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InterPro, progress and status in 2005

N. J. Mulder
2004 Nucleic Acids Research  
InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text-and sequencebased searches via a webserver (  ...  Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases.  ...  ACKNOWLEDGEMENTS The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) and the Integr8 grant (number QLRI-CT-2001000015) of the European Commission.  ... 
doi:10.1093/nar/gki106 pmid:15608177 pmcid:PMC540060 fatcat:ykhpocbakfck3elxzhjb7z34rm

The SWISS-MODEL Repository: new features and functionalities

J. Kopp
2006 Nucleic Acids Research  
As of September 2005, the repository contained 675 000 models for 604 000 different protein sequences of the UniProt database.  ...  Regular updates ensure that the content of the repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures  ...  Peitsch (Novartis AG, Basel, Switzerland) and to Nicolas Guex (GSK, Raleigh, NC)  ... 
doi:10.1093/nar/gkj056 pmid:16381875 pmcid:PMC1347419 fatcat:6gmxsbvpevffdctehjp3r7c5j4

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation

Yiannis A I Kourmpetis, Ate van der Burgt, Marco C A M Bink, Cajo J F Ter Braak, Roeland C H J van Ham
2007 In Silico Biology  
In contrast, an analysis of the occurrence of InterPro hits in the proteomes of the seven species, followed by a mapping of the hits to GO terms, did not reveal an aberrant pattern for the A. thaliana  ...  In this study we quantify the usage of multiple and hierarchically independent GO terms in the curated genome annotations of seven well-studied species.  ...  The use of multiple hierarchically independent Gene Ontology terms in gene function prediction and genome annotation References  ... 
pmid:18467770 fatcat:n3akgt72gnedhesigzti5zxfia

Expression of protein tyrosine kinase 6 (PTK6) in nonsmall cell lung cancer and their clinical and prognostic significance

Deng, Chao Zhao, Yan Chen, Weiwei Zhang, Jianrong Zhang, Yulian Xu, Wenjie Li, Sunxiao Chen
2013 OncoTargets and Therapy  
Aim: The aim of the study was to validate the expression of protein tyrosine kinase 6 (PTK6) in nonsmall cell lung cancer (NSCLC), and to evaluate its clinicopathological and prognostic significance.  ...  Conclusion: Our results validated that PTK6 was found to be overexpressed in a proportion of NSCLC samples, and was associated with a poor prognosis, suggesting that this subgroup of NSCLC patients might  ...  Disclosure The authors report no conflicts of interest in this work.  ... 
doi:10.2147/ott.s41283 pmid:23525678 pmcid:PMC3596122 fatcat:b2ws65zrfvdylk3gqv3o5jo3le

Transcriptomic Basis of Metamorphic Competence in the Salt-Marsh-Dwelling Polychaete Capitella teleta

Robert Burns, Jan Pechenik
2017 The Biological Bulletin  
We studied gene expression patterns in precompetent and competent larvae of the salt-marshdwelling polychaete worm Capitella teleta (Blake, Grassle & Eckelbarger, 2009)-a species in which precompetent  ...  Serotonin and GABA (γ-aminobutyric acid) receptors are among the genes that were upregulated in competent larvae; both have been shown to induce larvae of C. teleta and other marine invertebrates to metamorphose  ...  to gene ontologies that reflect this status of continued growth and development (Table 2) .  ... 
doi:10.1086/692829 pmid:28898599 fatcat:podcgsf6vjhnjgr32zogfydzte

Page 690 of Psychological Abstracts Vol. 93, Issue 2 [page]

2006 Psychological Abstracts  
Students need to be chal- lenged with progressively more complex tasks and those tasks need to reflect the reality in which they will be working.  ...  By using increasingly complex and relevant cases in cooperative groups with an experiential learning process interpro- fessional education can be successful—Journal abstract. 5533. DeLuca, Ellen K.  ... 

The Repertoires of Ubiquitinating and Deubiquitinating Enzymes in Eukaryotic Genomes

Andrew Paul Hutchins, Shaq Liu, Diego Diez, Diego Miranda-Saavedra
2013 Molecular biology and evolution  
In yeast, we predict 85 UBE and 24 DUB genes, for 814 UBE and 107 DUB genes in the human genome.  ...  35% additional UBE and DUB genes in yeast and human, which had not been reported before.  ...  Japan Society for the Promotion of Science (JSPS) through the WPI-IFReC Research Program and a Kakenhi grant; the Kishimoto Foundation; and the ETHZ-JST Japanese-Swiss Cooperative Program.  ... 
doi:10.1093/molbev/mst022 pmid:23393154 pmcid:PMC3670738 fatcat:oowgk7m2cfbqtno3m35uqwyxmy

FuncBase : a resource for quantitative gene function annotation

J. E. Beaver, M. Tasan, F. D. Gibbons, W. Tian, T. R. Hughes, F. P. Roth
2010 Bioinformatics  
Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system.  ...  Cherry and E. Hong; MGI members, including J. Blake and D. Hill; Roth lab members, including G. Berriz and R. Deo.  ...  Funding: National Institues of Health (grants NS054052, NS035611, HL081341, HG001715, HG004233 and HG003224); A Canadian Institute for Advanced Research Fellowship (to F.P.R.).  ... 
doi:10.1093/bioinformatics/btq265 pmid:20495000 pmcid:PMC2894510 fatcat:q5wm5rewxjfp5h2v7aod4qkvoy

