EXAMPLE: SULFUR-RELATED GENES

Using a filtered list of C. reinhardtii genes derived from transcriptome se­quencing of the green alga under sulfur-depleted conditions [26], the Algal Functional Annotation Tool found enrichment for annotations related to sulfur metabolism, cysteine and methionine metabolism, and sulfur com­pound biosynthesis. For each annotation, the results may be expanded to reveal the genes containing that particular annotation. Furthermore, there is significant overlap between terms directly assigned to C. reinhardtii pro­teins and those inferred from A. thaliana orthology. Visualization of the sulfur metabolism KEGG pathway shows that a majority of the enzymes involved in this biological process is in the sample list, and the reactions they catalyze may be seen on the pathway map. The results for any enrich­ment analysis may be downloaded as a tab-delimited text file. Taking a gene found to be associated with the KEGG pathway ‘Sulfur metabolism’ by this enrichment analysis (JGI v. 3 ID 206154) as a starting input into the gene similarity search tool, the genes corresponding to sulfate transport­er, methionine synthase reductase, and cysteine dioxygenase were found within the top 15 results using the correlation metric between log counts.

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