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1. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

Author

de Jong, Tristan V, Pan, Yanchao, Rastas, Pasi, Munro, Daniel, Tutaj, Monika, Akil, Huda, Benner, Chris, Chen, Denghui, Chitre, Apurva S, Chow, William, Colonna, Vincenza, Dalgard, Clifton L, Demos, Wendy M, Doris, Peter A, Garrison, Erik, Geurts, Aron M, Gunturkun, Hakan M, Guryev, Victor, Hourlier, Thibaut, Howe, Kerstin, Huang, Jun, Kalbfleisch, Ted, Kim, Panjun, Li, Ling, Mahaffey, Spencer, Martin, Fergal J, Mohammadi, Pejman, Ozel, Ayse Bilge, Polesskaya, Oksana, Pravenec, Michal, Prins, Pjotr, Sebat, Jonathan, Smith, Jennifer R, Woods, Leah C Solberg, Tabakoff, Boris, Tracey, Alan, Uliano-Silva, Marcela, Villani, Flavia, Wang, Hongyang, Sharp, Burt M, Telese, Francesca, Jiang, Zhihua, Saba, Laura, Wang, Xusheng, Murphy, Terence D, Palmer, Abraham A, Kwitek, Anne E, Dwinell, Melinda R, Williams, Robert W, Li, Jun Z, and Chen, Hao

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Good Health and Well Being, Rats, Animals, Genome, Molecular Sequence Annotation, Genomics, Whole Genome Sequencing, Genetic Variation, Rnor_6.0, genetic map, heterogeneous stock, hybrid rat diversity panel, inbred strains, mRatBN7.2, phylogenetic tree, rat, recombinant inbred, reference genome
Abstract

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Published
2024

2. The Gene Ontology knowledgebase in 2023

Author

Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, and Berardini, Tanya Z

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Gene Ontology, Proteins, Molecular Sequence Annotation, Databases, Genetic, Computational Biology, gene annotation, gene function, knowledgebase, knowledge graphs, Gene Ontology Consortium, Developmental Biology, Biochemistry and cell biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023

3. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A, Alexander, Micheal, Anagnostopoulos, Anna V, Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M, Blake, Judith A, Blodgett, Olin, Bradford, Yvonne M, Bult, Carol J, Cain, Scott, Calvi, Brian R, Carbon, Seth, Chan, Juancarlos, Chen, Wen J, Cherry, J Michael, Cho, Jaehyoung, Christie, Karen R, Crosby, Madeline A, Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L, D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E, dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R, Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C, Gondwe, Felix, Goodman, Josh, Gramates, L Sian, Grove, Christian A, Hale, Paul, Harris, Todd, Hayman, G Thomas, Hill, David P, Howe, Douglas G, Howe, Kevin L, Hu, Yanhui, Jha, Sagar, Kadin, James A, Kaufman, Thomas C, Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E, Laulederkind, Stanley JF, Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A, Martin, Ryan, Marygold, Steven J, Matthews, Beverley, McAndrews, Monica S, Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J, Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S, Nash, Robert S, Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E, Gelbart, Susan Russo, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R, Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M, and Smith, Cynthia L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.5 Resources and infrastructure (underpinning), Alleles, Animals, Caenorhabditis elegans, Databases, Genetic, Drosophila, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomycetales, Zebrafish, Alliance of Genome Resources Consortium, biocuration, data mining, gene expression, gene function, gene interaction, genome, knowledgebase, phenotype, variants, Developmental Biology, Biochemistry and cell biology
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2022

5. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin CC, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit HM, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, and Karra, Kalpana

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Animals, Arabidopsis, Caenorhabditis elegans, Dictyostelium, Drosophila melanogaster, Escherichia coli, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomyces cerevisiae, Schizosaccharomyces, User-Computer Interface, Zebrafish, Gene Ontology Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

7. Long-term Metabolic Dysfunction Programming in Female Mice by Serial Moderate Restriction of a High-fat High-sucrose Diet.

Author

Wildes, Micah P, Fernando, Deemantha G, Grobe, Connie C, Reho, John J, Grobe, Justin L, Kidambi, Srividya, Kindel, Tammy L, Kwitek, Anne E, Segar, Jeffrey L, Williams, Joni S, and Morselli, Lisa L

Subjects
DIETARY patterns, GLUCOSE tolerance tests, INTERMITTENT fasting, LOW-calorie diet, BODY composition
Abstract

