We extend classic diagnostic allele counting measures of geneflow across a barrier between taxa to genome-scale data. This is achieved by combining two different operators to form a device that functions as a genetic AND gate: the assembly of the LacI and LuxR operators integrates inputs from the inducers IPTG and AHL into a transcription output.

Gene Sets

Gene sets are collections of genes that share common characteristics, such as membership in a specific pathway or co-expression in a particular gene expression experiment. Such gene sets are often used as molecular signatures to identify biologically meaningful patterns of genetic variation.

The ability to detect genetic risk factors with gene set analysis is of substantial interest for a variety of reasons. First, gene set analyses may help to overcome the small sample size and directional biases inherent in individual variant-association studies. Second, testing for enrichment of functionally related genes may be more effective than individual genes, given the polygenic nature of complex diseases.

genegateuae supports a number of different methods for gene set enrichment analysis, including GO and KEGG. Moreover, the site also provides the ability to upload and analyze gene set lists that have been manually curated or generated using other methods such as GATHER or manual literature search.

Using genegateuae, users can choose which of the 26 databases to use as backend annotation for their enrichment analysis (Fig. 2). Enrichment analysis results are displayed on the screen along with a corresponding heat map and can be viewed as downloadable tables. Detailed information about the intersection between the enriched gene sets is also provided, as well as a link to the original database from which the gene set was compiled if it has been made publicly available.

Data

yrGATE provides a new, community alternative to traditional manual gene structure annotation and is highly adaptable to various input data. It enables a large, nonexclusive group of annotators to investigate genome sequence evidence, and is particularly well suited to emerging species such as maize. The software's user-friendly character contributes to its potential for widespread community adoption.

The yrGATE tool is available for most major operating systems, and runs on most web browsers. Input data is delivered as spliced alignments of cDNA and EST sequences, or as genomic coordinates for annotated gene models. Annotation output is deposited in local database tables or as simple text or GFF3 [25] files.

Annotation tools are presented as interactive graphs of genomic regions, with form fields for defining exons and constructing gene structures. For example, a screenshot of the yrGATE Annotation Tool window from ZmGDB (Figure 2a) shows a completed gene structure annotation. The annotation was based on pre-computed transcript evidence that consists of two groups of ESTs (9, circled) separated by a region with no spanning evidence (160260-160664). The annotator defined three user defined exons using portals to both GENSCAN and GeneSeqer@PlantGDB portals (2 in Figure 2a).

Once an annotator has finished a gene structure, it is saved as an annotation record (1 in Figure 2), which can be modified or deleted at will. Alternatively, the annotator can choose to submit it to a community database for public access.