Gene Expression Atlas

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Gene Expression Atlas

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Gene Expression Atlas

Overview

<table class="infobox infobox-gene">
<tr>
<th class="infobox-header" colspan="2">Gene Expression Atlas</th>
</tr>
<tr>
<td class="label">Gene</td>
<td>eQTL Tissue</td>
</tr>
<tr>
<td class="label">AP0E</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">CLU</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">CR1</td>
<td>Blood</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">Gene</td>
<td>eQTL Tissue</td>
</tr>
<tr>
<td class="label">SNCA</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">LRRK2</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">GBA1</td>
<td>Blood</td>
</tr>
</table>

This page provides a comprehensive reference for gene expression patterns in the brain across neurodegenerative diseases, leveraging data from the Allen Brain Atlas and other comprehensive expression studies. Understanding where genes are expressed in the brain is fundamental to interpreting GWAS findings, identifying cell-type-specific vulnerability, and developing targeted therapies. [@allen2024]

Gene expression patterns reveal which cell types express disease-relevant genes, providing insights into mechanism and potential therapeutic windows. Single-cell RNA sequencing has revolutionized our understanding of cell-type-specific expression in neurodegenerative diseases. [@seaad2023]

--- [@brain2021]

Brain Region Expression Patterns

Alzheimer Disease Expression Signatures

...

Gene Expression Atlas

Overview

<table class="infobox infobox-gene">
<tr>
<th class="infobox-header" colspan="2">Gene Expression Atlas</th>
</tr>
<tr>
<td class="label">Gene</td>
<td>eQTL Tissue</td>
</tr>
<tr>
<td class="label">AP0E</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">CLU</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">CR1</td>
<td>Blood</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">Gene</td>
<td>eQTL Tissue</td>
</tr>
<tr>
<td class="label">SNCA</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">LRRK2</td>
<td>Brain</td>
</tr>
<tr>
<td class="label">GBA1</td>
<td>Blood</td>
</tr>
</table>

This page provides a comprehensive reference for gene expression patterns in the brain across neurodegenerative diseases, leveraging data from the Allen Brain Atlas and other comprehensive expression studies. Understanding where genes are expressed in the brain is fundamental to interpreting GWAS findings, identifying cell-type-specific vulnerability, and developing targeted therapies. [@allen2024]

Gene expression patterns reveal which cell types express disease-relevant genes, providing insights into mechanism and potential therapeutic windows. Single-cell RNA sequencing has revolutionized our understanding of cell-type-specific expression in neurodegenerative diseases. [@seaad2023]

--- [@brain2021]

Brain Region Expression Patterns

Alzheimer Disease Expression Signatures

Hippocampal Expression: The [hippocampus](/brain-regions/hippocampus) shows early involvement in AD. Key genes with hippocampal expression include: [@gtex2020]

[APP](/entities/app-protein): High expression in pyramidal [neurons](/entities/neurons), moderate in interneurons
[MAPT](/proteins/tau) (Tau): High expression in pyramidal neurons; isoform expression shifts in AD
[APOE](/proteins/apoe): Expressed in [astrocytes](/entities/astrocytes) and [microglia](/cell-types/microglia-neuroinflammation); APOE4 carriers show altered expression
[TREM2](/proteins/trem2): Microglia-specific expression; expression increases in AD

[Entorhinal Cortex](/brain-regions/entorhinal-cortex) Expression: The entorhinal [cortex](/brain-regions/cortex) is the earliest affected region: [@eqtl2022]

SNCA: Low baseline expression but increases with pathology
GRN: High expression in microglia; progranulin deficiency leads to [TDP-43](/mechanisms/tdp-43-proteinopathy) pathology
[C9orf72](/entities/c9orf72): Moderate neuronal expression; hexanucleotide expansions cause toxicity

Cortical Expression: Neocortex shows later involvement:

NEFL, NEFM (Neurofilament): Released in neurodegeneration; biomarkers
CLU (Clusterin): Astrocyte expression; clearance of debris

Parkinson Disease Expression Signatures

Substantia Nigra Expression: The substantia nigra pars compacta is selectively vulnerable:

SNCA: High expression in dopaminergic neurons; aggregation triggers cell death
LRRK2: Neuronal expression; kinase activity increases in disease
PARKIN: Ubiquitous but essential in dopaminergic neurons
PINK1: Mitochondrial expression; loss leads to mitophagy defects
GBA1: Lysosomal expression; mutations increase PD risk

Striatal Expression: Target of dopaminergic therapy:

DRD1, DRD2: High striatal expression; targets of dopaminergic drugs
DARPP32: Medium spiny neuron marker; dopamine signaling

