Literature DB >> 14988118

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.

Wolfgang Huber1, Robert Gentleman.   

Abstract

UNLABELLED: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation of data packages for curating, distributing and working with probe sequence data in a uniform, across-types-of-microarrays manner. While the implementation is specific to the Bioconductor project, the ideas and general strategies are more general and could be easily adopted by other projects. AVAILABILITY: The R package matchprobes is available under LGPL at http://www.bioconductor.org SUPPLEMENTARY INFORMATION: The package contains documentation in the form of a vignette and manual pages.

Mesh:

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Year:  2004        PMID: 14988118     DOI: 10.1093/bioinformatics/bth133

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  17 in total

1.  Consistent annotation of gene expression arrays.

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2.  From ORFeome to biology: a functional genomics pipeline.

Authors:  Stefan Wiemann; Dorit Arlt; Wolfgang Huber; Ruth Wellenreuther; Simone Schleeger; Alexander Mehrle; Stephanie Bechtel; Mamatha Sauermann; Ulrike Korf; Rainer Pepperkok; Holger Sültmann; Annemarie Poustka
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

Review 3.  [Research strategies towards a holistic characterization of rheumatoid arthritis--a systems biology approach].

Authors:  A Thiel; H-J Thiesen
Journal:  Z Rheumatol       Date:  2005-09       Impact factor: 1.372

4.  Autocrine expression of the epidermal growth factor receptor ligand heparin-binding EGF-like growth factor in cervical cancer.

Authors:  Marlies Schrevel; E Michelle Osse; Frans A Prins; J Baptist M Z Trimbos; Gert Jan Fleuren; Arko Gorter; Ekaterina S Jordanova
Journal:  Int J Oncol       Date:  2017-05-03       Impact factor: 5.650

5.  Activation of the NOTCH pathway in head and neck cancer.

Authors:  Wenyue Sun; Daria A Gaykalova; Michael F Ochs; Elizabeth Mambo; Demetri Arnaoutakis; Yan Liu; Myriam Loyo; Nishant Agrawal; Jason Howard; Ryan Li; Sun Ahn; Elana Fertig; David Sidransky; Jeffery Houghton; Kalyan Buddavarapu; Tiffany Sanford; Ashish Choudhary; Will Darden; Alex Adai; Gary Latham; Justin Bishop; Rajni Sharma; William H Westra; Patrick Hennessey; Christine H Chung; Joseph A Califano
Journal:  Cancer Res       Date:  2013-12-18       Impact factor: 12.701

6.  Epithelial-mesenchymal transition-derived cells exhibit multilineage differentiation potential similar to mesenchymal stem cells.

Authors:  Venkata Lokesh Battula; Kurt William Evans; Brett George Hollier; Yuexi Shi; Frank C Marini; Ayyakkannu Ayyanan; Rui-Yu Wang; Cathrin Brisken; Rudy Guerra; Michael Andreeff; Sendurai A Mani
Journal:  Stem Cells       Date:  2010-08       Impact factor: 6.277

7.  Large scale analysis of positional effects of single-base mismatches on microarray gene expression data.

Authors:  Fenghai Duan; Mark A Pauley; Eliot R Spindel; Li Zhang; Robert B Norgren
Journal:  BioData Min       Date:  2010-04-29       Impact factor: 2.522

8.  Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma.

Authors:  Valeria R Mas; Daniel G Maluf; Kellie J Archer; Kenneth Yanek; Xiangrong Kong; Laura Kulik; Chris E Freise; Kim M Olthoff; Rafik M Ghobrial; Paula McIver; Robert Fisher
Journal:  Mol Med       Date:  2008-12-15       Impact factor: 6.354

9.  SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.

Authors:  Adam J Bass; Hideo Watanabe; Craig H Mermel; Soyoung Yu; Sven Perner; Roel G Verhaak; So Young Kim; Leslie Wardwell; Pablo Tamayo; Irit Gat-Viks; Alex H Ramos; Michele S Woo; Barbara A Weir; Gad Getz; Rameen Beroukhim; Michael O'Kelly; Amit Dutt; Orit Rozenblatt-Rosen; Piotr Dziunycz; Justin Komisarof; Lucian R Chirieac; Christopher J Lafargue; Veit Scheble; Theresia Wilbertz; Changqing Ma; Shilpa Rao; Hiroshi Nakagawa; Douglas B Stairs; Lin Lin; Thomas J Giordano; Patrick Wagner; John D Minna; Adi F Gazdar; Chang Qi Zhu; Marcia S Brose; Ivan Cecconello; Ulysses Ribeiro; Suely K Marie; Olav Dahl; Ramesh A Shivdasani; Ming-Sound Tsao; Mark A Rubin; Kwok K Wong; Aviv Regev; William C Hahn; David G Beer; Anil K Rustgi; Matthew Meyerson
Journal:  Nat Genet       Date:  2009-10-04       Impact factor: 38.330

10.  Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data.

Authors:  Jun Yin; Sarah McLoughlin; Ian B Jeffery; Antonino Glaviano; Breandan Kennedy; Desmond G Higgins
Journal:  BMC Genomics       Date:  2010-01-20       Impact factor: 3.969

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