A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts

Abstract

Using a spotted 65-mer oligonucleotide microarray, we have characterized the developmental expression profile from mid-gastrulation (75% epiboly) to 5 days post-fertilization (dpf) for >16,000 unique transcripts in the zebrafish genome. Microarray profiling data sets are often immense, and one challenge is validating the results and prioritizing genes for further study. The purpose of the current study was to address such issues, as well as to generate a publicly available resource for investigators to examine the developmental expression profile of any of the over 16,000 zebrafish genes on the array. On the chips, there are 16,459 printed spots corresponding to 16,288 unique transcripts and 172 β-actin (AF025305) spots spatially distributed throughout the chip as a positive control. We have collected 55 microarray gene expression profiling results from various zebrafish laboratories and created a Perl/CGI-based software tool ( http://serine.umdnj.edu/∼ouyangmi/cgi-bin/zebrafish/profile.htm) for researchers to look for the expression patterns of their gene of interest. Users can search for their genes of interest by entering the accession numbers or the nucleotide sequences and the expression profiling will be reported in the form of expression intensities versus time-course graphical displays. In order to validate this web tool, we compared 74 genes’ expression results between our web tool and the in situ hybridization results from Thisse et al. [Thisse, B., Heyer, V., Lux, A., Alunni, A., Degrave, A., Seiliez, I., Kirchner, J., Parkhill, J.-P., Thisse, C., 2004. Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening. Meth. Cell. Biol. 77, 505–519] as well as those reported by Mathavan et al. [Mathavan, S., Lee, S.G., mark, A., Miller, L.D., Murthy, K.R., Tong, Y., Wu, Y.L., Lam, S.H., Yang, H., Ruan, Y., Korzh, V., Gong, Z., Liu, E.T., Lufkin, T., 2005. Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet. 1, 260–276]. The comparison indicates that our microarray-derived expression patterns are 80% and 75% in agreement with the in situ database (Thisse et al., 2004) and previously published microarray data (Mathavan et al., 2005), respectively. Those genes that conflict between our web tool and the in situ database either have high sequence similarity with other genes or the in situ probes are not reliable. Among those genes that disagree between our web tool and those reported by Mathavan et al. (2005), 93% of the genes are in agreement between our web tool and the in situ database, indicating our web tool results are quite reliable. Thus, this resource provides a user-friendly web based platform for researchers to determine the developmental profile of their gene of interest and to prioritize genes identified in microarray analyses by their developmental expression profile.