Cell Type Expression

Neuronal Expression

Excitatory neurons: High expression of synaptic proteins, ion channels
Inhibitory neurons: GABAergic signaling components, calcium-binding proteins
Dopaminergic neurons: SNCA, LRRK2, tyrosine hydroxylase (TH)
Cholinergic neurons: Choline acetyltransferase (CHAT), vesicular transporters

Glial Expression

Astrocytes: APOE, [GFAP](/entities/gfap), CLU, excitatory amino acid transporters (EAATs)
Microglia: TREM2, CX3CR1, CD33, [complement system](/entities/complement-system) components
Oligodendrocytes: MBP, PLP, myelin-related genes
Oligodendrocyte precursor cells (OPCs): PDGFRA, NG2 (CSPG4)

Single-Cell Expression Resources

Allen Brain Cell Atlas

The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) provides single-nucleus RNA sequencing of AD brains:

Cell type populations: All major neuron and glial types identified
Disease states: Comparison of AD vs. healthy aging
Regional coverage: Multiple brain regions including hippocampus, cortex
Data access: https://portal.brain-map.org/explore/atlases/sea-ad

Key Findings from Single-Cell Studies

Cell-Type Vulnerability in AD

Upper-layer excitatory neurons show earliest tau pathology
Oligodendrocyte precursor cells increase proliferation
Microglia show disease-specific transcriptional states (disease-associated microglia - DAM)
Astrocytes adopt reactive phenotypes

Cell-Type Vulnerability in PD

Dopaminergic neurons in substantia nigra show mitochondrial dysfunction signatures
Microglia show chronic activation patterns
Oligodendrocytes show reduced myelin gene expression

Expression Quantitative Trait Loci (eQTLs)

AD eQTLs

PD eQTLs

Expression-Based Therapeutic Target Identification

Overexpressed Targets

Genes with high brain expression that are also GWAS hits represent priority targets:

LRRK2: High neuronal expression, strong PD GWAS signal

TREM2: Microglial expression, strong AD GWAS signal

SNCA: Neuronal expression, strong PD GWAS signal

Cell-Type Specific Targets

Neuronal targets: Synaptic proteins, ion channels, neurotransmitter receptors Microglial targets: TREM2, CD33, complement components Astrocytic targets: APOE, glutamate transporters Oligodendroglial targets: Myelin genes, cholesterol metabolism

Expression Database Resources

Allen Brain Atlas: https://portal.brain-map.org/
Human Cell Atlas: https://www.humancellatlas.org/
BrainSpan Atlas: https://brainspan.org/
GTEx Portal: https://gtexportal.org/
SEA-AD: https://portal.brain-map.org/explore/atlases/sea-ad
AMP-AD: https://ampadportal.org/

External Links

[PubMed](https://pubmed.ncbi.nlm.nih.gov/)
[KEGG Pathways](https://www.genome.jp/kegg/pathway.html)

References

Unknown, Allen Brain Atlas Data Portal (2024) (2024)

[Unknown, SEA-AD Single-Cell Atlas (2023) (2023)](https://doi.org/10.1101/2023.02.27.530901)

[Unknown, Brain Cell Type Atlas (2021) (2021)](https://doi.org/10.1126/science.abb4596)

[Unknown, GTEx Consortium (2020) (2020)](https://doi.org/10.1126/science.aaz1776)

[Unknown, AD eQTL Meta-Analysis (2022) (2022)](https://doi.org/10.1038/s41588-022-01084-1)

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Related Entities

GENEEXPRESSIONATLAS

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slug	genes-gene-expression-atlas
kg_node_id	GENEEXPRESSIONATLAS
entity_type	gene
origin_type	v1_polymorphic_backfill
source_table	wiki_pages
wiki_page_id	wp-acbe356b3c9e
__merged_from	{'merged_at': '2026-05-13', 'unprefixed_id': 'genes-gene-expression-atlas'}
_schema_version	1

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Gene Expression Atlas

Gene Expression Atlas

Overview

Brain Region Expression Patterns

Alzheimer Disease Expression Signatures

Gene Expression Atlas

Overview

Brain Region Expression Patterns

Alzheimer Disease Expression Signatures

Parkinson Disease Expression Signatures

Cell Type Expression

Single-Cell Expression Resources

Allen Brain Cell Atlas

Key Findings from Single-Cell Studies

Expression Quantitative Trait Loci (eQTLs)

AD eQTLs

PD eQTLs

Expression-Based Therapeutic Target Identification

Overexpressed Targets

Cell-Type Specific Targets

Expression Database Resources

See Also

External Links

References

💬 Discussion