title: Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.
abstract: Alternative splicing allows a single gene to produce multiple transcript-level splice isoforms from which the translated proteins may show differences in their expression and function. Identifying the major functional or canonical isoform is important for understanding gene and protein functions. Identification and characterization of splice isoforms is a stated goal of the HUPO Human Proteome Project and of neXtProt. Multiple efforts have catalogued splice isoforms as "dominant", "principal", or "major" isoforms based on expression or evolutionary traits. In contrast, we recently proposed highest connected isoforms (HCIs) as a new class of canonical isoforms that have the strongest interactions in a functional network and revealed their significantly higher (differential) transcript-level expression compared to nonhighest connected isoforms (NCIs) regardless of tissues/cell lines in the mouse. HCIs and their expression behavior in the human remain unexplored. Here we identified HCIs for 6157 multi-isoform genes using a human isoform network that we constructed by integrating a large compendium of heterogeneous genomic data. We present examples for pairs of transcript isoforms of ABCC3, RBM34, ERBB2, and ANXA7. We found that functional networks of isoforms of the same gene can show large differences. Interestingly, differential expression between HCIs and NCIs was also observed in the human on an independent set of 940 RNA-seq samples across multiple tissues, including heart, kidney, and liver. Using proteomic data from normal human retina and placenta, we showed that HCIs are a promising indicator of expressed protein isoforms exemplified by NUDFB6 and M6PR. Furthermore, we found that a significant percentage (20%, p = 0.0003) of human and mouse HCIs are homologues, suggesting their conservation between species. Our identified HCIs expand the repertoire of canonical isoforms and are expected to facilitate studying main protein products, understanding gene regulation, and possibly evolution. The network is available through our web server as a rich resource for investigating isoform functional relationships (http://guanlab.ccmb.med.umich.edu/hisonet). All MS/MS data were available at ProteomeXchange Web site (http://www.proteomexchange.org) through their identifiers (retina: PXD001242, placenta: PXD000754).
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Hong-Dong
authors.initials: HD
authors.lastname: Li
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Brandon
authors.initials: B
authors.lastname: Govindarajoo
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Bharat
authors.initials: B
authors.lastname: Panwar
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.affiliation: Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Yuanfang
authors.initials: Y
authors.lastname: Guan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D002886:Chromosomes, Human, Pair 17; D006801:Humans; D051379:Mice; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics*; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D020543:Proteome; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D020033:Protein Isoforms; D011506:Proteins; D020543:Proteome; D012333:RNA, Messenger
keywords: alternative splicing; canonical isoforms; highest connected isoforms; isoform networks