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Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data

BMC BIOINFORMATICS 2007年第1期8卷 1-14页

作者： Chen, James J. Hsueh, Huey-Miin Delongchamp, Robert R. Lin, Chien-Ju Tsai, Chen-An US FDA Natl Ctr Toxicol Res Div Personalized Nutr & Med Jefferson AR 72079 USA Natl Chengchi Univ Dept Stat Taipei 11623 Taiwan Univ Arkansas Med Sci Dept Epidemiol Little Rock AR 72205 USA China Med Univ Dept Publ Hlth Taichung Taiwan China Med Univ Ctr Biostat Taichung Taiwan

Background: Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the microarray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. The MAQC analysis presented for the conclusion of inter- and intra-platform comparability/reproducibility of microarray gene expression measurements is inadequate. We evaluate the reproducibility/comparability of the MAQC data for 12901 common genes in four titration samples generated from five high-density one-color microarray platforms and the TaqMan technology. We discuss some of the problems with the use of correlation coefficient as metric to evaluate the inter- and intra-platform reproducibility and the percent of overlapping genes (POG) as a measure for evaluation of a gene selection procedure by MAQC. Results: A total of 293 arrays were used in the intra- and inter-platform analysis. A hierarchical cluster analysis shows distinct differences in the measured intensities among the five platforms. A number of genes show a small fold-change in one platform and a large fold-change in another platform, even though the correlations between platforms are high. An analysis of variance shows thirty percent of gene expressions of the samples show inconsistent patterns across the five platforms. We illustrated that POG does not reflect the accuracy of a selected gene list. A non-overlapping gene can be truly differentially expressed with a stringent cut, and an overlapping gene can be non-differentially expressed with non-stringent cutoff. In addition, POG is an unusable selection criterion. POG can increase or decrease irregularly as cutoff changes;there is no criterion to determine a cutoff so that POG is optimized. Conclusion: Using various statistical methods we demonstrate that there are differences in the intensities measured by different platforms and diffe

关键词： microarray platform Gold Standard Data microarray Quality Control MAQC Project Individual platform

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Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

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BMC BIOINFORMATICS 2006年第1期7卷 1-20页

作者： Holloway, Andrew J. Oshlack, Alicia Diyagama, Dileepa S. Bowtell, David D. L. Smyth, Gordon K. Walter & Eliza Hall Inst Med Res Melbourne Vic 3050 Australia Peter MacCallum Canc Ctr Ian Potter Fdn Ctr Canc Genom & Predict Med Melbourne Vic 3002 Australia

Background: Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results: A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. Conclusion: The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome.

关键词： Fold Change microarray platform Titration Series Affymetrix platform Commercial platform

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An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)

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BMC GENOMICS 2009年第1期10卷 1-15页

作者： Mascarell-Creus, Albert Canizares, Joaquin Vilarrasa-Blasi, Josep Mora-Garcia, Santiago Blanca, Jose Gonzalez-Ibeas, Daniel Saladie, Montserrat Roig, Cristina Deleu, Wim Pico-Silvent, Belen Lopez-Bigas, Nuria Aranda, Miguel A. Garcia-Mas, Jordi Nuez, Fernando Puigdomenech, Pere Cano-Delgado, Ana I. CSIC IRTA UAB Dept Mol Genet CRAG Barcelona 08034 Spain CSIC IRTA UAB Dept Plant Genet CRAG Cabrils 08348 Spain CSIC Dept Biol Estres & Patol Vegetal CEBAS Murcia 30100 Spain COMAV UPV Inst Conservac & Mejora Agrodiversidad Valenciana CPI Valencia 46022 Spain Univ Pompeu Fabra Res Unit Biomed Informat GRIB Expt & Hlth Sci Dept Barcelona 08080 Spain

Background: Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression. Results: We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study. Conclusion: The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.

关键词： Gene Ontology Melon Cucumber Mosaic Virus microarray platform Functional Genomic Study

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Optimization and clinical validation of a pathogen detection microarray

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GENOME BIOLOGY 2007年第5期8卷 1-13页

作者： Wong, Christopher W. Heng, Charlie Lee Wah Yee, Leong Wan Soh, Shirlena W. L. Kartasasmita, Cissy B. Simoes, Eric A. F. Hibberd, Martin L. Sung, Wing-Kin Miller, Lance D. Genome Inst Singapore Singapore Singapore Padjadjaran State Univ Fac Med Dept Pediat Hasan Saikin Hosp Bandung Indonesia Univ Colorado Sect Infect Dis Denver CO 80202 USA Univ Colorado Hlth Sci Ctr Denver CO 80206 USA Childrens Hosp Denver CO 80218 USA

DNA microarrays used as "genomic sensors" have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.

关键词： Respiratory Syncytial Virus Additional Data File microarray platform Pathogen Detection Lower Respiratory Tract Infection

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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

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GENOME BIOLOGY 2005年第7期6卷 1-12页

作者： Carter, MG Sharov, AA VanBuren, V Dudekula, DB Carmack, CE Nelson, C Ko, MSH NIA Dev Genom & Aging Sect Genet Lab Baltimore MD 21224 USA Agilent Technol Palo Alto CA 94304 USA

The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome ( made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

关键词： Transcript Abundance Additional Data File Oligonucleotide Probe microarray platform microarray Design

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Whole genome microarray analysis, from neonatal blood cards

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BMC GENETICS 2009年第1期10卷 1-8页

作者： Hardin, Jill Finnell, Richard H. Wong, David Hogan, Michael E. Horovitz, Joy Shu, Jenny Shaw, Gary M. Univ Calif Berkeley Sch Publ Hlth Berkeley CA 94720 USA Inst Biosci & Technol Texas A&M Houston TX 77030 USA Childrens Hosp Oakland Res Inst Calif Res Div Oakland CA 94609 USA GenVault Corp Carlsbad CA 92011 USA Express Anal Corp Durham NC 27713 USA

Background: Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. Results: A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40(th) of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250(th) of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Conclusion: Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.

关键词： microarray platform Neonatal Screening Genome Amplification Neonatal Blood Guthrie Card

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Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes

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BMC GENOMICS 2009年第1期10卷 1-12页

作者： Numata, Koji Osada, Yuko Okada, Yuki Saito, Rintaro Hiraiwa, Noriko Nakaoka, Hajime Yamamoto, Naoyuki Watanabe, Kazufumi Okubo, Kazue Kohama, Chihiro Kanai, Akio Abe, Kuniya Kiyosawa, Hidenori RIKEN Tsukuba Inst Technol & Dev Team Mammalian Cellular Dynam BRC Tsukuba 3050074 Japan Keio Univ Inst Adv Biosci Yamagata 9970017 Japan Keio Univ Dept Environm Informat Fujisawa Kanagawa 2528520 Japan RIKEN Tsukuba Inst Expt Anim Div BRC Tsukuba 3050074 Japan Cs Lab Co Ltd Kita Ku Sapporo Hokkaido 0600002 Japan Hokkaido Syst Sci Co Ltd Custom Biotechnol Serv Grp Kita Ku Sapporo Hokkaido 0010932 Japan Genostaff Inc Bunkyo Ku Tokyo 1130031 Japan Univ Tsukuba Grad Sch Life & Environm Sci Tsukuba Ibaraki 3050006 Japan RIKEN Tsukuba Inst Technol & Dev Team BioSignal Program BRC Tsukuba 3050074 Japan

Background: Recent transcriptomic analyses in mammals have uncovered the widespread occurrence of endogenous antisense transcripts, termed natural antisense transcripts (NATs). NATs are transcribed from the opposite strand of the gene locus and are thought to control sense gene expression, but the mechanism of such regulation is as yet unknown. Although several thousand potential sense-antisense pairs have been identified in mammals, examples of functionally characterized NATs remain limited. To identify NAT candidates suitable for further functional analyses, we performed DNA microarray-based NAT screening using mouse adult normal tissues and mammary tumors to target not only the sense orientation but also the complementary strand of the annotated genes. Results: First, we designed microarray probes to target the complementary strand of genes for which an antisense counterpart had been identified only in human public cDNA sources, but not in the mouse. We observed a prominent expression signal from 66.1% of 635 target genes, and 58 genes of these showed tissue-specific expression. Expression analyses of selected examples (Acaa1b and Aard) confirmed their dynamic transcription in vivo. Although interspecies conservation of NAT expression was previously investigated by the presence of cDNA sources in both species, our results suggest that there are more examples of human-mouse conserved NATs that could not be identified by cDNA sources. We also designed probes to target the complementary strand of well-characterized genes, including oncogenes, and compared the expression of these genes between mammary cancerous tissues and non-pathological tissues. We found that antisense expression of 95 genes of 404 well-annotated genes was markedly altered in tumor tissue compared with that in normal tissue and that 19 of these genes also exhibited changes in sense gene expression. These results highlight the importance of NAT expression in the regulation of cellular events and in

关键词： microarray platform Antisense Transcript Mouse Mammary Tumor Virus Complementary Strand Antisense Transcription

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Electrochemical microarray for Identification Pathogens: A Review

