Literature DB >> 15684227

CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.

Sek Won Kong1, Kyu-Baek Hwang, Richard D Kim, Byoung-Tak Zhang, Steven A Greenberg, Isaac S Kohane, Peter J Park.   

Abstract

SUMMARY: To increase compatibility between different generations of Affymetrix GeneChip arrays, we propose a method of filtering probes based on their sequences. Our method is implemented as a web-based service for downloading necessary materials for converting the raw data files (*.CEL) for comparative analysis. The user can specify the appropriate level of filtering by setting the criteria for the minimum overlap length between probe sequences and the minimum number of usable probe pairs per probe set. Our website supports a within-species comparison for human and mouse GeneChip arrays. AVAILABILITY: http://www.crosschip.org

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Year:  2005        PMID： 15684227      PMCID： PMC2819168          DOI： 10.1093/bioinformatics/bti288

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


  4 in total

1.  Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.

Authors:  Brigham H Mecham; Gregory T Klus; Jeffrey Strovel; Meena Augustus; David Byrne; Peter Bozso; Daniel Z Wetmore; Thomas J Mariani; Isaac S Kohane; Zoltan Szallasi
Journal:  Nucleic Acids Res       Date:  2004-05-25       Impact factor: 16.971

2.  Analysis of matched mRNA measurements from two different microarray technologies.

Authors:  Winston Patrick Kuo; Tor-Kristian Jenssen; Atul J Butte; Lucila Ohno-Machado; Isaac S Kohane
Journal:  Bioinformatics       Date:  2002-03       Impact factor: 6.937

3.  Combining gene expression data from different generations of oligonucleotide arrays.

Authors:  Kyu-Baek Hwang; Sek Won Kong; Steve A Greenberg; Peter J Park
Journal:  BMC Bioinformatics       Date:  2004-10-25       Impact factor: 3.169

4.  Reproducibility of gene expression across generations of Affymetrix microarrays.

Authors:  Ashish Nimgaonkar; Despina Sanoudou; Atul J Butte; Judith N Haslett; Louis M Kunkel; Alan H Beggs; Isaac S Kohane
Journal:  BMC Bioinformatics       Date:  2003-06-25       Impact factor: 3.169
  4 in total
  9 in total

1.  DSGeo: software tools for cross-platform analysis of gene expression data in GEO.

Authors:  Ronilda Lacson; Erik Pitzer; Jihoon Kim; Pedro Galante; Christian Hinske; Lucila Ohno-Machado
Journal:  J Biomed Inform       Date:  2010-05-07       Impact factor: 6.317

2.  AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm.

Authors:  Jihoon Kim; Kiltesh Patel; Hyunchul Jung; Winston P Kuo; Lucila Ohno-Machado
Journal:  BMC Bioinformatics       Date:  2011-03-17       Impact factor: 3.307

3.  A-MADMAN: annotation-based microarray data meta-analysis tool.

Authors:  Andrea Bisognin; Alessandro Coppe; Francesco Ferrari; Davide Risso; Chiara Romualdi; Silvio Bicciato; Stefania Bortoluzzi
Journal:  BMC Bioinformatics       Date:  2009-06-29       Impact factor: 3.169

4.  Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior.

Authors:  Shyama Majumdar; Edward M Gong; Dolores Di Vizio; Jonathan Dreyfuss; David J Degraff; Martin H Hager; Peter J Park; Joaquim Bellmunt; Robert J Matusik; Jonathan E Rosenberg; Rosalyn M Adam
Journal:  Neoplasia       Date:  2013-07       Impact factor: 5.715

5.  ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

Authors:  Christopher C Overall; D Andrew Carr; Ehsan S Tabari; Kevin J Thompson; Jennifer W Weller
Journal:  BMC Bioinformatics       Date:  2011-05-06       Impact factor: 3.307

6.  virtualArray: a R/bioconductor package to merge raw data from different microarray platforms.

Authors:  Andreas Heider; Rüdiger Alt
Journal:  BMC Bioinformatics       Date:  2013-03-02       Impact factor: 3.169

7.  Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.

Authors:  Donna M Toleno; Gabriel Renaud; Tyra G Wolfsberg; Munirul Islam; Derek E Wildman; Kimberly D Siegmund; Joseph G Hacia
Journal:  BMC Bioinformatics       Date:  2009-03-05       Impact factor: 3.169

8.  A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.

Authors:  Henrik Bengtsson; Amrita Ray; Paul Spellman; Terence P Speed
Journal:  Bioinformatics       Date:  2009-02-04       Impact factor: 6.937

Review 9.  Microarray probes and probe sets.

Authors:  Hongfang Liu; Ionut Bebu; Xin Li
Journal:  Front Biosci (Elite Ed)       Date:  2010-01-01
  9 in total

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