Exploring data collections and gene signatures with projection analysis

The central notion behind our approach is to:

1. Create a compendium of transcriptomic datasets focused on neuroinflammation and neurodegeneration: "Transcriptomic data collections" below. And:
2. Collect functionally relevant gene lists to explore across many datasets. This can be from lab or published experiments, or matrix decomposition approaches (SJD) to define robust transcriptomic dynamics that are shared across selected datasets: "Gene signatures" below. Followed by:
3. Molecular dissection of the broad transcriptomic data collections (1) by projection into gene signatures (2): Table of ”Projection links“ below.

1. Transcriptomics data collections in NeMO Analytics

The central notion behind our approach is to:

Neuroinflammation: A collection of bulk and single-cell studies of human tissue and rodent models in diverse neuroinflammatory contexts, along with RNA-seq of sorted cell types for perspective.

Alzheimer's disease - Brain Tissue: Bulk and scRNA-seq in human brain tissue from AD and control samples.

Alzheimer's disease - Brain Vasculature: RNA-seq studies focusing on cell types of the vasculature.

Alzheimer's disease - Mouse models: Bulk and scRNA-seq in mouse models of AD.

Peripheral Immune: Diverse RNA-seq studies of peripheral immune cells.

2. Gene signatures to dissect data collections

NPTX2 expression correlations: Genes correlating with NPTX2 message and protein in the medial temporal gyrus of control and AD brain tissue from Lao et al 2025.

AD DEGs and age correlations: Genes differentially expressed in the medial temporal gyrus between AD and non-demented controls from Piras et al 2025.

UP in Disease Associated Microglial (DAM): 50 gene over-expressed in DAMs from Keren-Shaulet et al 2017.

DOWN in Disease Associated Microglial (DAM): 29 gene down-regulated in DAMs from Keren-Shaulet et al 2017.

Transcriptomic factors in microglia across neurodegenerative disease: 26 factors derived from microglia from 161 donors across diseases including, AD, ALS/FTD, PD, HD, MS, and epilepsy from Marshe et al 2025.

3. Projection links to explore gene signatures across the NeMO Analytics data collections