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1. Current status and new features of the Consensus Coding Sequence database

Author

Farrell, Catherine M, O’Leary, Nuala A, Harte, Rachel A, Loveland, Jane E, Wilming, Laurens G, Wallin, Craig, Diekhans, Mark, Barrell, Daniel, Searle, Stephen MJ, Aken, Bronwen, Hiatt, Susan M, Frankish, Adam, Suner, Marie-Marthe, Rajput, Bhanu, Steward, Charles A, Brown, Garth R, Bennett, Ruth, Murphy, Michael, Wu, Wendy, Kay, Mike P, Hart, Jennifer, Rajan, Jeena, Weber, Janet, Snow, Catherine, Riddick, Lillian D, Hunt, Toby, Webb, David, Thomas, Mark, Tamez, Pamela, Rangwala, Sanjida H, McGarvey, Kelly M, Pujar, Shashikant, Shkeda, Andrei, Mudge, Jonathan M, Gonzalez, Jose M, Gilbert, James GR, Trevanion, Stephen J, Baertsch, Robert, Harrow, Jennifer L, Hubbard, Tim, Ostell, James M, Haussler, David, and Pruitt, Kim D

Subjects
Human Genome, Genetics, Animals, Databases, Genetic, Exons, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Proteins, Sequence Analysis, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

Published
2014

2. 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

5. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Author

Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi

Published
2009

7. Complete MHC haplotype sequencing for common disease gene mapping

Author

Stewart, Andrew C., Ashurst, Jennifer L., Allcock, Richard J.N., Horton, Roger, Atrazhev, Alexey M., Hunt, Sarah, Humphray, Sean J., Howson, Joanna M.M., Halls, Karen, Forbes, Simon, Dunham, Ian, Coggill, Penny, Palmer, Sophie, Osoegawa, Kazutoyo, Mungall, Andrew J., Sims, Sarah, Rogers, Jane, Roberts, Anne N., Yu Wang, Todd, John A., Beck, Stephen, Trowsdale, John, Sawcer, Stephen, Jong, Peiter J. de, Elliott, John F., and Wilming, Laurens G.

Subjects
Nucleotide sequence -- Research, Chromosome mapping -- Research, Genetic research, Health
Abstract

A comparison between autoimmune-disease-associated-haplotypes HLA-A3-B7-Cw7-DR15 and HLA-A1-B8-Cw7-DR3 of human major histocompatibility sequence is conducted for determining the gene mapping of common diseases. Complete polymorphism maps can be obtained using clone-based approaches.

Published
2004

8. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection

Author

Numata, Koji, Kanai, Akio, Saito, Rintaro, Kondo, Shinji, Adachi, Jun, Wilming, Laurens G., Hume, David A., Hayashizaki, Yoshihide, Tomita, Masaru, Arakawa, Takahiro, Carninci, Piero, and Kawai, Jun

Subjects
Genomes -- Research, Genetic research -- Analysis, Genetic research -- Methods, DNA -- Genetic aspects, RNA -- Genetic aspects, Gene expression -- Physiological aspects, Genetic transcription -- Physiological aspects, Methodology -- Analysis, Health
Abstract

Research has been conducted on noncoding RNAs. The authors have identified the candidate functional noncoding RNAs from the RIKEN mouse full-length cDNA collection via the use of systematic computational filtering approach, and have reported the results.

Published
2003

10. The Vertebrate Genome Annotation browser 10 years on

Author

Harrow, Jennifer L., primary, Steward, Charles A., additional, Frankish, Adam, additional, Gilbert, James G., additional, Gonzalez, Jose M., additional, Loveland, Jane E., additional, Mudge, Jonathan, additional, Sheppard, Dan, additional, Thomas, Mark, additional, Trevanion, Stephen, additional, and Wilming, Laurens G., additional

Published
2013
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11. Current status and new features of the Consensus Coding Sequence database

Author

Farrell, Catherine M., primary, O’Leary, Nuala A., additional, Harte, Rachel A., additional, Loveland, Jane E., additional, Wilming, Laurens G., additional, Wallin, Craig, additional, Diekhans, Mark, additional, Barrell, Daniel, additional, Searle, Stephen M. J., additional, Aken, Bronwen, additional, Hiatt, Susan M., additional, Frankish, Adam, additional, Suner, Marie-Marthe, additional, Rajput, Bhanu, additional, Steward, Charles A., additional, Brown, Garth R., additional, Bennett, Ruth, additional, Murphy, Michael, additional, Wu, Wendy, additional, Kay, Mike P., additional, Hart, Jennifer, additional, Rajan, Jeena, additional, Weber, Janet, additional, Snow, Catherine, additional, Riddick, Lillian D., additional, Hunt, Toby, additional, Webb, David, additional, Thomas, Mark, additional, Tamez, Pamela, additional, Rangwala, Sanjida H., additional, McGarvey, Kelly M., additional, Pujar, Shashikant, additional, Shkeda, Andrei, additional, Mudge, Jonathan M., additional, Gonzalez, Jose M., additional, Gilbert, James G. R., additional, Trevanion, Stephen J., additional, Baertsch, Robert, additional, Harrow, Jennifer L., additional, Hubbard, Tim, additional, Ostell, James M., additional, Haussler, David, additional, and Pruitt, Kim D., additional