Background While intermittent fasting leads to weight loss and improved glucose metabolism, food insecurity, the insufficient access to food for a healthy life, is associated with obesity and adverse cardiometabolic health, especially in women. We aimed to characterize the effects of intermittently restricted feeding on energy balance and glucose tolerance in female mice. Methods Female C57BL/6J mice were fed a high-fat, high-sucrose diet and intermittently food restricted to 60% of control littermates' ad libitum intake, starting at weaning and until week 19. Restricted mice were subsequently allowed ad libitum access to the same diet. Body composition and energy balance were measured at weeks 18.5, 19, 30, and 40. At week 42, mice underwent an intraperitoneal glucose tolerance test and plasma appetitive hormones measurements after nutrient gavage. Results During the food restriction phase, restricted mice accrued lower weight and fat mass than controls despite periodic ad libitum food access. Reintroduction of continuous ad libitum food caused increased food intake during the light phase and increased body mass in restricted mice. Minor differences in body composition-adjusted energy expenditure between groups were observed at week 40. At week 42, glucose tolerance was impaired in restricted mice compared to controls, and trends toward lower levels of postprandial anorexigenic hormones glucagon-like peptide-1 and pancreatic polypeptide were observed. Conclusion Our findings suggest that repeated intermittent food restriction leads to changes in eating behavior that predispose to glucose intolerance when food is freely available. Future studies are needed to elucidate the specific mechanisms underlying these changes. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Krüppel-like factor 4 (KLF4) in Transcriptional Control of The Three Unique Isoforms of Agouti-Related Peptide (Agrp) in Mice

Author

Ritter, McKenzie L., primary, Wagner, Valerie A., additional, Balapattabi, Kirthikaa, additional, Opichka, Megan A., additional, Lu, Ko-Ting, additional, Wackman, Kelsey K., additional, Reho, John J., additional, Keen, Henry L., additional, Kwitek, Anne E, additional, Morselli, Lisa L, additional, Geurts, Aron M., additional, Sigmund, Curt D., additional, and Grobe, Justin L., additional

Published
2023
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13. Krüppel-like factor 4 in transcriptional control of the three unique isoforms of Agouti-related peptide in mice.

Author

Ritter, McKenzie L., Wagner, Valerie A., Balapattabi, Kirthikaa, Opichka, Megan A., Ko-Ting Lu, Wackman, Kelsey K., Reho, John J., Keen, Henry L., Kwitek, Anne E., Morselli, Lisa L., Geurts, Aron M., Sigmund, Curt D., and Grobe, Justin L.

Subjects
KRUPPEL-like factors, PEPTIDES, WEIGHT gain, ZINC-finger proteins, BODY composition, FAT, MICE, GENE expression
Abstract

This article explores the role of Krüppel-like factor 4 (KLF4) in the transcriptional control of Agouti-related peptide (AgRP) isoforms in mice. The study found that KLF4 promotes the transcription of AgRP in lean mice, but this mechanism is altered during diet-induced obesity. The findings suggest that the expression of AgRP isoforms is dependent on cell type and that KLF4 plays a context-dependent role in AgRP control. Further research is needed to investigate the differential regulation of Agrp isoforms by KLF4. The article also provides information about the funding and support received for the research project, as well as a list of references to other scientific articles and databases related to the study of energy homeostasis, gene expression, and neuroendocrinology. [Extracted from the article]

Published
2024
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26. Rare Disease Research Resources at the Rat Genome Database

Author

Kaldunski, Mary L, primary, Smith, Jennifer R, additional, Brodie, Kent C, additional, De Pons, Jeffrey L, additional, Demos, Wendy M, additional, Gibson, Adam C, additional, Hayman, G Thomas, additional, Lamers, Logan, additional, Laulederkind, Stanley J F, additional, Thorat, Ketaki, additional, Thota, Jyothi, additional, Tutaj, Marek A, additional, Tutaj, Monika, additional, Vedi, Mahima, additional, Wang, Shur-Jen, additional, Zacher, Stacy, additional, Dwinell, Melinda R, additional, and Kwitek, Anne E, additional

Published
2023
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27. 2022 Updates to the Rat Genome Database: A FAIR Resource

Author

Vedi, Mahima, primary, Smith, Jennifer R, additional, Hayman, G Thomas, additional, Tutaj, Monika, additional, Brodie, Kent C, additional, De Pons, Jeffrey L, additional, Demos, Wendy M, additional, Gibson, Adam C, additional, Kaldunski, Mary L, additional, Lamers, Logan, additional, Laulederkind, Stanley J F, additional, Thota, Jyothi, additional, Thorat, Ketaki, additional, Tutaj, Marek A, additional, Wang, Shur-Jen, additional, Zacher, Stacy, additional, Dwinell, Melinda R, additional, and Kwitek, Anne E, additional

Published
2023
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28. The Gene Ontology knowledgebase in 2023.

Author

Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, and Bakker, Erika

Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023

29. Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal

Author

Wang, Shur-Jen, primary, Brodie, Kent C., additional, De Pons, Jeffrey L., additional, Demos, Wendy M., additional, Gibson, Adam C., additional, Hayman, G. Thomas, additional, Hill, Morgan L., additional, Kaldunski, Mary L., additional, Lamers, Logan, additional, Laulederkind, Stanley J. F., additional, Nalabolu, Harika S., additional, Thota, Jyothi, additional, Thorat, Ketaki, additional, Tutaj, Marek A., additional, Tutaj, Monika, additional, Vedi, Mahima, additional, Zacher, Stacy, additional, Smith, Jennifer R., additional, Dwinell, Melinda R., additional, and Kwitek, Anne E., additional

Published
2022
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30. The Gene Ontology knowledgebase in 2023

Author

Consortium, Gene Ontology, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte

