Figure 5

Comparison of the germline-specific/enriched genes identified by SAGE with the germline-enriched genes identified by the microarray. (A) Overview of the comparison between SAGE and microarray. Germline-specific/enriched SAGE data were generated by selecting genes that are identified only by the germline library (germline-specific) and genes that have a 2-fold enrichment of the tag counts in the germline library over the soma library (germline-enriched). Genes were further selected to have a germline tag count ≥ 9. Data correspond to 330 germline-specific genes and 733 germline-enriched genes. Microarray data used were the adult data, with wt/glp-4 F.I. ≥ 2 (99% confidence >0). (B) SAGE data for the germline-enriched genes identified only by microarray. 'Ambiguous genes' are genes that were not identified as germline-specific due to having an ambiguous tag in the soma (Short-SAGE) library, or that have an ambiguous Long-SAGE tag (Germline SAGE library). 'No SAGE tags' do not have an assigned Long and/or Short-SAGE tag. 'SAGE tags available but not identified' are genes that do have an associated Long-SAGE tag and Short-SAGE tag, and the tags are not ambiguous, but no tags were identified in either library. 'Germline tag < 9' are genes identified in the germline SAGE library, and either were not identified in the soma SAGE library or have a tag count ratio ≥ 2, but have a germline tag count < 9. '1 ≤ germline/soma < 2' refers to genes that were identified in both the germline and the soma SAGE libraries and have a germline/soma tag ratio ≥ 1 and < 2. The expanded category are genes that are only identified in the soma SAGE library, or genes that are identified in both the germline and the soma SAGE libraries with a soma/germline tag ratio > 1. (C) The corresponding microarray data for the germline-specific/enriched genes identified only by the SAGE. 'Microarray F.I.' refers to the adult/glp-4 fold induction value. 'Below confidence level' refers to genes with a 99% confidence level < 0. (D) Germline-specific or (E) germline-enriched genes identified by SAGE compared to germline-enriched genes identified by microarray plotted against the distribution of transcript levels based on tag counts.