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INTERNATIONAL JOURNAL OF ELECTROCHEMICAL SCIENCE 2014年第7期9卷 3431-3439页

作者： Rodrigo, Miguel Angel Merlos Zitka, Ondrej Krejcova, Ludmila Hynek, David Masarik, Michal Kynicky, Jindrich Heger, Zbynek Adam, Vojtech Kizek, Rene Mendel Univ Brno Fac Agron Dept Chem & Biochem CZ-61300 Brno Czech Republic Brno Univ Technol Cent European Inst Technol CZ-61600 Brno Czech Republic Karel Englis Coll CZ-60200 Brno Czech Republic

Numerous analytical methods are used to detect pathogens agents including methods based on the direct isolation followed by real time-polymerase chain reaction, or immunology tests. There have not been published numerous papers on the using of electrochemical microarrays for detection of viruses and/or bacteria but there is a great potential. Electrochemical detection has been developed and assay performances studied for the CombiMatrix oligonucleotide microarray platform. CombiMatrix core technology is based on a specially modified semiconductor adapted for biological applications, which contains arrays of platinum microelectrodes. The ElectraSense (TM) principle is the detection of redox active chemistries proximal to specific electrodes. The target molecules are labelled with a redox enzyme via biotin-streptavidin (or avidin) interaction. Enzymatic oxidation of an electron donor substrate then occurs. The detection current is generated due to electro-reduction of the enzymatic reaction product. Thus, the ElectraSense (TM) platform has been used to develop nucleic acid assays for highly accurate genotyping of a variety of pathogens including bio-threat agents. In this review we summarize recent studies on the detection and identification of pathogens by electrochemical microarrays technology and discuss the advantages and disadvantages.

关键词： Electrochemical detection microarray platform Viruses, Influenza virus Human papillomavirus

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Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

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BMC GENOMICS 2011年第1期12卷 1-11页

作者： Toepel, Joerg Albaum, Stefan P. Arvidsson, Samuel Goesmann, Alexander la Russa, Marco Rogge, Kristin Kruse, Olaf Univ Bielefeld Dept Biol Ctr Biotechnol CeBiTec D-33615 Bielefeld Germany Max Planck Inst Mol Plant Physiol AG Bioinformat GoFORSYS D-14476 Potsdam Germany

Background: Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptomic studies, however a new microarray platform was needed. Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models. Results: In total 44000 probes were determined (3 independent probes per transcript model) covering 93% of the transcriptome. Alignment studies with the recently published AUGUSTUS 10.2 annotation confirmed 11000 transcript models resulting in a very good coverage of 70% of the transcriptome (17000). Following the estimation of 10000 predicted genes in Chlamydomonas reinhardtii our new microarray, nevertheless, covers the expected genome by 90-95%. Conclusions: To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport.

关键词： microarray platform Nitrogen Starvation Aryl Sulfatase Nutrient Starvation Sulfur Starvation

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Comparison and consolidation of microarray data sets of human tissue expression

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BMC GENOMICS 2010年第1期11卷 1-17页

作者： Russ, Jenny Futschik, Matthias E. Humboldt Univ Charite Inst Theoret Biol D-10115 Berlin Germany Univ Algarve Ctr Mol & Struct Biomed Lab Associado Inst Biotechnol & Bioengn P-8005139 Faro Portugal

Background: Human tissue displays a remarkable diversity in structure and function. To understand how such diversity emerges from the same DNA, systematic measurements of gene expression across different tissues in the human body are essential. Several recent studies addressed this formidable task using microarray technologies. These large tissue expression data sets have provided us an important basis for biomedical research. However, it is well known that microarray data can be compromised by high noise level and various experimental artefacts. Critical comparison of different data sets can help to reveal such errors and to avoid pitfalls in their application. Results: We present here the first comparison and integration of four freely available tissue expression data sets generated using three different microarray platforms and containing a total of 377 microarray hybridizations. When assessing the tissue expression of genes, we found that the results considerably depend on the chosen data set. Nevertheless, the comparison also revealed statistically significant similarity of gene expression profiles across different platforms. This enabled us to construct consolidated lists of platform-independent tissue-specific genes using a set of complementary measures. Follow-up analyses showed that results based on consolidated data tend to be more reliable. Conclusions: Our study strongly indicates that the consolidation of the four different tissue expression data sets can increase data quality and can lead to biologically more meaningful results. The provided compendium of platform-independent gene lists should facilitate the identification of novel tissue-specific marker genes.

关键词： Gene Ontology False Discovery Rate Gene List microarray platform Tissue Class

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