Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox
Summary: The integration of neuroimaging and transcriptomics data, Imaging Transcriptomics, is becoming increasingly popular but standardized workflows for its implementation are still lacking. We describe the Imaging Transcriptomics toolbox, a new package that implements a full imaging transcriptom...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722001952 |
| _version_ | 1818022799014363136 |
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| author | Alessio Giacomel Daniel Martins Matteo Frigo Federico Turkheimer Steven C.R. Williams Ottavia Dipasquale Mattia Veronese |
| author_facet | Alessio Giacomel Daniel Martins Matteo Frigo Federico Turkheimer Steven C.R. Williams Ottavia Dipasquale Mattia Veronese |
| author_sort | Alessio Giacomel |
| collection | DOAJ |
| description | Summary: The integration of neuroimaging and transcriptomics data, Imaging Transcriptomics, is becoming increasingly popular but standardized workflows for its implementation are still lacking. We describe the Imaging Transcriptomics toolbox, a new package that implements a full imaging transcriptomics pipeline using a user-friendly, command line interface. This toolbox allows the user to identify patterns of gene expression which correlates with a specific neuroimaging phenotype and perform gene set enrichment analyses to inform the biological interpretation of the findings using up-to-date methods.For complete details on the use and execution of this protocol, please refer to Martins et al. (2021). |
| first_indexed | 2024-12-10T03:34:10Z |
| format | Article |
| id | doaj.art-adf72fee2a22400a99eb9bea4645e1a1 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-10T03:34:10Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-adf72fee2a22400a99eb9bea4645e1a12022-12-22T02:03:45ZengElsevierSTAR Protocols2666-16672022-06-0132101315Integrating neuroimaging and gene expression data using the imaging transcriptomics toolboxAlessio Giacomel0Daniel Martins1Matteo Frigo2Federico Turkheimer3Steven C.R. Williams4Ottavia Dipasquale5Mattia Veronese6Department of Neuroimaging, IoPPN, King’s College London, London, UK; Corresponding authorDepartment of Neuroimaging, IoPPN, King’s College London, London, UK; Corresponding authorCorsmed AB, Stockholm, Sweden; ATHENA Project Team, Inria Sophia Antipolis - Mediterranée, Université Côte d’Azur, Nice, FranceDepartment of Neuroimaging, IoPPN, King’s College London, London, UKDepartment of Neuroimaging, IoPPN, King’s College London, London, UKDepartment of Neuroimaging, IoPPN, King’s College London, London, UKDepartment of Neuroimaging, IoPPN, King’s College London, London, UK; Department of Information Engineering, University of Padova, Padova, ItalySummary: The integration of neuroimaging and transcriptomics data, Imaging Transcriptomics, is becoming increasingly popular but standardized workflows for its implementation are still lacking. We describe the Imaging Transcriptomics toolbox, a new package that implements a full imaging transcriptomics pipeline using a user-friendly, command line interface. This toolbox allows the user to identify patterns of gene expression which correlates with a specific neuroimaging phenotype and perform gene set enrichment analyses to inform the biological interpretation of the findings using up-to-date methods.For complete details on the use and execution of this protocol, please refer to Martins et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166722001952BioinformaticsSequence analysisHealth SciencesNeuroscienceComputer sciences |
| spellingShingle | Alessio Giacomel Daniel Martins Matteo Frigo Federico Turkheimer Steven C.R. Williams Ottavia Dipasquale Mattia Veronese Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox STAR Protocols Bioinformatics Sequence analysis Health Sciences Neuroscience Computer sciences |
| title | Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| title_full | Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| title_fullStr | Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| title_full_unstemmed | Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| title_short | Integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| title_sort | integrating neuroimaging and gene expression data using the imaging transcriptomics toolbox |
| topic | Bioinformatics Sequence analysis Health Sciences Neuroscience Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722001952 |
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