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Sternberg PW, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M, Arnaboldi V, Becerra A, Brown S, Cain S, Chan J, Chen WJ, Cho J, Davis P, Diamantakis S, Dyer S, Grigoriadis D, Grove CA, Harris T, Howe K, Kishore R, Lee R, Longden I, Luypaert M, Müller HM, Nuin P, Quinton-Tulloch M, Raciti D, Schedl T, Schindelman G, Stein L. WormBase 2024: status and transitioning to Alliance infrastructure. Genetics 2024; 227:iyae050. [PMID: 38573366 PMCID: PMC11075546 DOI: 10.1093/genetics/iyae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
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Affiliation(s)
- Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stephanie Brown
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | | | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ian Longden
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Hans-Michael Müller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
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Zhang XQ, Li L. Biological Function and Clinical Value of VPS13A in Pan-Cancer Based on Bioinformatics Analysis. Int J Gen Med 2021; 14:6825-6838. [PMID: 34690502 PMCID: PMC8530525 DOI: 10.2147/ijgm.s330256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose Vacuolar protein sorting-associated protein 13A (VPS13A) has been shown to be associated with rhabdomyosarcoma, gastric cancer and ovarian cancer, but the pan cancer analysis of VPS13A is still lacking, and the bioinformatics function of VPS13A has not been studied yet. Methods We used TCGA and GEO databases to investigate the distribution, expression and prognosis of VPS13A in 33 tumors for the first time. We used TIMER2, ULCAN databases to obtain the expression differences of VPS13A in tumor tissues and corresponding normal tissues, and further obtain the gene expression in different pathological stages of tumors from the GEPIA database. Mutation types and survival analysis of VPS13A were obtained from cBioPortal database. The relationship between VPS13A and immune infiltration was explored using TIMER2. We used the String website to obtain VPS13A binding proteins and draw the protein–protein interaction network map. JVENN was used for cross analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used for gene enrichment analysis. Results VPS13A is highly expressed in most tumors, and gene expression is associated with prognosis in patients with tumors. The expression level of VPS13A was correlated with the infiltration depth of CD8+T cells in DLBC, LUAD, SKCM and TGCT, and was correlated with carcinoma-associated fibroblasts in BRCA, CESC, LIHC and THYM. Compared with normal tissue, VPS13A methylation levels were higher in some primary tumors. KEGG gene enrichment indicates that VPS13A is involved in RNA degradation, autophagy, cell senescence, cell cycle, apoptosis and other pathways. Conclusion VPS13A is closely related to the occurrence and progression of tumors and can be used as a biomarker for tumor screening and diagnosis. The level of VPS13A expression and the presence of mutations affect the prognosis of patients with certain cancers, which can be determined by early genetic testing.
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Affiliation(s)
- Xue Qin Zhang
- Department of Gynecology and Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, People's Republic of China
| | - Li Li
- Department of Gynecology and Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, People's Republic of China
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