Limits...
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.

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.


Characterization of correlations between individual donor profiles and the median profile. (A) Histogram of donor-to-median profile correlations. The dashed red line marks a correlation of 0.446, which corresponds to one sided p < 0.05 (derived from random simulations of donor expression profiles). Mean expression levels and overlaps with the “synaptic transmission” and “neuron part” gene ontology groups are provided for genes in four correlation ranges (marked as dotted vertical lines). Expression profiles for four representative genes that lie at the midpoints of each range are provided in (B) and marked in (A) with arrows (HTR1F, MRPS6, SOCS6, and NUP210L). The solid black line represents the median profile and the six donor profiles as dotted lines in (B). Each region is color-coded to indicate its cortical lobe: frontal (red), parietal (blue), temporal (purple) and occipital (green). Each symbol shape represents a specific donor.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4584957&req=5

Figure 1: Characterization of correlations between individual donor profiles and the median profile. (A) Histogram of donor-to-median profile correlations. The dashed red line marks a correlation of 0.446, which corresponds to one sided p < 0.05 (derived from random simulations of donor expression profiles). Mean expression levels and overlaps with the “synaptic transmission” and “neuron part” gene ontology groups are provided for genes in four correlation ranges (marked as dotted vertical lines). Expression profiles for four representative genes that lie at the midpoints of each range are provided in (B) and marked in (A) with arrows (HTR1F, MRPS6, SOCS6, and NUP210L). The solid black line represents the median profile and the six donor profiles as dotted lines in (B). Each region is color-coded to indicate its cortical lobe: frontal (red), parietal (blue), temporal (purple) and occipital (green). Each symbol shape represents a specific donor.

Mentions: The third stage involved averaging values of gene expression across all voxels mapped into a specific FreeSurfer region; for each individual brain, median values were obtained for each gene and each cortical region. These values were then summarized across the individual brains; for the group of six brains, median values were calculated for each gene and region (see Figure 1 for examples). The result is seven gene-expression profiles (six donors and one median profile). These profiles can be represented as a vector of regional expression values for each gene. Mean Spearman correlation between these vectors (or profiles) of the individual brains and the median result is used to provide a measure of variance across the individuals for a specific gene (referred to as consistency).


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

French L, Paus T - Front Neurosci (2015)

Characterization of correlations between individual donor profiles and the median profile. (A) Histogram of donor-to-median profile correlations. The dashed red line marks a correlation of 0.446, which corresponds to one sided p < 0.05 (derived from random simulations of donor expression profiles). Mean expression levels and overlaps with the “synaptic transmission” and “neuron part” gene ontology groups are provided for genes in four correlation ranges (marked as dotted vertical lines). Expression profiles for four representative genes that lie at the midpoints of each range are provided in (B) and marked in (A) with arrows (HTR1F, MRPS6, SOCS6, and NUP210L). The solid black line represents the median profile and the six donor profiles as dotted lines in (B). Each region is color-coded to indicate its cortical lobe: frontal (red), parietal (blue), temporal (purple) and occipital (green). Each symbol shape represents a specific donor.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Characterization of correlations between individual donor profiles and the median profile. (A) Histogram of donor-to-median profile correlations. The dashed red line marks a correlation of 0.446, which corresponds to one sided p < 0.05 (derived from random simulations of donor expression profiles). Mean expression levels and overlaps with the “synaptic transmission” and “neuron part” gene ontology groups are provided for genes in four correlation ranges (marked as dotted vertical lines). Expression profiles for four representative genes that lie at the midpoints of each range are provided in (B) and marked in (A) with arrows (HTR1F, MRPS6, SOCS6, and NUP210L). The solid black line represents the median profile and the six donor profiles as dotted lines in (B). Each region is color-coded to indicate its cortical lobe: frontal (red), parietal (blue), temporal (purple) and occipital (green). Each symbol shape represents a specific donor.
Mentions: The third stage involved averaging values of gene expression across all voxels mapped into a specific FreeSurfer region; for each individual brain, median values were obtained for each gene and each cortical region. These values were then summarized across the individual brains; for the group of six brains, median values were calculated for each gene and region (see Figure 1 for examples). The result is seven gene-expression profiles (six donors and one median profile). These profiles can be represented as a vector of regional expression values for each gene. Mean Spearman correlation between these vectors (or profiles) of the individual brains and the median result is used to provide a measure of variance across the individuals for a specific gene (referred to as consistency).

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.