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Kristina M. Hettne Mark Thompson Herman H. H. B. M. van Haagen Eelke van der Horst Rajaram Kaliyaperumal Eleni Mina Zuotian Tatum Jeroen F. J. Laros Erik M. van Mulligen Martijn Schuemie Emmelien Aten Tong Shu Li Richard Bruskiewich Benjamin M. Good Andrew I. Su Jan A. Kors Johan den Dunnen Gert-Jan B. van Ommen Marco Roos Peter A.C. ‘t Hoen Barend Mons Erik A. Schultes 《PloS one》2016,11(2)
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations. 相似文献
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Mark?A?HerbertEmail author Catriona?JE?Beveridge David?McCormick Emmelien?Aten Nicola?Jones Lori?AS?Snyder Nigel?J?Saunders 《BMC microbiology》2005,5(1):31
Background
Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively. 相似文献3.
Olivier De Clerck Shu-Min Kao Kenny A. Bogaert Jonas Blomme Fatima Foflonker Michiel Kwantes Emmelien Vancaester Lisa Vanderstraeten Eylem Aydogdu Jens Boesger Gianmaria Califano Benedicte Charrier Rachel Clewes Andrea Del Cortona Sofie D’Hondt Noe Fernandez-Pozo Claire M. Gachon Marc Hanikenne John H. Bothwell 《Current biology : CB》2018,28(18):2921-2933.e5
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Yu Sun Rowida Almomani Emmelien Aten Jaap van der Heijden Stephen P. Robertson Brunella Franco Lina Basel-Vanagaite Ricardo Drut Johan T. den Dunnen Martijn H. Breuning 《American journal of human genetics》2010,87(1):146-5937
Terminal osseous dysplasia (TOD) is an X-linked dominant male-lethal disease characterized by skeletal dysplasia of the limbs, pigmentary defects of the skin, and recurrent digital fibroma with onset in female infancy. After performing X-exome capture and sequencing, we identified a mutation at the last nucleotide of exon 31 of the FLNA gene as the most likely cause of the disease. The variant c.5217G>A was found in six unrelated cases (three families and three sporadic cases) and was not found in 400 control X chromosomes, pilot data from the 1000 Genomes Project, or the FLNA gene variant database. In the families, the variant segregated with the disease, and it was transmitted four times from a mildly affected mother to a more seriously affected daughter. We show that, because of nonrandom X chromosome inactivation, the mutant allele was not expressed in patient fibroblasts. RNA expression of the mutant allele was detected only in cultured fibroma cells obtained from 15-year-old surgically removed material. The variant activates a cryptic splice site, removing the last 48 nucleotides from exon 31. At the protein level, this results in a loss of 16 amino acids (p.Val1724_Thr1739del), predicted to remove a sequence at the surface of filamin repeat 15. Our data show that TOD is caused by this single recurrent mutation in the FLNA gene. 相似文献
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Xenia Latypova Marie Vincent Alice Mollé Oluwadamilare A. Adebambo Cynthia Fourgeux Tahir N. Khan Alfonso Caro Monica Rosello Carmen Orellana Dmitriy Niyazov Damien Lederer Marie Deprez Yline Capri Peter Kannu Anne Claude Tabet Jonathan Levy Emmelien Aten Nicolette den Hollander Bertrand Isidor 《American journal of human genetics》2021,108(5):929-941
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