Appendix 1 of
Hackam, Mol Vis 2004;
Appendix 1. Supplemental information
Three files are provided as supplemental information for this article. This caption describes the content and structure of the files and details how to obtain the files.
DifferentialExpression.txt: This file contains the differential expression lists from each of the retina, brain, and liver comparisons, and the SAGE and library database analyses. Unigene identifying numbers (or accession numbers where unigene clusters were not available) are in the ID column. Gene names and SAM scores are also provided. The table is divided into subsections, containing data from the following analyses: (A) Retina enriched genes from the retina/brain comparison, using a false discovery rate of 4.5%; (B) Brain enriched genes from the retina/brain comparison, using a false discovery rate of 4.5%; (C) Retina enriched genes from the retina/liver comparison, using a false discovery rate of 1.2%; (D) Liver enriched genes from the retina/liver comparison, using a false discovery rate of 1.2%; (E) Total retina enriched genes identified in retina/brain and retina/liver comparisons; (F) Brain enriched genes from brain/liver comparison, using a false discovery rate of 1.2%; (G) Liver enriched genes from brain/liver comparison, using a false discovery rate of 1.2%; (H) Genes from the microarray found in the SAGE reference dataset of retina enriched genes; (I) Genes from the microarray found in the EST library reference dataset of retina enriched genes.
CandidateGenes.txt: Identification of candidate retina enriched genes that map within retina disease critical regions (from the retina/brain and retina/liver comparisons). Clones that map within the critical region of various human retina diseases were identified. Shown for each disease region are the Unigene cluster ID, the corresponding human Unigene cluster ID, and mouse gene name. The disease intervals were obtained from the RetNet database. Each retinal disease is listed with its corresponding mapped chromosomal locus. The retina-enriched genes identified in the microarray that map to these intervals are listed by mouse unigene cluster (or accession) number, human unigene homolog and gene name.
GeneAnnotations.txt: Functions included in the gene annotations. The keywords listed were used in querying SOURCE and GO databases. Genes annotated manually were included in these categories based on the primary function of the gene.
To access this data, click or select the words "Hackam Appendix". This will initiate the download of a compressed (zip) archive. This file should be uncompressed with an appropriate program (the particular program will depend on your operating system). Once extracted, you will have a folder (or directory) containing three files described above. The files are tab delimited text. Most spreadsheet programs will import files in this format.