Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment
文献类型：期刊论文
| 作者 | Hui, LJ; Zhang, X; Wu, X; Lin, ZX; Wang, QK; Li, YX; Hu, GX |
| 刊名 | ONCOGENE
 |
| 出版日期 | 2004 |
| 卷号 | 23期号:17页码:3013-3023 |
| 关键词 | alternative splicing prediction database cancer EST alignment |
| 通讯作者 | Li, YX (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, State Key Lab Mol Biol, Room 400,Cell Bldg,Yueyang Rd 320, Shanghai 200031, Peoples R China.,yxli@sibs.ac.cn ; xbshu@sunm.shcnc.ac.cn |
| 英文摘要 | Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocelluar carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed. |
| 学科主题 | Biochemistry & Molecular Biology; Oncology; Cell Biology; Genetics & Heredity |
| 类目[WOS] | Biochemistry & Molecular Biology ; Oncology ; Cell Biology ; Genetics & Heredity |
| 关键词[WOS] | EXPRESSED SEQUENCE TAGS ; HUMAN GENES ; COMPUTATIONAL ANALYSIS ; DATABASE ; PROTEIN ; INFORMATION ; CARCINOMAS ; TUMORS ; EXON |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000220845200005 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/2170]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Hui, LJ,Zhang, X,Wu, X,et al. Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment[J]. ONCOGENE,2004,23(17):3013-3023. |
| APA | Hui, LJ.,Zhang, X.,Wu, X.,Lin, ZX.,Wang, QK.,...&Hu, GX.(2004).Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.ONCOGENE,23(17),3013-3023. |
| MLA | Hui, LJ,et al."Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment".ONCOGENE 23.17(2004):3013-3023. |
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