| Status | 已發表Published |
| Computational Analysis of Gene Identi cation with SAGE | |
Wang, S. M.
| |
| 2002 | |
| Source Publication | JOURNAL OF COMPUTATIONAL BIOLOGY
 |
| ISSN | 1066-5277 |
| Pages | 513-526 |
| Abstract | SAGE is one of the few techniques capable of uniformly probing gene expression at a genome level irrespective of mRNA abundance and without a priori knowledge of the transcripts present. However, individual SAGE tags can match many sequences in the reference database, complicating gene identi cation. We perform a baseline evaluation of gene identi cation with SAGE using UniGene Human as the reference database by analyzing 1) the distributions of tags for various length tag sets formed for UniGene Human and 2) the tagto- sequence mapping using a SAGE tag set consisting of 37,522 tags derived from human myeloid cells. The extensive multiplicity of the dbEST component of UniGene signi cantly detracts from gains that might be expected by extending tags within the scope of the SAGE protocol. In order to achieve reasonable sequence speci city for gene identi cation with the content of the commonly used UniGene sequence collection, tags on the order of hundreds of bases in length are required. One way to produce tags of such lengths is with GLGI, which extends SAGE tags to the 30 end of cDNA. We show that the longer sequences produced by GLGI relieve signi cantly the multiple match condition. In the myeloid sample, we also found a correlation between multiple match severity and high copy number. We extrapolate these ndings, providing insights into the use of UniGene Human as a reference for gene identi cation. |
| Keyword | SAGE computation mapping specificity |
| Language | 英語English |
| The Source to Article | PB_Publication |
| PUB ID | 43518 |
| Document Type | Journal article |
| Collection | DEPARTMENT OF PUBLIC HEALTH AND MEDICINAL ADMINISTRATION |
| Recommended Citation GB/T 7714 | Wang, S. M.. Computational Analysis of Gene Identi cation with SAGE[J]. JOURNAL OF COMPUTATIONAL BIOLOGY, 2002, 513-526. |
| APA | Wang, S. M..(2002). Computational Analysis of Gene Identi cation with SAGE. JOURNAL OF COMPUTATIONAL BIOLOGY, 513-526. |
| MLA | Wang, S. M.."Computational Analysis of Gene Identi cation with SAGE".JOURNAL OF COMPUTATIONAL BIOLOGY (2002):513-526. |
| Files in This Item: | There are no files associated with this item. | |||||
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment