title: Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.
abstract: Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed.
authors.affiliation: Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan.
authors.forename: Huai-Kuang
authors.initials: HK
authors.lastname: Tsai
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Pei-Ying
authors.initials: PY
authors.lastname: Huang
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Cheng-Yan
authors.initials: CY
authors.lastname: Kao
authors.affiliation: Biodiversity Research Center, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan.
authors.forename: Daryi
authors.initials: D
authors.lastname: Wang
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic; D015027:Zebrafish / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D029961:Zebrafish Proteins