WormBase: a cross-species database for comparative genomics

Abstract

WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.

Requirement for a conserved Toll/interleukin-1 resistance domain protein in the Caenorhabditis elegans immune response

“…As described above, tir-1 is the only C. elegans gene identified by bioinformatic analysis that encodes an intracellular TIR domain-containing protein that could potentially function as an adapter in TLR signaling (37). However, the tir-1 gene has five known isoforms confirmed by partial cDNAs, tir-1a, tir-1b, tir-1c, tir-1d, and tir-1e (Fig.…”

“…However, the tir-1 gene has five known isoforms confirmed by partial cDNAs, tir-1a, tir-1b, tir-1c, tir-1d, and tir-1e (Fig. 4A) (37). In addition to the TIR domain, the proteins encoded by all five TIR-1 isoforms contain two sterile ␣ motifs (SAM), which have previously been shown to mediate proteinprotein interactions in large protein complexes (47).…”

“…For example, the lipopolysaccharide response of transgenic mice is abrogated by a single point mutation in the DNA sequence encoding the TIR domain of TLR4 that blocks the interaction of TLR4 with downstream TIR domaincontaining adapter proteins (36). In C. elegans, only two genes encode TIR domain proteins (37). tol-1 encodes a Toll receptor homologue, and tir-1 (F13B10.1) encodes a protein that is homologous to the mammalian gene known as SARM.…”

DAF-16-Dependent Suppression of Immunity During Reproduction in Caenorhabditis elegans

“…ag17 showed strong linkage to the central region of chromosome I within a 0.25-MU interval bounded by SNP markers F21C3 and H15M21. Of 61 genes that were found within this region according to WormBase (Harris et al 2003), 50 RNAi clones were available in the Ahringer library and were analyzed for their role in pathogen resistance. Nine RNAi clones (F21C3.5, F52A8.5, F07A5.1, T28F4.1, C26C6.1, C26C6.2, C26C6.5, T25G3.3, and D2030.3) caused pathogen resistance phenotype in wild-type animals; however, four of the nine RNAi clones also exhibited obvious anatomical defects and were not analyzed further.…”

“…From the resulting PCR product, each exon of the age-1 PCR product in the wild-type and mutant genomic DNA was sequenced in both the forward and reverse direction and analyzed using the Vector NTI Suite 7 software package (InforMax, Bethesda, MD). The sequences obtained from wild-type and ag12 DNA were compared to the published sequence in WormBase (Harris et al 2003). Sequence alignments of homologous Ras-binding domains (RBDs) from other PI3 kinases were obtained from the Conserved Domain Database (Marchler-Bauer et al 2005).…”