Published
2013
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12. Sequencing and comparative analysis of the gorilla MHC genomic sequence

Author

Wilming, Laurens G., primary, Hart, Elizabeth A., additional, Coggill, Penny C., additional, Horton, Roger, additional, Gilbert, James G. R., additional, Clee, Chris, additional, Jones, Matt, additional, Lloyd, Christine, additional, Palmer, Sophie, additional, Sims, Sarah, additional, Whitehead, Siobhan, additional, Wiley, David, additional, Beck, Stephan, additional, and Harrow, Jennifer L., additional

Published
2013
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13. Pseudo-messenger RNA : Phantoms of the transcriptome

Author

Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Tan, Sin Lam, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L., Huminiecki, Lukasz, Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Tan, Sin Lam, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L., and Huminiecki, Lukasz

Abstract

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein- coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo - messenger RNAs ( approximately half of which are transposonassociated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein- coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense- mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non- standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.

Published
2006
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16. Discovery of Candidate Disease Genes in ENU–Induced Mouse Mutants by Large-Scale Sequencing, Including a Splice-Site Mutation in Nucleoredoxin

Author

Boles, Melissa K., primary, Wilkinson, Bonney M., additional, Wilming, Laurens G., additional, Liu, Bin, additional, Probst, Frank J., additional, Harrow, Jennifer, additional, Grafham, Darren, additional, Hentges, Kathryn E., additional, Woodward, Lanette P., additional, Maxwell, Andrea, additional, Mitchell, Karen, additional, Risley, Michael D., additional, Johnson, Randy, additional, Hirschi, Karen, additional, Lupski, James R., additional, Funato, Yosuke, additional, Miki, Hiroaki, additional, Marin-Garcia, Pablo, additional, Matthews, Lucy, additional, Coffey, Alison J., additional, Parker, Anne, additional, Hubbard, Tim J., additional, Rogers, Jane, additional, Bradley, Allan, additional, Adams, David J., additional, and Justice, Monica J., additional

Published
2009
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18. Pseudo–Messenger RNA: Phantoms of the Transcriptome

Author

Frith, Martin C, primary, Wilming, Laurens G, additional, Forrest, Alistair, additional, Kawaji, Hideya, additional, Tan, Sin Lam, additional, Wahlestedt, Claes, additional, Bajic, Vladimir B, additional, Kai, Chikatoshi, additional, Kawai, Jun, additional, Carninci, Piero, additional, Hayashizaki, Yoshihide, additional, Bailey, Timothy L, additional, and Huminiecki, Lukasz, additional

Published
2006
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19. Genetic Analysis of Completely Sequenced Disease-Associated MHC Haplotypes Identifies Shuffling of Segments in Recent Human History

Author

Traherne, James A, primary, Horton, Roger, additional, Roberts, Anne N, additional, Miretti, Marcos M, additional, Hurles, Matthew E, additional, Stewart, C. Andrew, additional, Ashurst, Jennifer L, additional, Atrazhev, Alexey M, additional, Coggill, Penny, additional, Palmer, Sophie, additional, Almeida, Jeff, additional, Sims, Sarah, additional, Wilming, Laurens G, additional, Rogers, Jane, additional, de Jong, Pieter J., additional, Carrington, Mary, additional, Elliott, John F, additional, Sawcer, Stephen, additional, Todd, John A, additional, Trowsdale, John, additional, and Beck, Stephan, additional

Published
2006
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23. Pseudo-Messenger RNA: Phantoms of the Transcriptome.

Author

Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Sin Lam Tan, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L., and Huminiecki, Lukasz

Subjects
*MESSENGER RNA, *GENETIC code, *PROTEINS, *NUCLEOTIDE sequence, *CIRCULAR DNA, *GENETIC transcription, *TRANSPOSONS, *GENOMES
Abstract

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo-messenger RNAs (approximately half of which are transposon-associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein-coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense-mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non-standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level. [ABSTRACT FROM AUTHOR]

Published
2006
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25. A novel member of the transmembrane serine/threonine kinase receptor family is specifically expressed in the gonads and in mesenchymal cells adjacent to the müllerian duct

Author

Baarends, Willy M., Helmond, Marjolein J. L. van, Post, Miriam, Schoot, Pieter J. C. M. van der, Hoogerbrugge, Jos W., Winter, Johan P. de, Uilenbroek, Jan Th. J., Karels, Bas, Wilming, Laurens G., Meijers, J. H. Carel, Themmen, Axel P. N., and Grootegoed, J. Anton

