TY - JOUR A1 - Jiang, Yuxiang A1 - Oron, Tal Ronnen A1 - Clark, Wyatt T. A1 - Bankapur, Asma R. A1 - D'Andrea, Daniel A1 - Lepore, Rosalba A1 - Funk, Christopher S. A1 - Kahanda, Indika A1 - Verspoor, Karin M. A1 - Ben-Hur, Asa A1 - Koo, Da Chen Emily A1 - Penfold-Brown, Duncan A1 - Shasha, Dennis A1 - Youngs, Noah A1 - Bonneau, Richard A1 - Lin, Alexandra A1 - Sahraeian, Sayed M. E. A1 - Martelli, Pier Luigi A1 - Profiti, Giuseppe A1 - Casadio, Rita A1 - Cao, Renzhi A1 - Zhong, Zhaolong A1 - Cheng, Jianlin A1 - Altenhoff, Adrian A1 - Skunca, Nives A1 - Dessimoz, Christophe A1 - Dogan, Tunca A1 - Hakala, Kai A1 - Kaewphan, Suwisa A1 - Mehryary, Farrokh A1 - Salakoski, Tapio A1 - Ginter, Filip A1 - Fang, Hai A1 - Smithers, Ben A1 - Oates, Matt A1 - Gough, Julian A1 - Törönen, Petri A1 - Koskinen, Patrik A1 - Holm, Liisa A1 - Chen, Ching-Tai A1 - Hsu, Wen-Lian A1 - Bryson, Kevin A1 - Cozzetto, Domenico A1 - Minneci, Federico A1 - Jones, David T. A1 - Chapman, Samuel A1 - BKC, Dukka A1 - Khan, Ishita K. A1 - Kihara, Daisuke A1 - Ofer, Dan A1 - Rappoport, Nadav A1 - Stern, Amos A1 - Cibrian-Uhalte, Elena A1 - Denny, Paul A1 - Foulger, Rebecca E. A1 - Hieta, Reija A1 - Legge, Duncan A1 - Lovering, Ruth C. A1 - Magrane, Michele A1 - Melidoni, Anna N. A1 - Mutowo-Meullenet, Prudence A1 - Pichler, Klemens A1 - Shypitsyna, Aleksandra A1 - Li, Biao A1 - Zakeri, Pooya A1 - ElShal, Sarah A1 - Tranchevent, Léon-Charles A1 - Das, Sayoni A1 - Dawson, Natalie L. A1 - Lee, David A1 - Lees, Jonathan G. A1 - Sillitoe, Ian A1 - Bhat, Prajwal A1 - Nepusz, Tamás A1 - Romero, Alfonso E. A1 - Sasidharan, Rajkumar A1 - Yang, Haixuan A1 - Paccanaro, Alberto A1 - Gillis, Jesse A1 - Sedeño-Cortés, Adriana E. A1 - Pavlidis, Paul A1 - Feng, Shou A1 - Cejuela, Juan M. A1 - Goldberg, Tatyana A1 - Hamp, Tobias A1 - Richter, Lothar A1 - Salamov, Asaf A1 - Gabaldon, Toni A1 - Marcet-Houben, Marina A1 - Supek, Fran A1 - Gong, Qingtian A1 - Ning, Wei A1 - Zhou, Yuanpeng A1 - Tian, Weidong A1 - Falda, Marco A1 - Fontana, Paolo A1 - Lavezzo, Enrico A1 - Toppo, Stefano A1 - Ferrari, Carlo A1 - Giollo, Manuel A1 - Piovesan, Damiano A1 - Tosatto, Silvio C. E. A1 - del Pozo, Angela A1 - Fernández, José M. A1 - Maietta, Paolo A1 - Valencia, Alfonso A1 - Tress, Michael L. A1 - Benso, Alfredo A1 - Di Carlo, Stefano A1 - Politano, Gianfranco A1 - Savino, Alessandro A1 - Rehman, Hafeez Ur A1 - Re, Matteo A1 - Mesiti, Marco A1 - Valentini, Giorgio A1 - Bargsten, Joachim W. A1 - van Dijk, Aalt D. J. A1 - Gemovic, Branislava A1 - Glisic, Sanja A1 - Perovic, Vladmir A1 - Veljkovic, Veljko A1 - Almeida-e-Silva, Danillo C. A1 - Vencio, Ricardo Z. N. A1 - Sharan, Malvika A1 - Vogel, Jörg A1 - Kansakar, Lakesh A1 - Zhang, Shanshan A1 - Vucetic, Slobodan A1 - Wang, Zheng A1 - Sternberg, Michael J. E. A1 - Wass, Mark N. A1 - Huntley, Rachael P. A1 - Martin, Maria J. A1 - O'Donovan, Claire A1 - Robinson, Peter N. A1 - Moreau, Yves A1 - Tramontano, Anna A1 - Babbitt, Patricia C. A1 - Brenner, Steven E. A1 - Linial, Michal A1 - Orengo, Christine A. A1 - Rost, Burkhard A1 - Greene, Casey S. A1 - Mooney, Sean D. A1 - Friedberg, Iddo A1 - Radivojac, Predrag A1 - Veljkovic, Nevena T1 - An expanded evaluation of protein function prediction methods shows an improvement in accuracy JF - Genome Biology N2 - Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. KW - Protein function prediction KW - Disease gene prioritization Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166293 VL - 17 IS - 184 ER - TY - JOUR A1 - Majounie, Elisa A1 - Renton, Alan E. A1 - Mok, Kin A1 - Dopper, Elise G. P. A1 - Waite, Adrian A1 - Rollinson, Sara A1 - Chiò, Adriano A1 - Restagno, Gabriella A1 - Nicolaou, Nayia A1 - Simon-Sanchez, Javier A1 - van Swieten, John C. A1 - Abramzon, Yevgeniya A1 - Johnson, Janel O. A1 - Sendtner, Michael A1 - Pamphlett, Roger A1 - Orrell, Richard W. A1 - Mead, Simon A1 - Sidle, Katie C. A1 - Houlden, Henry A1 - Rohrer, Jonathan D. A1 - Morrison, Karen E. A1 - Pall, Hardev A1 - Talbot, Kevin A1 - Ansorge, Olaf A1 - Hernandez, Dena G. A1 - Arepalli, Sampath A1 - Sabatelli, Mario A1 - Mora, Gabriele A1 - Corbo, Massimo A1 - Giannini, Fabio A1 - Calvo, Andrea A1 - Englund, Elisabet A1 - Borghero, Giuseppe A1 - Floris, Gian Luca A1 - Remes, Anne M. A1 - Laaksovirta, Hannu A1 - McCluskey, Leo A1 - Trojanowski, John Q. A1 - Van Deerlin, Vivianna M. A1 - Schellenberg, Gerard D. A1 - Nalls, Michael A. A1 - Drory, Vivian E. A1 - Lu, Chin-Song A1 - Yeh, Tu-Hsueh A1 - Ishiura, Hiroyuki A1 - Takahashi, Yuji A1 - Tsuji, Shoji A1 - Le Ber, Isabelle A1 - Brice, Alexis A1 - Drepper, Carsten A1 - Williams, Nigel A1 - Kirby, Janine A1 - Shaw, Pamela A1 - Hardy, John A1 - Tienari, Pentti J. A1 - Heutink, Peter A1 - Morris, Huw R. A1 - Pickering-Brown, Stuart A1 - Traynor, Bryan J. T1 - Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study JF - The Lancet Neurology N2 - Background We aimed to accurately estimate the frequency of a hexanucleotide repeat expansion in C9orf72 that has been associated with a large proportion of cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Methods We screened 4448 patients diagnosed with ALS (El Escorial criteria) and 1425 patients with FTD (Lund-Manchester criteria) from 17 regions worldwide for the GGGGCC hexanucleotide expansion using a repeat-primed PCR assay. We assessed familial disease status on the basis of self-reported family history of similar neurodegenerative diseases at the time of sample collection. We compared haplotype data for 262 patients carrying the expansion with the known Finnish founder risk haplotype across the chromosomal locus. We calculated age-related penetrance using the Kaplan-Meier method with data for 603 individuals with the expansion. Findings In patients with sporadic ALS, we identified the repeat expansion in 236 (7·0%) of 3377 white individuals from the USA, Europe, and Australia, two (4·1%) of 49 black individuals from the USA, and six (8·3%) of 72 Hispanic individuals from the USA. The mutation was present in 217 (39·3%) of 552 white individuals with familial ALS from Europe and the USA. 59 (6·0%) of 981 white Europeans with sporadic FTD had the mutation, as did 99 (24·8%) of 400 white Europeans with familial FTD. Data for other ethnic groups were sparse, but we identified one Asian patient with familial ALS (from 20 assessed) and two with familial FTD (from three assessed) who carried the mutation. The mutation was not carried by the three Native Americans or 360 patients from Asia or the Pacific Islands with sporadic ALS who were tested, or by 41 Asian patients with sporadic FTD. All patients with the repeat expansion had (partly or fully) the founder haplotype, suggesting a one-off expansion occurring about 1500 years ago. The pathogenic expansion was non-penetrant in individuals younger than 35 years, 50% penetrant by 58 years, and almost fully penetrant by 80 years. Interpretation A common Mendelian genetic lesion in C9orf72 is implicated in many cases of sporadic and familial ALS and FTD. Testing for this pathogenic expansion should be considered in the management and genetic counselling of patients with these fatal neurodegenerative diseases. KW - DNA repeat expansion KW - C9orf72 KW - amyotrophic lateral sclerosis KW - frontotemporal dementia KW - cross-sectional studies Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-154644 VL - 11 SP - 323 EP - 330 ER - TY - JOUR A1 - Iyengar, Sudha K. A1 - Sedor, John R. A1 - Freedman, Barry I. A1 - Kao, W. H. Linda A1 - Kretzler, Matthias A1 - Keller, Benjamin J. A1 - Abboud, Hanna E. A1 - Adler, Sharon G. A1 - Best, Lyle G. A1 - Bowden, Donald W. A1 - Burlock, Allison A1 - Chen, Yii-Der Ida A1 - Cole, Shelley A. A1 - Comeau, Mary E. A1 - Curtis, Jeffrey M. A1 - Divers, Jasmin A1 - Drechsler, Christiane A1 - Duggirala, Ravi A1 - Elston, Robert C. A1 - Guo, Xiuqing A1 - Huang, Huateng A1 - Hoffmann, Michael Marcus A1 - Howard, Barbara V. A1 - Ipp, Eli A1 - Kimmel, Paul L. A1 - Klag, Michael J. A1 - Knowler, William C. A1 - Kohn, Orly F. A1 - Leak, Tennille S. A1 - Leehey, David J. A1 - Li, Man A1 - Malhotra, Alka A1 - März, Winfried A1 - Nair, Viji A1 - Nelson, Robert G. A1 - Nicholas, Susanne B. A1 - O’Brien, Stephen J. A1 - Pahl, Madeleine V. A1 - Parekh, Rulan S. A1 - Pezzolesi, Marcus G. A1 - Rasooly, Rebekah S. A1 - Rotimi, Charles N. A1 - Rotter, Jerome I. A1 - Schelling, Jeffrey R. A1 - Seldin, Michael F. A1 - Shah, Vallabh O. A1 - Smiles, Adam M. A1 - Smith, Michael W. A1 - Taylor, Kent D. A1 - Thameem, Farook A1 - Thornley-Brown, Denyse P. A1 - Truitt, Barbara J. A1 - Wanner, Christoph A1 - Weil, E. Jennifer A1 - Winkler, Cheryl A. A1 - Zager, Philip G. A1 - Igo, Jr, Robert P. A1 - Hanson, Robert L. A1 - Langefeld, Carl D. T1 - Genome-wide association and trans-ethnic meta-analysis for advanced diabetic kidney disease: Family Investigation of Nephropathy and Diabetes (FIND) JF - PLoS Genetics N2 - Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10\(^{−9}\)). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10\(^{−8}\)), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD. KW - diabetic kidney disease KW - genome-wide association study KW - Family Investigation of Nephropathy and Diabetes Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180545 VL - 11 IS - 8 ER - TY - CHAP A1 - Brown, C. C. A1 - Heinze, B. A1 - Krüger, Hans-Peter T1 - Der exakte 2x2x2-Felder-Kontingenztest. (Brown-Heinze-Krüger-Tafeln) N2 - No abstract available Y1 - 1975 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40933 ER - TY - CHAP A1 - Brown, C. C. A1 - Heinze, B. A1 - Krüger, Hans-Peter T1 - Tafel des exakten 2x2x2-Felder-Kontingenztests N2 - No abstract available KW - Biostatistik KW - Nichtparametrischer Test Y1 - 1975 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40952 ER - TY - JOUR A1 - Perrella, Gina A1 - Montague, Samantha J. A1 - Brown, Helena C. A1 - Garcia Quintanilla, Lourdes A1 - Slater, Alexandre A1 - Stegner, David A1 - Thomas, Mark A1 - Heemskerk, Johan W. M. A1 - Watson, Steve P. T1 - Role of tyrosine kinase Syk in thrombus stabilisation at high shear JF - International Journal of Molecular Sciences N2 - Understanding the pathways involved in the formation and stability of the core and shell regions of a platelet-rich arterial thrombus may result in new ways to treat arterial thrombosis. The distinguishing feature between these two regions is the absence of fibrin in the shell which indicates that in vitro flow-based assays over thrombogenic surfaces, in the absence of coagulation, can be used to resemble this region. In this study, we have investigated the contribution of Syk tyrosine kinase in the stability of platelet aggregates (or thrombi) formed on collagen or atherosclerotic plaque homogenate at arterial shear (1000 s\(^{−1}\)). We show that post-perfusion of the Syk inhibitor PRT-060318 over preformed thrombi on both surfaces enhances thrombus breakdown and platelet detachment. The resulting loss of thrombus stability led to a reduction in thrombus contractile score which could be detected as early as 3 min after perfusion of the Syk inhibitor. A similar loss of thrombus stability was observed with ticagrelor and indomethacin, inhibitors of platelet adenosine diphosphate (ADP) receptor and thromboxane A\(_2\) (TxA\(_2\)), respectively, and in the presence of the Src inhibitor, dasatinib. In contrast, the Btk inhibitor, ibrutinib, causes only a minor decrease in thrombus contractile score. Weak thrombus breakdown is also seen with the blocking GPVI nanobody, Nb21, which indicates, at best, a minor contribution of collagen to the stability of the platelet aggregate. These results show that Syk regulates thrombus stability in the absence of fibrin in human platelets under flow and provide evidence that this involves pathways additional to activation of GPVI by collagen. KW - disaggregation KW - platelet KW - Syk KW - thrombus KW - tyrosine kinase Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284243 SN - 1422-0067 VL - 23 IS - 1 ER -