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A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas.

French L, Paus T - Front Neurosci (2015)

View Article: PubMed Central - PubMed

Affiliation: Rotman Research Institute, Baycrest Toronto, ON, Canada.

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The Allen Human Brain Atlas provides an anatomically comprehensive view of gene expression in the brain (Hawrylycz et al., )... Adding the perspective of gene expression could facilitate interpretation of these reports... For example, we recently found that the magnitude of group differences in cortical thickness between cannabis users and non-users correlates with regional variations in expression levels of cannabis receptor 1 (CNR1) (French et al., )... The number of donors per region varied between all six donors for 28/34 regions to three donors for 1/34 region... The number of samples per region ranged from 6 (bankssts) to 100 (superiorfrontal) (details in DKRegionStatistics.tsv)... This figure represents a summarized and filtered view of 329,478 CNR1 expression measurements provided in the Allen Brain Atlas and processed with the tools described in this report; creating this figure involved downloading two files and executing the R script, all provided in this report... These properties possibly result in low correlations across the donors due a lower signal to noise ratio... Reassuringly, neural associated genes show consistent spatial patterns across the six brains... AllenHBA_to_DKRegion_Map.xls—Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions... This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers... AllenHBA_DK_ExpressionMatrix.tsv—Tab separated file containing correlation to the median values across the donors (left hemisphere only, column named “Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns)... This file can be opened with read.table in R or as a tab separated file in a spreadsheet program... ConsistentGOGroups.tsv—Gene Ontology enrichment analyses results for the consistency measure... InconsistentGOGroups.tsv—Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency).

No MeSH data available.


Lateral (left) and medial (right) views of CNR1 gene expression data projected onto the FreeSurfer cortical regions in the left hemisphere of the fsaverage brain template. Expression (log2 intensity) ranges from 5 (blue), 5.92 (white), and red (6.83).
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Figure 2: Lateral (left) and medial (right) views of CNR1 gene expression data projected onto the FreeSurfer cortical regions in the left hemisphere of the fsaverage brain template. Expression (log2 intensity) ranges from 5 (blue), 5.92 (white), and red (6.83).

Mentions: Figure 2 presents a cortical surface map of CNR1 expression. This example image was created using our R script that creates color lookup tables for the TkSurfer tool (CreateExpressionLUT.r). In the case of CNR1, consistency across the six individual brains is high (Spearman's ρ = 0.82, 98 percentile). This figure represents a summarized and filtered view of 329,478 CNR1 expression measurements provided in the Allen Brain Atlas and processed with the tools described in this report; creating this figure involved downloading two files and executing the R script, all provided in this report. While similar visualizations are provided by the Allen Institute website (http://human.brain-map.org/) and Brain Explorer 2 3D viewer they do not provide a single view that summarizes across donors, probes or FreeSurfer cortical regions (Figure S1). We hope that our technique will help facilitate interpretation of neuroimaging findings in a molecular context.


A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas.

French L, Paus T - Front Neurosci (2015)

Lateral (left) and medial (right) views of CNR1 gene expression data projected onto the FreeSurfer cortical regions in the left hemisphere of the fsaverage brain template. Expression (log2 intensity) ranges from 5 (blue), 5.92 (white), and red (6.83).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584957&req=5

Figure 2: Lateral (left) and medial (right) views of CNR1 gene expression data projected onto the FreeSurfer cortical regions in the left hemisphere of the fsaverage brain template. Expression (log2 intensity) ranges from 5 (blue), 5.92 (white), and red (6.83).
Mentions: Figure 2 presents a cortical surface map of CNR1 expression. This example image was created using our R script that creates color lookup tables for the TkSurfer tool (CreateExpressionLUT.r). In the case of CNR1, consistency across the six individual brains is high (Spearman's ρ = 0.82, 98 percentile). This figure represents a summarized and filtered view of 329,478 CNR1 expression measurements provided in the Allen Brain Atlas and processed with the tools described in this report; creating this figure involved downloading two files and executing the R script, all provided in this report. While similar visualizations are provided by the Allen Institute website (http://human.brain-map.org/) and Brain Explorer 2 3D viewer they do not provide a single view that summarizes across donors, probes or FreeSurfer cortical regions (Figure S1). We hope that our technique will help facilitate interpretation of neuroimaging findings in a molecular context.

View Article: PubMed Central - PubMed

Affiliation: Rotman Research Institute, Baycrest Toronto, ON, Canada.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

The Allen Human Brain Atlas provides an anatomically comprehensive view of gene expression in the brain (Hawrylycz et al., )... Adding the perspective of gene expression could facilitate interpretation of these reports... For example, we recently found that the magnitude of group differences in cortical thickness between cannabis users and non-users correlates with regional variations in expression levels of cannabis receptor 1 (CNR1) (French et al., )... The number of donors per region varied between all six donors for 28/34 regions to three donors for 1/34 region... The number of samples per region ranged from 6 (bankssts) to 100 (superiorfrontal) (details in DKRegionStatistics.tsv)... This figure represents a summarized and filtered view of 329,478 CNR1 expression measurements provided in the Allen Brain Atlas and processed with the tools described in this report; creating this figure involved downloading two files and executing the R script, all provided in this report... These properties possibly result in low correlations across the donors due a lower signal to noise ratio... Reassuringly, neural associated genes show consistent spatial patterns across the six brains... AllenHBA_to_DKRegion_Map.xls—Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions... This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers... AllenHBA_DK_ExpressionMatrix.tsv—Tab separated file containing correlation to the median values across the donors (left hemisphere only, column named “Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns)... This file can be opened with read.table in R or as a tab separated file in a spreadsheet program... ConsistentGOGroups.tsv—Gene Ontology enrichment analyses results for the consistency measure... InconsistentGOGroups.tsv—Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency).

No MeSH data available.