High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa

Paulo José Pereira Lima Teixeira, Daniela Paula de Toledo Thomazella, Osvaldo Reis, Paula Favoretti Vital do Prado, Maria Carolina Scatolin do Rio, Gabriel Lorencini Fiorin, Juliana José, Gustavo Gilson Lacerda Costa, Victor Augusti Negri, Jorge Maurício Costa Mondego, Piotr Mieczkowski, Gonçalo Amarante Guimarães Pereira
2014 The Plant Cell  
We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors.  ...  in the infected shoots.  ...  progression in fruits, WBD progression in shoots, nongerminating and germinating spores, and basidiomata).  ... 
doi:10.1105/tpc.114.130807 pmid:25371547 pmcid:PMC4277218 fatcat:j5nxmqlyirhsveduruegiob2im

Patterns of Selection and Tissue-Specific Expression among Maize Domestication and Crop Improvement Loci

K. M. Hufford, P. Canaran, D. H. Ware, M. D. McMullen, B. S. Gaut
2007 Plant Physiology  
Electronic northern analysis revealed that candidate genes are significantly overexpressed in the maize ear relative to vegetative tissues such as maize shoot, leaf, and root tissue.  ...  Using an expanded dataset of 48 candidate selected and 658 neutral reference loci, we tested the hypothesis that candidate selected genes in maize are more likely to have transcriptional functions than  ...  Using the InterPro database, we functionally annotated genes in the selected and reference sets, and made GO assignments.  ... 
doi:10.1104/pp.107.098988 pmid:17496114 pmcid:PMC1914116 fatcat:msyiz5b5dfegzkdvroetquc4j4

Mutated genes, pathways and processes in tumours

A. Baudot, A. Valencia
2010 New Biotechnology  
Literature searches identify pathways and processes that are covered sparsely in the literature, and invite the proposal of new hypotheses to investigate cancer initiation and progression.  ...  From this, we draw a map of the altered processes, and their combinations, in more than 10 tumours types.  ...  Real and D. Rico for valuable comments and suggestions.  ... 
doi:10.1016/j.nbt.2010.01.070 fatcat:7xf7djt3nzenth7aoxadoxcmxm

Mutated genes, pathways and processes in tumours

Anaïs Baudot, Victor de la Torre, Alfonso Valencia
2010 EMBO Reports  
Literature searches identify pathways and processes that are covered sparsely in the literature, and invite the proposal of new hypotheses to investigate cancer initiation and progression.  ...  From this, we draw a map of the altered processes, and their combinations, in more than 10 tumours types.  ...  Real and D. Rico for valuable comments and suggestions.  ... 
doi:10.1038/embor.2010.133 pmid:20847737 pmcid:PMC2948187 fatcat:rpxitirfdzedlbyfkyeu4y2ida

Edifice of vitiDB: A first ever structured portal for vitiligo protein repository and its assessment

Anvita Gupta Malhotra
2017 Bioscience Biotechnology Research Communications  
In addition, the database throws light on interectome of proteins and their targetability assessment.  ...  The additional information in the form of derived data can potentially assist in the drug discovery process.  ...  Acknowledgments The authors thankfully acknowledge the help, support and guidance provided by Dr. Ajay Pandey, Department of Mechanical Engineering, MANIT, Bhopal.  ... 
doi:10.21786/bbrc/10.2/3 fatcat:zcbgruwetbgdzkutkvvjeiqfem

Inter-Species Validation for Domain Combination Based Protein-Protein Interaction Prediction Method

Woo-Hyuk Jang, Dong-Soo Han, Hong-Soog Kim, Sung-Doke Lee
2005 Genome Informatics Series  
Interactions of proteins in Human, Mouse, H. pylori, E. coli, and C. elegans are predicted and validated using the protein interaction and domain data in Yeast, Fly, and the combination of Yeast and Fly  ...  In this paper, we report the validation results of applying the DCPPIP method for Fly and Human proteins.  ...  Acknowledgments This work is funded by 'Nano-Bio technology development project' of Korea Science and Engineering Foundation(Grant No. M10529000011-05N2900-01110), and Dr. S. D.  ... 
doi:10.11234/gi1990.16.2_136 fatcat:2xtiggmie5e2vg6msuh27avpii

An overview of human protein databases and their application to functional proteomics in health and disease

YanQiong Zhang, YunPing Zhu, FuChu He
2011 Science China Life Sciences  
This work was supported by the National Basic Research Program of China (Grant Nos. 2010CB912700 and 2011CB910601).  ...  PRIDE was established as a production service in 2005.  ...  roles in the progression of various human cancers.  ... 
doi:10.1007/s11427-011-4247-x pmid:22173304 fatcat:hgveej677vgrleolzt7pqcpohu
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