Abstract

The activin and TGF-β type II receptors are members of a separate subfamily of transmembrane receptors with intrinsic protein kinase activity, which also includes the recently cloned TGF-β type I receptor. We have isolated and characterized a cDNA clone (C14) encoding a new member of this subfamily. The domain structure of the C14-encoded protein corresponds with the structure of the other known transmembrane serine/threonine kinase receptors. It also contains the two inserts in the kinase domain that are characteristic for this subfamily. Using in situ hybridization, C14 mRNA was detected in the mesenchymal cells located adjacent to the müllerian ducts of males and females at day 15 (E15) of embryonic development. Marked C14 mRNA expression was also detected in the female gonads. In female E16 embryos, the C14 mRNA expression pattern remained similar to that in E15 embryos. However, in male E16 embryos C14 mRNA was detected in a circular area that includes the degenerating müllerian duct. The expression of C14 mRNA was also studied using RNase protection assays. At E15 and E16, C14 mRNA is expressed in the female as well as in the male urogenital ridge. However, at E19, a high C14 mRNA level in the female urogenital ridge contrasts with a lack of C14 mRNA in the male urogenital ridge. This correlates with the almost complete degeneration of the müllerian ducts in male embryos at E19. C14 mRNA expression was also detected in embryonic testes at E15, E16 and E19 using RNase protection assays, but at much lower levels than those found in the developing ovaries. In eleven other tissues no C14 mRNA was observed. The results point to anti-müllerian hormone (AMH) being the most likely candidate ligand for C14. The embryonic C14 mRNA expression pattern in the urogenital ridge correlates with the expected site of AMH action, and C14 mRNA expression in the fetal ovary is in agreement with known effects of AMH on gonadal differentiation. Postnatal C14 mRNA expression in rats was found to be confined mainly to the gonads. In the testis, C14 mRNA expression occurs in Sertoli cells. This testicular expression markedly increases during the first 3 weeks after birth, concurrent with the onset of spermatogenesis.

Published
1994
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26. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin

Author

Boles, Melissa K, Wilkinson, Bonney M, Wilming, Laurens G, Liu, Bin, Probst, Frank J, Harrow, Jennifer, Grafham, Darren, Hentges, Kathryn E, Woodward, Lanette P, Maxwell, Andrea, Mitchell, Karen, Risley, Michael D, Johnson, Randy, Hirschi, Karen, Lupski, James R, Funato, Yosuke, Miki, Hiroaki, Marin-Garcia, Pablo, Matthews, Lucy, Coffey, Alison J, Parker, Anne, Hubbard, Tim J, Rogers, Jane, Bradley, Allan, Adams, David J, and Justice, Monica J

Subjects
Mice, Ethylnitrosourea, Gene Expression Profiling, Mutation, Animals, Chromosome Mapping, Nuclear Proteins, Genes, Lethal, Exons, Oxidoreductases, Mice, Mutant Strains, 3. Good health
Abstract

An accurate and precisely annotated genome assembly is a fundamental requirement for functional genomic analysis. Here, the complete DNA sequence and gene annotation of mouse Chromosome 11 was used to test the efficacy of large-scale sequencing for mutation identification. We re-sequenced the 14,000 annotated exons and boundaries from over 900 genes in 41 recessive mutant mouse lines that were isolated in an N-ethyl-N-nitrosourea (ENU) mutation screen targeted to mouse Chromosome 11. Fifty-nine sequence variants were identified in 55 genes from 31 mutant lines. 39% of the lesions lie in coding sequences and create primarily missense mutations. The other 61% lie in noncoding regions, many of them in highly conserved sequences. A lesion in the perinatal lethal line l11Jus13 alters a consensus splice site of nucleoredoxin (Nxn), inserting 10 amino acids into the resulting protein. We conclude that point mutations can be accurately and sensitively recovered by large-scale sequencing, and that conserved noncoding regions should be included for disease mutation identification. Only seven of the candidate genes we report have been previously targeted by mutation in mice or rats, showing that despite ongoing efforts to functionally annotate genes in the mammalian genome, an enormous gap remains between phenotype and function. Our data show that the classical positional mapping approach of disease mutation identification can be extended to large target regions using high-throughput sequencing.

27. Meeting report: a workshop on Best Practices in Genome Annotation.

Author

Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P, and Hannick LI

Abstract

Efforts to annotate the genomes of a wide variety of model organisms are currently carried out by sequencing centers, model organism databases and academic/institutional laboratories around the world. Different annotation methods and tools have been developed over time to meet the needs of biologists faced with the task of annotating biological data. While standardized methods are essential for consistent curation within each annotation group, methods and tools can differ between groups, especially when the groups are curating different organisms. Biocurators from several institutes met at the Third International Biocuration Conference in Berlin, Germany, April 2009 and hosted the 'Best Practices in Genome Annotation: Inference from Evidence' workshop to share their strategies, pipelines, standards and tools. This article documents the material presented in the workshop.

Published
2010
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