We are analyzing https://link.springer.com/article/10.1186/1471-2105-8-461.

Title:
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation | BMC Bioinformatics
Description:
Background Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. Results We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. Conclusion The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
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Keywords {🔍}

probe, reporters, set, expression, gene, correlation, pubmed, article, offtarget, genes, google, scholar, reporter, data, transcript, sets, microarray, figure, analysis, sequence, crosshybridization, transcripts, alignment, target, affymetrix, cdf, signal, pairs, cas, results, sensitivity, show, central, signals, custommade, score, arabidopsis, scores, bioinformatics, genome, coefficients, study, authors, model, atg, networks, calculated, multiple, coefficient, dataset,

Topics {✒️}

tineke casneuf & wolfgang huber org/resources/microarray/atgenexpress/atge_dev_samples van de peer /auth/analysis/downloads/na21/ivt/ath1–121501 view author information authors wolfgang huber article download pdf open access article summarized expression profile /support/downloads/manuals/data_analysis_fundamentals_manual high-density oligonucleotide arrays author correspondence /support/technical/manual/alignments_psl_manual /support/technical/technotes/plier_technote /support/technical/whitepapers/sadd_whitepaper highest needleman-wunsch scores signal profile expression profile chip description file article casneuf /products/arrays/specific/arab arabidopsis information resource[http chip description files stefanie de bodt large-scale analysis profile corresponds open software development functionally related genes privacy choices/manage cookies normalized signal profiles european economic area authors’ original file full size image tissue microarray dataset background-passified microarrays search related subjects high signal correlation probe set cross-hybridize biomed central bolstad bm stress dataset global alignment algorithm ath1 affymetrix genechip reporter alignment score alignment scores {a1 integrated modeling-cogrim graphical gaussian models gap open penalty

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Schema {🗺️}

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         headline:In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
         description:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
         datePublished:2007-11-26T00:00:00Z
         dateModified:2007-11-26T00:00:00Z
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            Stress Dataset
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            Microarrays
            Computational Biology/Bioinformatics
            Computer Appl. in Life Sciences
            Algorithms
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      headline:In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
      description:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
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         Expression Correlation
         Signal Profile
         Microarray Gene Expression Profile
         Stress Dataset
         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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            name:Ghent University
            address:
               name:Department of Molecular Genetics, Ghent University, Ghent, Belgium
               type:PostalAddress
            type:Organization
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            address:
               name:EMBL – European Bioinformatics Institute, Cambridge, U
               type:PostalAddress
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      name:VIB, Department of Plant Systems Biology, Ghent, Belgium
      name:Department of Molecular Genetics, Ghent University, Ghent, Belgium
      name:EMBL – European Bioinformatics Institute, Cambridge, U

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