Wnt signaling in C. elegans, both canonical and non-canonical, governs cell polarity and asymmetric cell divisions that ultimately affect endoderm specification, vulva and gonad development, neuroblast migration, neuron branching and outgrowth, formation of the postdeirid sensilla and male tail ray and spicule formation (see WormBook chapters on Wnt signaling for reviews). For the WS246 and WS247 releases of WormBase, WormBase curators have focused on curating papers directly relevant to Wnt signaling in C. elegans. This curation includes Wnt-related genetic and regulatory interactions, anatomy function, mutant phenotypes (by allele and RNAi), expression patterns, Gene Ontology annotations, and cross-species gene orthology and gene models for other nematode species.
New in WS246: Automatically generated gene descriptions
WormBase has been writing concise descriptions of genes that appear in the Overview widget of the gene page. Written in prose, these descriptions provide a quick overview of gene function. Since the process of manually writing gene descriptions is a relatively slow process, many genes lacked such descriptions.
A new experimental tool at WormBase aims to fill these gaps by automatically creating gene descriptions which are visible in the Overview widget of gene pages. The semi-automated process of generating these descriptions relies on pre-existing orthology and Gene Ontology annotations (biological process, molecular function, and cellular component) in WormBase. This process offers a broad coverage for genes lacking manually drafted descriptions.
New Features for WS246
Human Disease Data Update
As part of WormBase efforts to curate genes that are potential models for inherited human diseases, 867 genes have been predicted as potential disease genes. In addition curation efforts added publications on experiments using C.elegans genes to investigate human genetic diseases to 181 genes. And 244 genes have been identified from publications as being relevant to research in that field.
WormBase curates human disease relevance data by designating genes as ‘Experimental models’ for a specific human disease based on experimental data published in the literature. In addition to manual curation, an automated data pipeline designates genes as ‘Potential models’ based on orthology with the human gene. Detailed text descriptions called ‘Human disease relevance’ descriptions describe how the elegans gene is a genetic model for the human disease. All human disease relevant data can be found in the ‘Human Diseases’ widget and in the ‘Overview’ section on gene pages.
Focus on Parasite Papers
For the upcoming WS246 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.
Zang X, Atmadja AK, Gray P, Allen JE, Gray CA, Lawrence RA, Yazdanbakhsh M,
Maizels RM. The serpin secreted by Brugia malayi microfilariae, Bm-SPN-2, elicits strong, but short-lived, immune responses in mice and humans. J Immunol. 2000 Nov 1;165(9):5161-9.
linked genes: Bma-srp-2
ParaSite: Bma-srp-2
Zang X, Yazdanbakhsh M, Jiang H, Kanost MR, Maizels RM. A novel serpin expressed by blood-borne microfilariae of the parasitic nematode Brugia malayi inhibits human neutrophil serine proteinases. Blood. 1999 Aug 15;94(4):1418-28.
linked genes: Bma-srp-2
ParaSite: Bma-srp-2
Manoury B, Gregory WF, Maizels RM, Watts C. Bm-CPI-2, a cystatin homolog secreted by the filarial parasite Brugia malayi, inhibits class II MHC-restricted antigen processing. Curr Biol. 2001 Mar 20;11(6):447-51.
linked genes: cpi-2 , Bm5160 , Bm10669
ParaSite: Bm5160 , Bm10669
Focus on Parasite Papers
For the upcoming WS246 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.
Yadav S, Gupta S, Selvaraj C, Doharey PK, Verma A, Singh SK, Saxena JK. In silico and in vitro studies on the protein-protein interactions between Brugia malayi immunomodulatory protein calreticulin and human C1q. PLoS One. 2014 Sep 3;9(9):e106413.
linked genes: Bm6412
ParaSite: Bma6412
Galvin BD, Li Z, Villemaine E, Poole CB, Chapman MS, Pollastri MP, Wyatt PG, Carlow CK. A target repurposing approach identifies N-myristoyltransferase as a new candidate drug target in filarial nematodes. PLoS Negl Trop Dis. 2014 Sep 4;8(9):e3145.
linked genes: Bma-nmt-1 , nmt-1
ParaSite: Bma-nmt-1
Terry FE, Moise L, Martin RF, Torres M, Pilotte N, Williams SA, De Groot AS. Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases. Expert Rev Vaccines. 2014 Sep 5:1-15.
linked genes: Bma-prdx-2
ParaSite: Bma-prdx-2