novel peptides in rat brain microglia representing novel proteoforms for 249 gene loci in the rat genome. These novel peptides aided in the discovery of novel exons, translation of annotated untranslated regions, pseudogenes, and splice variants for various loci; many of which have known disease associations, including neurological disorders like schizophrenia, amyotrophic lateral sclerosis, etc. Novel isoforms were also discovered for genes implicated in cardiovascular diseases and breast cancer for which rats are considered model organisms. Our integrative multi-omics data analysis not only enables the discovery of new proteoforms but also generates an improved reference for human disease studies in the rat model.
authors.affiliation: From the ‡G. N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, India;
authors.forename: Dhirendra
authors.initials: D
authors.lastname: Kumar
authors.affiliation: From the ‡G. N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, India;
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Yadav
authors.affiliation: ¶Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors.forename: Xinying
authors.initials: X
authors.lastname: Jia
authors.affiliation: ¶Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors.forename: Jason
authors.initials: J
authors.lastname: Mulvenna
authors.affiliation: From the ‡G. N. Ramachandran Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, India; ddash@igib.res.in.
authors.forename: Debasis
authors.initials: D
authors.lastname: Dash
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D020022:Genetic Predisposition to Disease / Q000235:genetics; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods; D051379:Mice; D017628:Microglia / Q000378:metabolism; D058977:Molecular Sequence Annotation / Q000379:methods; D010455:Peptides / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D051381:Rats; D015203:Reproducibility of Results; D012984:Software; D057188:Workflow
chemical_list: D010455:Peptides; D020543:Proteome