An efficient and high-throughput approach for experimental validation of novel human gene predictions
| Autor: | Charles Larry, Michael Harris, Chunlin Xiao, Valentina Di Francisco, Toni L. Ceccardi, Sarah Perkins, Fangqi Hu, Clark Brown, Mark Shannon, Jason Evans, Sonny Young, Sergei Maltchenko, Marion Webster-Laig, Pius Brzoska, Karl J. Guegler, Raymond R. Samaha, Gene Spier, Dennis A. Gilbert, Rixun Fang, Karen Poulter, Alex Dubman, Peter W. Li, Michael Malicdem, Jeffrey Hoover, Michael Cassel |
|---|---|
| Rok vydání: | 2006 |
| Předmět: |
Microarray
RT-PCR Ab initio Genomics Biology Genome Transcriptome Predictive Value of Tests Genetics RefSeq Humans Gene Oligonucleotide Array Sequence Analysis Genome Human Reverse Transcriptase Polymerase Chain Reaction Gene Expression Profiling Computational Biology Proteins Reproducibility of Results Sequence Analysis DNA Alternative Splicing RNA splicing Algorithms Software Novel human genes |
| Zdroj: | Genomics. 87:437-445 |
| ISSN: | 0888-7543 |
| Popis: | A highly automated RT-PCR-based approach has been established to validate novel human gene predictions with no prior experimental evidence of mRNA splicing (ab initio predictions). Ab initio gene predictions were selected for high-throughput validation using predicted protein classification, sequence similarity to other genomes, colocalization with an MPSS tag, or microarray expression. Initial microarray prioritization followed by RT-PCR validation was the most efficient combination, resulting in approximately 35% of the ab initio predictions being validated by RT-PCR. Of the 7252 novel genes that were prioritized and processed, 796 constituted real transcripts. In addition, high-throughput RACE successfully extended the 5′ and/or 3′ ends of >60% of RT-PCR-validated genes. Reevaluation of these transcripts produced 574 novel transcripts using RefSeq as a reference. RT-PCR sequencing in combination with RACE on ab initio gene predictions could be used to define the transcriptome across all species. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect