AMDA 2.13: A major update for automated cross-platform microarray data analysis
Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2012-07-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/0000113889 |
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| author | Dimos Kapetis Ferdinando Clarelli Federico Vitulli Nicole Kerlero de Rosbo Ottavio Beretta Maria Foti Paola Ricciardi-Castagnoli Francesca Zolezzi |
| author_facet | Dimos Kapetis Ferdinando Clarelli Federico Vitulli Nicole Kerlero de Rosbo Ottavio Beretta Maria Foti Paola Ricciardi-Castagnoli Francesca Zolezzi |
| author_sort | Dimos Kapetis |
| collection | DOAJ |
| description | Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3′ IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix (cartridges and plates) and whole transcript probe design (Gene 1.0/1.1 ST and Exon 1.0 ST GeneChips), Illumina Bead Arrays, and one-channel Agilent 4×44 arrays. Relative to early versions, it supports various experimental designs and delivers more insightful biological understanding and up-to-date annotations. |
| format | Article |
| id | doaj-art-e3644f933d8f4299871047cd7a1dd628 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2012-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-e3644f933d8f4299871047cd7a1dd6282025-08-20T02:25:58ZengTaylor & Francis GroupBioTechniques0736-62051940-98182012-07-01531334010.2144/0000113889AMDA 2.13: A major update for automated cross-platform microarray data analysisDimos Kapetis0Ferdinando Clarelli1Federico Vitulli2Nicole Kerlero de Rosbo3Ottavio Beretta4Maria Foti5Paola Ricciardi-Castagnoli6Francesca Zolezzi71Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy2Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, Milan, 20133 , Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, Italy1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 220126 Milan, ItalyMicroarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3′ IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix (cartridges and plates) and whole transcript probe design (Gene 1.0/1.1 ST and Exon 1.0 ST GeneChips), Illumina Bead Arrays, and one-channel Agilent 4×44 arrays. Relative to early versions, it supports various experimental designs and delivers more insightful biological understanding and up-to-date annotations.https://www.future-science.com/doi/10.2144/0000113889data analysismicroarraysanalytical pipelinesautomationopen-source software |
| spellingShingle | Dimos Kapetis Ferdinando Clarelli Federico Vitulli Nicole Kerlero de Rosbo Ottavio Beretta Maria Foti Paola Ricciardi-Castagnoli Francesca Zolezzi AMDA 2.13: A major update for automated cross-platform microarray data analysis BioTechniques data analysis microarrays analytical pipelines automation open-source software |
| title | AMDA 2.13: A major update for automated cross-platform microarray data analysis |
| title_full | AMDA 2.13: A major update for automated cross-platform microarray data analysis |
| title_fullStr | AMDA 2.13: A major update for automated cross-platform microarray data analysis |
| title_full_unstemmed | AMDA 2.13: A major update for automated cross-platform microarray data analysis |
| title_short | AMDA 2.13: A major update for automated cross-platform microarray data analysis |
| title_sort | amda 2 13 a major update for automated cross platform microarray data analysis |
| topic | data analysis microarrays analytical pipelines automation open-source software |
| url | https://www.future-science.com/doi/10.2144/0000113889 |
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