Genealyzer: web application for the analysis and comparison of gene expression data
Abstract Background Gene expression profiling is a widely adopted method in areas like drug development or functional gene analysis. Microarray data of gene expression experiments is still commonly used and widely available for retrospective analyses. However, due to to changes of the underlying tec...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05266-4 |
| _version_ | 1797840810505404416 |
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| author | Kristina Lietz Babak Saremi Lena Wiese |
| author_facet | Kristina Lietz Babak Saremi Lena Wiese |
| author_sort | Kristina Lietz |
| collection | DOAJ |
| description | Abstract Background Gene expression profiling is a widely adopted method in areas like drug development or functional gene analysis. Microarray data of gene expression experiments is still commonly used and widely available for retrospective analyses. However, due to to changes of the underlying technologies data sets from different technologies are often difficult to compare and thus a multitude of already available data becomes difficult to use. We present a web application that abstracts away mathematical and programmatical details in order to enable a convenient and customizable analysis of microarray data for large-scale reproducibility studies. In addition, the web application provides a feature that allows easy access to large microarray repositories. Results Our web application consists of three basic steps which are necessary for a differential gene expression analysis as well as Gene Ontology (GO) enrichment analysis and the comparison of multiple analysis results. Genealyzer can handle Affymetrix data as well as one-channel and two-channel Agilent data. All steps are visualized with meaningful plots. The application offers flexible analysis while being intuitively operable. Conclusions Our web application provides a unified platform for analysing microarray data, while allowing users to compare the results of different technologies and organisms. Beyond reproducibility, this also offers many possibilities for gaining further insights from existing study data, especially since data from different technologies or organisms can also be compared. The web application can be accessed via this URL: https://genealyzer.item.fraunhofer.de/ . Login credentials can be found at the end. |
| first_indexed | 2024-04-09T16:20:45Z |
| format | Article |
| id | doaj.art-b55a276bf2b6436f856df202ff6bcc73 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T16:20:45Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b55a276bf2b6436f856df202ff6bcc732023-04-23T11:29:57ZengBMCBMC Bioinformatics1471-21052023-04-0124111710.1186/s12859-023-05266-4Genealyzer: web application for the analysis and comparison of gene expression dataKristina Lietz0Babak Saremi1Lena Wiese2Research Group Bioinformatics, Fraunhofer ITEMResearch Group Bioinformatics, Fraunhofer ITEMResearch Group Bioinformatics, Fraunhofer ITEMAbstract Background Gene expression profiling is a widely adopted method in areas like drug development or functional gene analysis. Microarray data of gene expression experiments is still commonly used and widely available for retrospective analyses. However, due to to changes of the underlying technologies data sets from different technologies are often difficult to compare and thus a multitude of already available data becomes difficult to use. We present a web application that abstracts away mathematical and programmatical details in order to enable a convenient and customizable analysis of microarray data for large-scale reproducibility studies. In addition, the web application provides a feature that allows easy access to large microarray repositories. Results Our web application consists of three basic steps which are necessary for a differential gene expression analysis as well as Gene Ontology (GO) enrichment analysis and the comparison of multiple analysis results. Genealyzer can handle Affymetrix data as well as one-channel and two-channel Agilent data. All steps are visualized with meaningful plots. The application offers flexible analysis while being intuitively operable. Conclusions Our web application provides a unified platform for analysing microarray data, while allowing users to compare the results of different technologies and organisms. Beyond reproducibility, this also offers many possibilities for gaining further insights from existing study data, especially since data from different technologies or organisms can also be compared. The web application can be accessed via this URL: https://genealyzer.item.fraunhofer.de/ . Login credentials can be found at the end.https://doi.org/10.1186/s12859-023-05266-4MicroarrayWebapplicationGene expression |
| spellingShingle | Kristina Lietz Babak Saremi Lena Wiese Genealyzer: web application for the analysis and comparison of gene expression data BMC Bioinformatics Microarray Webapplication Gene expression |
| title | Genealyzer: web application for the analysis and comparison of gene expression data |
| title_full | Genealyzer: web application for the analysis and comparison of gene expression data |
| title_fullStr | Genealyzer: web application for the analysis and comparison of gene expression data |
| title_full_unstemmed | Genealyzer: web application for the analysis and comparison of gene expression data |
| title_short | Genealyzer: web application for the analysis and comparison of gene expression data |
| title_sort | genealyzer web application for the analysis and comparison of gene expression data |
| topic | Microarray Webapplication Gene expression |
| url | https://doi.org/10.1186/s12859-023-05266-4 |
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