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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Kelkar, Dhanashree S. Provost, Elayne Chaerkady, Raghothama Muthusamy, Babylakshmi Manda, Srikanth S. Subbannayya, Tejaswini Selvan, Lakshmi Dhevi N. Wang, Chieh-Huei Datta, Keshava K. Woo, Sunghee Dwivedi, Sutopa B. Renuse, Santosh Getnet, Derese Huang, Tai-Chung Kim, Min-Sik Pinto, Sneha M. Mitchell, Christopher J. Madugundu, Anil K. Kumar, Praveen Sharma, Jyoti Advani, Jayshree Dey, Gourav Balakrishnan, Lavanya Syed, Nazia Nanjappa, Vishalakshi Subbannayya, Yashwanth Goel, Renu Prasad, T. S. Keshava Bafna, Vineet Sirdeshmukh, Ravi Gowda, Harsha Wang, Charles Leach, Steven D. Pandey, Akhilesh |
| Description | Author Affiliation: Kelkar DS ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Provost E ( §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205); Chaerkady R ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Muthusamy B ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Manda SS ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Subbannayya T ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Selvan LD ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Wang CH ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Datta KK ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Woo S ( §§Department of Computer Science, University of California, San Diego, California 92093); Dwivedi SB ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Renuse S ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Getnet D ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Huang TC ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Kim MS ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Pinto SM ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Mitchell CJ ( ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205); Madugundu AK ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Kumar P ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Sharma J ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Advani J ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Dey G ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Balakrishnan L ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Syed N ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Nanjappa V ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Subbannayya Y ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Goel R ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Prasad TS ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Bafna V ( §§Department of Computer Science, University of California, San Diego, California 92093); Sirdeshmukh R ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Gowda H ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India); Wang C ( The Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350); Leach SD ( §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205); Pandey A ( From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India) |
| Abstract | Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and â¼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes. |
| File Format | HTM / HTML |
| ISSN | 15359476 |
| e-ISSN | 15359484 |
| DOI | 10.1074/mcp.M114.038299 |
| Journal | Molecular & Cellular Proteomics |
| Issue Number | 11 |
| Volume Number | 13 |
| Language | English |
| Publisher | American Society for Biochemistry and Molecular Biology |
| Publisher Date | 2014-11-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Discipline Proteomics Genome Genetics Proteome Transcriptome Zebrafish Amino Acid Sequence Animals Gene Expression Profiling High-throughput Nucleotide Sequencing Mass Spectrometry Molecular Sequence Annotation Proteomics Sequence Analysis, Rna Research Support, Non-u.s. Gov't Validation Studies |
| Content Type | Text |
| Resource Type | Article |
| Subject | Medicine Analytical Chemistry Molecular Biology Biochemistry |
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