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Literature DB >> 17387043

Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.

Raad Z Gharaibeh¹, Anthony A Fodor, Cynthia J Gibas.

Abstract

High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays.

Entities: Chemical

Mesh：

Substances：
Oligonucleotide Probes

Year: 2007 PMID： 17387043 PMCID： PMC2043163 DOI： 10.1016/j.compbiolchem.2007.02.008

Source DB: PubMed Journal: Comput Biol Chem ISSN： 1476-9271 Impact factor: 2.877

28 in total

1. A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations.

Authors: Felix Naef; Nicholas D Socci; Marcelo Magnasco
Journal: Bioinformatics Date: 2003-01-22 Impact factor: 6.937

2. Modeling of DNA microarray data by using physical properties of hybridization.

Authors: G A Held; G Grinstein; Y Tu
Journal: Proc Natl Acad Sci U S A Date: 2003-06-13 Impact factor: 11.205

3. Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

Authors: Rafael A Irizarry; Bridget Hobbs; Francois Collin; Yasmin D Beazer-Barclay; Kristen J Antonellis; Uwe Scherf; Terence P Speed
Journal: Biostatistics Date: 2003-04 Impact factor: 5.899

4. A model of molecular interactions on short oligonucleotide microarrays.

Authors: Li Zhang; Michael F Miles; Kenneth D Aldape
Journal: Nat Biotechnol Date: 2003-06-08 Impact factor: 54.908

5. Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays.

Authors: Felix Naef; Marcelo O Magnasco
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2003-07-16

6. Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection.

Authors: R M Anthony; A R J Schuitema; A B Chan; P J Boender; P R Klatser; L Oskam
Journal: Biotechniques Date: 2003-05 Impact factor: 1.993

7. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

Authors: C Li; W H Wong
Journal: Proc Natl Acad Sci U S A Date: 2001-01-02 Impact factor: 11.205

8. Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays.

Authors: Eugene Chudin; Randal Walker; Alan Kosaka; Sue X Wu; Douglas Rabert; Thomas K Chang; Dirk E Kreder
Journal: Genome Biol Date: 2001-12-14 Impact factor: 13.583

9. Discovery of gene function by expression profiling of the malaria parasite life cycle.

Authors: Karine G Le Roch; Yingyao Zhou; Peter L Blair; Muni Grainger; J Kathleen Moch; J David Haynes; Patricia De La Vega; Anthony A Holder; Serge Batalov; Daniel J Carucci; Elizabeth A Winzeler
Journal: Science Date: 2003-07-31 Impact factor: 47.728

10. Towards the uniform distribution of null P values on Affymetrix microarrays.

Authors: Anthony A Fodor; Timothy L Tickle; Christine Richardson
Journal: Genome Biol Date: 2007 Impact factor: 13.583

8 in total

1. Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression.

Authors: Rita M Graze; Lauren M McIntyre; Bradley J Main; Marta L Wayne; Sergey V Nuzhdin
Journal: Genetics Date: 2009-08-10 Impact factor: 4.562

Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.

1. A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations.

2. Modeling of DNA microarray data by using physical properties of hybridization.

3. Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

4. A model of molecular interactions on short oligonucleotide microarrays.

5. Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays.

6. Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection.

7. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

8. Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays.

9. Discovery of gene function by expression profiling of the malaria parasite life cycle.

10. Towards the uniform distribution of null P values on Affymetrix microarrays.

1. Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression.

2. Free energy estimation of short DNA duplex hybridizations.

3. Application of equilibrium models of solution hybridization to microarray design and analysis.

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

5. Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.

6. Correction of spatial bias in oligonucleotide array data.

7. Background correction using dinucleotide affinities improves the performance of GCRMA.

8. Design and analysis of mismatch probes for long oligonucleotide microarrays.