Paper of Interest: OrthoList 2

The new comparative genomic analysis between C. elegans and humans, OrthoList 2 (OL2), was just published early online in GENETICS.  OL2 comes with a new web-based tool that allows for rapid searches of OL2 by worm or human gene identifiers, protein domains (InterPro and SMART), or human-disease associations (OMIM), and also includes updated RNAi resources. The paper describes OL2 and various findings, including how the content of OL2 compares with the original OrthoList tool. The web-based tool for accessing OL2 is here.

Please specify allele and strain names in publications

WormBase curates data from published papers and attaches different types of data such as phenotype, overview, expression, human disease model, etc., to genetic entities such as genes, alleles, strains or transgenes. These are also bonafide  ‘objects’ in our database which allow us to attach data to them.  If we cannot find these named genetic entities in your paper it becomes extremely difficult for us to curate the paper.  It is not enough to just specify the amino acid or nucleic acid change of a mutation, we need either the strain or allele name to curate the paper.

WS249: Parasite Papers I

For the upcoming WS249 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Winter AD, Weir W, Hunt M, Berriman M, Gilleard JS, Devaney E, Britton C.Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. BMC Genomics. 2012 Jan 4;13:4.

miRNA genes are referenced from the WBPaper00040579 entry.

Winter AD, Gillan V, Maitland K, Emes RD, Roberts B, McCormack G, Weir W, Protasio AV, Holroyd N, Berriman M, Britton C, Devaney E. A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites. BMC Genomics. 2015 Apr 22;16(1):331.

referenced genes: let-7, Bm6643, Bm5914, Bma-tag-97, Bma-mir-5364

Cinkornpumin JK, Wisidagama DR, Rapoport V, Go JL, Dieterich C, Wang X, Sommer RJ, Hong RL. A host beetle pheromone regulates development and behavior in the nematode Pristionchus pacificus. Elife. 2014 Oct 15;3

referenced genes: C06G1.1, Ppa-obi-1, CBG16343, CRE27642, CJA06526, Bm2019

WS248: Parasite Papers II

For the upcoming WS248 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Doharey PK, Suthar MK, Verma A, Kumar V, Yadav S, Balaramnavar VM, Rathaur S, Saxena AK, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Brugia malayi thymidylate kinase. Acta Trop. 2014 May;133:83-92. doi:10.1016/j.actatropica.2014.02.003. Epub 2014 Feb 17.

genes referred to: Bm5401

Singh VK, Doharey PK, Kumar V, Saxena JK, Siddiqi MI, Rathaur S, Narender T.
Synthesis, molecular docking and Brugia malayi thymidylate kinase (BmTMK) enzyme inhibition study of novel derivatives of [6]-shogaol. Eur J Med Chem. 2015 Mar 26;93:74-82. doi: 10.1016/j.ejmech.2015.01.035. Epub 2015 Jan 20.

genes referred to: Bm5401

Bulman CA, Bidlow CM, Lustigman S, Cho-Ngwa F, Williams D, Rascón AA Jr, Tricoche N, Samje M, Bell A, Suzuki B, Lim KC, Supakorndej N, Supakorndej P, Wolfe AR, Knudsen GM, Chen S, Wilson C, Ang KH, Arkin M, Gut J, Franklin C,
Marcellino C, McKerrow JH, Debnath A, Sakanari JA. Repurposing auranofin as a lead candidate for treatment of lymphatic filariasis and onchocerciasis. PLoS Negl Trop Dis. 2015 Feb 20;9(2):e0003534. doi: 10.1371/journal.pntd.0003534. eCollection 2015 Feb.

genes referred to: Bma-trxr-1