nhihin/ire

Code to reproduce analyses in Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease (Hin et al.)

Code to reproduce analyses in Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease (Hin et al. DOI: 10.3233/JAD-210200)

Citation: Hin, N., Newman, M., Pederson, S. and Lardelli, M., 2021. Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease. Journal of Alzheimer's Disease. vol. Pre-press, no. Pre-press, pp. 1-34. https://pubmed.ncbi.nlm.nih.gov/34719489/

Media Release: "Ironing out the cause of Alzheimer's disease", The University of Adelaide. https://sciences.adelaide.edu.au/news/list/2021/11/12/ironing-out-the-cause-of-alzheimers-disease, online 12 Nov 2021.

IRE Gene Sets

Human, mouse and zebrafish IRE gene sets are available in the output/IRE_genesets directory in the following formats:

• ireGenes.rds: R Object file containing lists of 3' and 5' IRE gene sets with Ensembl gene identifier format that can be imported into R using the readRDS() function.

• ireGenes.xlsx: Lists of 3' and 5' IRE gene sets in Excel spreadsheet, including various gene identifiers.

• utr3.fa.gz and utr5.fa.gz: Fasta format sequences of UTR sequences from reference transcriptomes, used as input to SIREs.

• utr3_sires.gff and utr5_sires.gff: GFF format of predicted IRE and IRE-like motifs from SIREs.

Gene Set Testing

• Gene set testing with bulk RNA-seq or microarray data can be used with conventional methods (e.g. GSEA, or the fry, roast, or camera functions implemented in the limma package, etc.). Example code is provided in the code/combinedGSEA.R script. This script was used to perform gene set tests for the analyses described in the paper.

• For single-cell RNA-seq (scRNA-seq), the enrichIt function from the escape package allows custom gene sets to be used to perform GSEA-like gene set testing on individual cells. The R objects supplied (ireGenes.rds as described above) are in a suitable format for use with this function.

Description of Analysis Workflow + Files

• Analysis R Markdown notebooks can be found in the analysis directory.
• Wrapper function to perform gene set enrichment using combined p-values from three methods (fry, camera, and fgsea) is located in the code directory as code/combinedGSEA.R.
• Raw data files can be found in the data directory.
• IRE gene sets (described above) are available in the output directory.