GeneTools – application for functional annotation and statistical hypothesis testing

Abstract

Background: Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.

Functional analysis of a zebrafishmyd88mutant identifies key transcriptional components of the innate immune system

“…The table displays the enrichment of immune-related GO terms following infection of myd88 −/− (Mu) and wild-type (Wt) embryos with E. tarda (Et) or S. typhimurium (St). GO-term enrichment in the gene lists upregulated by infection was determined by master-target statistical testing using eGOn (Beisvag et al, 2006) with the Danio rerio UniGene build number 124 as background. The numbers of genes associated with each GO term and the P -values for enrichment are indicated.…”

“…For heat map construction, the fold change values of significant probes representing the same gene were averaged. GO analysis was performed using the GeneTools eGOn v2.0 web-based gene ontology analysis software (http://www.genetools.microarray.ntnu.no) (Beisvag et al, 2006). …”

Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells

“…Gene ontology classification of these 35 differentially expressed genes was performed by using GeneBank accession number, Operon ID, and annotation tools database available on-line [28,29]. The gene sets were classified according to their putative main molecular function.…”

“…Genes were considered differentially expressed as a result of DDC overexpression if normalized values from induced LNCaP-DDC cells were at least 2-fold greater or 2-fold less than those from the control cells (LNCaP-DDC-Dox, LNCaP-pDEST- Dox, and LNCaP-pDEST+Dox). Functional classifications were based on gene ontology (GO) annotation obtained through the GeneTools database [28,29]. …”

Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

“…microarray.ntnu.no) at the level of the UniGene clusters (D. rerio UniGene build no. 105) [20]. Overlapping genes of Tag-Seq, microarray and RNA-Seq data sets were functionally annotated using the National Center for Biotechnology Information (NCBI) Gene Ontology Annotation (GOA), Entrez Gene, and HomoloGene databases and the AmiGO (http://amigo.geneontology.org/cgi-bin/ amigo/go.cgi) gene ontology database.…”