Subjects
Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Cell Biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023
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36. Cardiometabolic effects of DOCA-salt in male C57BL/6J mice are variably dependent on sodium and nonsodium components of diet

Author

Patil, Chetan N., primary, Ritter, McKenzie L., additional, Wackman, Kelsey K., additional, Oliveira, Vanessa, additional, Balapattabi, Kirthikaa, additional, Grobe, Connie C., additional, Brozoski, Daniel T., additional, Reho, John J., additional, Nakagawa, Pablo, additional, Mouradian, Gary C., additional, Kriegel, Alison J., additional, Kwitek, Anne E., additional, Hodges, Matthew R., additional, Segar, Jeffrey L., additional, Sigmund, Curt D., additional, and Grobe, Justin L., additional

Published
2022
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41. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A., Alexander, Micheal, Anagnostopoulos, Anna V., Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M., Blake, Judith A., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Christie, Karen R., Crosby, Madeline A., Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L., D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E., dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R., Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C., Gondwe, Felix, Goodman, Josh, Gramates, L. Sian, Grove, Christian A., Hale, Paul, Harris, Todd, Thomas Hayman, G., Hill, David P., Howe, Douglas G., Howe, Kevin L., Hu, Yanhui, Jha, Sagar, Kadin, James A., Kaufman, Thomas C., Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E., Laulederkind, Stanley J. F., Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A., Martin, Ryan, Marygold, Steven J., Matthews, Beverley, McAndrews, Monica S., Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Müller, Hans-Michael, Mungall, Christopher J., Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S., Nash, Robert S., Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E., Russo Gelbart, Susan, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R., Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M., Smith, Cynthia L., Smith, Jennifer R., Stein, Lincoln, Sternberg, Paul W., Tabone, Christopher J., Thomas, Paul D., Thorat, Ketaki, Thota, Jyothi, Toro, Sabrina, Tomczuk, Monika, Trovisco, Vitor, Tutaj, Marek A., Tutaj, Monika, Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Wang, Qinghua, Wang, Shur-Jen, Weng, Shuai, Westerfield, Monte, Williams, Gary, Wilming, Laurens G., Wong, Edith D., Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Zhou, Pinglei, and Zytkovicz, Mark

Subjects
Internet, Molecular Sequence Annotation, Rats, Mice, Gene Ontology, Databases, Genetic, Saccharomycetales, Genetics, Animals, Humans, Drosophila, Caenorhabditis elegans, Alleles, Zebrafish
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2021

42. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

Author

Howe, Kerstin, Dwinell, Melinda, Shimoyama, Mary, Corton, Craig, Betteridge, Emma, Dove, Alexander, Quail, Michael A, Smith, Michelle, Saba, Laura, Williams, Robert W, Chen, Hao, Kwitek, Anne E, McCarthy, Shane A, Uliano-Silva, Marcela, Chow, William, Tracey, Alan, Torrance, James, Sims, Ying, Challis, Richard, Threlfall, Jonathan, Blaxter, Mark, Howe, Kerstin [0000-0003-2237-513X], Saba, Laura [0000-0001-9649-1294], Williams, Robert W [0000-0001-8924-4447], Kwitek, Anne E [0000-0003-1024-4116], Tracey, Alan [0000-0002-4805-9058], Torrance, James [0000-0002-6117-8190], Challis, Richard [0000-0002-3502-1122], Threlfall, Jonathan [0000-0001-8599-4320], Blaxter, Mark [0000-0003-2861-949X], and Apollo - University of Cambridge Repository

Subjects
genome sequence, chromosomal, Rattus norvegicus, reference genome, Norway rat
Abstract

We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.

Published
2021

44. Methods for the Comprehensive in vivo Analysis of Energy Flux, Fluid Homeostasis, Blood Pressure, and Ventilatory Function in Rodents

Author

Reho, John J., primary, Nakagawa, Pablo, additional, Mouradian, Gary C., additional, Grobe, Connie C., additional, Saravia, Fatima L., additional, Burnett, Colin M. L., additional, Kwitek, Anne E., additional, Kirby, John R., additional, Segar, Jeffrey L., additional, Hodges, Matthew R., additional, Sigmund, Curt D., additional, and Grobe, Justin L., additional

Published
2022
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45. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses

Author

Vedi, Mahima, primary, Nalabolu, Harika S, additional, Lin, Chien-Wei, additional, Hoffman, Matthew J, additional, Smith, Jennifer R, additional, Brodie, Kent, additional, De Pons, Jeffrey L, additional, Demos, Wendy M, additional, Gibson, Adam C, additional, Hayman, G Thomas, additional, Hill, Morgan L, additional, Kaldunski, Mary L, additional, Lamers, Logan, additional, Laulederkind, Stanley J F, additional, Thorat, Ketaki, additional, Thota, Jyothi, additional, Tutaj, Monika, additional, Tutaj, Marek A, additional, Wang, Shur-Jen, additional, Zacher, Stacy, additional, Dwinell, Melinda R, additional, and Kwitek, Anne E, additional

Published
2022
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