JuGEx - Julich-Brain Gene Expression

バージョン 1.0.2 (5.4 MB) 作成者: Sebastian

Cytoarchitecture linked to gene expression to study multilevel human brain organization

https://www.fz-juelich.de/en/inm/inm-1/expertise/tools-services-and-research-data/jugex

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更新 2023/4/6

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JuGEx - Julich-Brain Gene Expression

Cytoarchitecture linked to gene expression to study multilevel human brain organization

Decoding the chain from genes to cognition requires detailed insights how areas with specific gene activities and microanatomical architectures contribute to brain function and dysfunction. The Allen Human Brain Atlas ^[1] contains regional gene expression data, while the Julich-Brain Atlas ^[2] offers three-dimensional cytoarchitectonic maps reflecting the interindividual variability. JuGEx offers an integrated framework that combines the analytical benefits of both repositories towards a multi-level brain atlas of adult humans. JuGEx is a new method for integrating tissue transcriptome and cytoarchitectonic segregation.

JuGEx finds differentially expressed genes based on a user-defined candidate gene list between two user-defined volumes of interest (Julich-Brain maps or other volume of interest in MNI152 reference space ^[3]). The tool downloads expression values via the Allen Brain API, which are further analysed using a permuted n-way ANOVA.

Important: Make sure that your VOIs are registered to the MNI152 reference space! If not, you will extract wrong and non-corresponding tissue samples through the Allen Brain API.

[1] Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL et al (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489:391–399. https://doi.org/10.1038/nature11405
[2] Amunts, K., Mohlberg, H., Bludau, S., Zilles, K. (2020). Julich-Brain – A 3D probabilistic atlas of human brain’s cytoarchitecture. Science 369, 988-992. DOI: 10.1126/science.abb4588
[3] Evans, A. C., Janke, A. L., Collins, D. L., Baillet, S. (2012). Brain templates and atlases. Neuroimage, 62(2):911-22. DOI: 10.1016/j.neuroimage.2012.01.024

Cite As

Bludau, Sebastian, et al. “Integration of Transcriptomic and Cytoarchitectonic Data Implicates a Role for MAOA and TAC1 in the Limbic-Cortical Network.” Brain Structure and Function, vol. 223, no. 5, Springer Science and Business Media LLC, Feb. 2018, pp. 2335–42, doi:10.1007/s00429-018-1620-6.

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JuGex

JuGex/analyze_AB_exp_Data

JuGex/extract_AB_exp_Data

JuGex/utility

JuGex/visualize_AB_exp_Data

バージョン	公開済み	リリースノート
1.0.2	2023/4/6	See release notes for this release on GitHub: https://github.com/INM-1-FZJ-Cytoarchitecture/jugex/releases/tag/1.0.2	ダウンロード
1.0.0	2020/10/9

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MLA	Bludau, Sebastian, et al. “Integration of Transcriptomic and Cytoarchitectonic Data Implicates a Role for MAOA and TAC1 in the Limbic-Cortical Network.” Brain Structure and Function, vol. 223, no. 5, Springer Science and Business Media LLC, Feb. 2018, pp. 2335–42, doi:10.1007/s00429-018-1620-6.
APA	Bludau, S., Mühleisen, T. W., Eickhoff, S. B., Hawrylycz, M. J., Cichon, S., & Amunts, K. (2018). Integration of transcriptomic and cytoarchitectonic data implicates a role for MAOA and TAC1 in the limbic-cortical network. Brain Structure and Function, 223(5), 2335–2342. Springer Science and Business Media LLC. Retrieved from https://doi.org/10.1007%2Fs00429-018-1620-6
BibTeX	@article{Bludau_2018, doi = {10.1007/s00429-018-1620-6}, url = {https://doi.org/10.1007%2Fs00429-018-1620-6}, year = 2018, month = {feb}, publisher = {Springer Science and Business Media {LLC}}, volume = {223}, number = {5}, pages = {2335--2342}, author = {Sebastian Bludau and Thomas W. Mühleisen and Simon B. Eickhoff and Michael J. Hawrylycz and Sven Cichon and Katrin Amunts}, title = {Integration of transcriptomic and cytoarchitectonic data implicates a role for {MAOA} and {TAC}1 in the limbic-cortical network}, journal = {Brain Structure and Function} }