GIDAS
Bioinformatics research analyzing differential gene expression in tuberculosis and Alzheimer's disease, using GEO microarray data and STRING protein-protein interaction networks. Output: a published-author credit on a paper about NMDA receptor phosphorylation and LTP impairment in Alzheimer's.
Differential expression on GSE19444.
Pulled the active-TB whole-blood microarray cohort (GSE19444), ran a standard limma-style differential expression pipeline, and ranked probes and genes by logFC and adjusted p-value.
| Output | Rows | Use |
|---|---|---|
| tuberculosis_GSE19444_ranked_genes.csv | ~22k | Top differentially-expressed genes for downstream analysis. |
| tuberculosis_GSE19444_ranked_probes.csv | ~54k | Probe-level resolution for ambiguous gene mappings. |
| tuberculosis_GSE19444_sample_groups.csv | ~54 | Active TB vs. latent vs. control labels. |
| tuberculosis_stringdb_top250_upregulated.csv | 250 | STRING-imported up-regulated subnetwork. |
| tuberculosis_stringdb_top250_downregulated.csv | 250 | STRING-imported down-regulated subnetwork. |
| tuberculosis_stringdb_top300_logFC_desc_with_stats.csv | 300 | Top hits with confidence + interaction stats for the writeup. |
NMDA receptor phosphorylation and LTP.
Parallel work on the Alzheimer's GEO datasets focused on the NMDA receptor signaling pathway. The analysis surfaced upregulated phosphorylation as a candidate contributor to long-term potentiation (LTP) impairment in early-stage AD.
The methodology mirrored the TB pipeline: pull the relevant GEO cohort, run differential expression, intersect with curated KEGG and Reactome pathways, then run STRING enrichment to see which protein-protein interaction modules cluster around the candidate genes. The combination of cross-cohort signal and pathway enrichment was the structure of the contribution to the eventual paper.
Author credit on the NMDA paper.
Listed as a contributing author on the publication titled "Upregulated phosphorylation in Alzheimer's disease, NMDA receptors and LTP". The contribution: differential expression analysis, STRING network construction, figure generation.