Bioinformatics and Gene Expression Analysis of the Human Chromosome 4q22-24 Region

Ueng-Cheng Yang ； Tai-Jay Chang

《Journal of Genetics and Molecular Biology》 11卷2期 (2000/06) Pp. 81-81

https://doi.org/10.30047/JGMB.200006.0007

並列摘要

Genome annotation is the first step toward functional analysis. We have analyzed the sequences from human chromosome 4q22-24 region, which is implicated in HCC pathogenesis, generated from the National Yang-Ming University Genome Research Center (YMGC). To increase the efficiency of analysis, most of the databases were installed locally. Codes and scripts were written to automate the analyses on a PC cluster. The annotation results are classified into 4 categories. Known gene encode protein that has been reported before, such as the ß-mannosidase locus. Related gene encodes protein that has similar sequence to known protein(s), like betatransducing-like protein homolog. These loci may represent a new member of a gene family. Predicted genes have the potential to express messenger RNA, such as the CCAAT-box-binding transcription factor. However, the sequence information is not sufficient to make exact assignment at this point. Pseudogenes are similar to known genes; however, they cannot be properly expressed. They are sometimes intronless and have a poly (A) tail, which may be formed by a retroposon-like integration mechanism. For example, a mRNA-like sequence similar to keratin-8 was found. We have found about 135 genes and have predicted about 200 genes in ten mega-basepair sequences in early May. The raw data and annotated results are both presented in web formats. The most update information can be found at “http://genome.ym.edu.tw/”. Since important databases keep updating at different frequencies, the bioinformatics core laboratory at YMGC will be updated the annotation about one week after each new release of UniGene database. To annotate those regions that do not have any protein or EST (expressed sequence tag) hits, computer programs were used to predict genes. These genes are called “program predicted genes” to avoid confusion with “predicted genes”. These genes are potentially novel and may have biological implications. Some of these genes are expressed in tumor tissues, but not normal tissue.