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Multiomics analysis:

Biological databases, software, and tools

Shiva Kazempour

PhD candidate at the lab

Neurepiomics workshop

PI: Dr. Habil Zare

October 9, 2023

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Link to slides:

Scroll down, and find “How to”

Types of biological databases

Primary

(archival database)

Secondary

Commposite

Nucleic acid databases

Combines different source of primary

Analyzed version of primary

Most common omics databases

ArrayExpress: stores data from high-throughput functional genomics experiments from EMBL-EBI
Ensembl: provides automatic annotation databases for vertebrate and eukaryote
FlyBase: genome of the model organism Drosophila melanogaster
GEO: a public functional genomics data repository from the U.S. National Cancer Institute (NCI), which supports array- and sequence-based data.
Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors.
UCSC genome browser
HumanMine: an integrated database of human genomics and proteomics data
Cancer genome atlas program (TCGA): over 20,000 primary cancer and matched normal samples spanning 33 cancer types.

Most common brain atlases

Allen brain map: Provides platform for visualizing multimodal single cell data that maps gene expression across the healthy human brain. Key features include an “all genes, all structures” RNA microarray survey that is spatially mapped to an MRI reference space, in situ hybridization image data at cellular resolution for selected genes
Human single cell atlas: Aiming to map every cell type in the human body
AMP-AD: Accelerating Medicines Partnership - Alzheimer’s Disease Target Discovery and Preclinical Validation

Search tools in Allen Brain Map: clustering genes vs clustering voxels

Correlation between genes

Correlation between voxels

TREM2 is a receptor primarily expressed on microglia. It functions to stimulate phagocytosis on one hand and to suppress cytokine production and inflammation on the other hand
TYROBP is an adaptor protein that associates with TREM2, helping to transmit signals when TREM2 is activated. This interaction is crucial for regulating microglial responses, including their phagocytic and inflammatory functions.