zur Hauptseite

Institut für Neurowissenschaften und Medizin

Navigation und Service


JuBrain 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 contains regional gene expression data, while the JuBrain Atlas offers three-dimensional cytoarchitectonic maps reflecting interindividual variability. To date, an integrated framework that combines the analytical benefits of both scientific platforms towards a multi-level brain atlas of adult humans was not available. We have therefore developed JuGEx, a new method for integrating tissue transcriptome and cytoarchitectonic segregation.



Animated visualization of a JuGEx result in a 3D reference space showing the localization of investigated tissue samples and regional expression differences of a candidate gene in the medial compared to the lateral frontal pole (enlarge video player to see further details).

JuGEx is an integrated framework of the AllenBrain and JuBrain atlases for statistical analysis of differential gene expression in the adult human brain.

JuGEx is an integrated framework of the AllenBrain and JuBrain atlas for statistical analysis of differential gene expression in the adult human brain.

Up to now, an integrated framework for combined analyses towards a multi-level human brain atlas has not been developed so far. To achieve this, we have developed JuGEx (JuBrain Gene Expression), a user-friendly workflow based on graphical user interfaces that enables multiple ways of analyses of differential gene expression and cytoarchitectonic data. The added value of our method is that different levels of information on brain architecture, e.g. structural and functional connectivity, brain activations, and neurotransmitter receptor density, can now be supplemented by transcriptional information to enlight biological aspects of brain organization and its diseases, spatially referring to the cytoarchitectonic JuBrain atlas. This allows analysis beyond approaches which rely on the traditional segregation of the brain into sulci and gyri, thereby lumping together functionally different microstructural areas. JuGex is publicly available to empower research from basic, cognitive and clinical neuroscience in further brain regions and disease models with regard to gene expression.


This research was supported by the European Union Seventh Framework program (FP7/2007-2013) Grant 604102 (Human Brain Project) to K.A. and S.C.


Sebastian Bludau, Thomas W. Mühleisen, Simon B. Eickhoff, Michael J. Hawrylycz, Sven Cichon, Katrin Amunts. Integration of transcriptomic and cytoarchitectonic data implicates a role for MAOA and TAC1 in the limbic-cortical network. 2018, Brain Structure and Function.

Code availability:

The workflow and GUIs of JuGex are based on a script distribution coded in Matlab (version R2015b, 64bit). JuGEx - download


JuGEx Download

The JuGEx workflow and the GUIs are based on a script distribution that was coded in Matlab (version R2015b, 64bit). All codes are freely available through a download at JuGEx download page.


Dr. Sebastian Bludau
Architecture and Brain Function

Dr. Thomas W. Mühleisen
Genomic Imaging