GOAL: A software tool for assessing biological significance of genes groups

Abstract

BackgroundModern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO), KEGG pathways, association between a transcription factor (TF) and its target genes, and/or gene networks.ResultsWe developed GOAL: Gene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application.ConclusionWe developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.

Digitization of trait representation in microarray data analysis of wheat infected by fusarium graminearum

“…Gene ontology enrichment analysis [30] revealed that genes down-regulated after Fusarium infection are predicted to mainly contribute toward growth and other primary metabolic …”

“…The association between Affy probe ID and UniGene from NCBI were updated, which resulted in 45,699 associations mapping to 26,674 unique UniGenes. Ensemble Plants (version 22) gene ontology association with wheat genes was analyzed for gene enrichment using the GOAL software [30].…”

biDCG: A New Method for Discovering Global Features of DNA Microarray Data via an Iterative Re-Clustering Procedure

“…aBiclusters identified by biDCG, as marked on Figure 5.bNumber of GO terms enriched in the gene set, with a significance level better than 0.05: GOAL [48] results.cNumber of functional terms enriched in the gene set, with a significance level better than 0.05: DAVID [49] results.dWe regrouped all genes from NL_A, NL_B, and NL_C, as those correspond to healthy patients.…”

Differences in Promoters of Orthologous Genes

“…The less conserved gene group consists of 171 human genes whose FPSIs are 0.0 (no common TF) when human is compared with both chimpanzee and mouse (Supplemental File 5). We then performed a gene functional characterization of each group using Gene Ontology AnaLyzer (GOAL) [36]. This reveals that the genes with more conserved promoters are closely related with various developmental process (GO:0007275, GO:0032502, GO:0048856, GO:0048731, GO:0009653, GO:0048513, GO:0001822), while genes with less conserved promoters are related with regulation of transport, protein binding and signalling (GO:0051050, GO:0005515, GO:0007242, GO:0019932, GO:0032501) and their functional representations are less significant even though there are twice number of genes in this group than in the most conserved group (Supplemental File 5).…”