README.md

Global Transcriptomic Profiling Identifies Differential Gene expression Signatures between Inflammatory and Non-inflammatory Aortic Aneurysms

DOI: 10.1002/art.42138

Authors: Benjamin Hur, Matthew J. Koster, Jin Sung Jang, Cornelia M. Weyand, Kenneth J. Warrington, and Jaeyun Sung

Contact: hur.benjamin@mayo.edu Corresponding Author: sung.jaeyun@mayo.edu

Transcriptome comparisons between inflammatory and non-inflammatory aortic aneurysms

Differentially expressed genes (DEGs) and volcano plot:

analysis_with3Meta/gene_set/01_run_deseq_multi_level.sh

analysis_with3Meta/gene_set/02_geneset.sh

analysis_with3Meta/gene_set/03_draw_vocano.sh

Note: DESeq2 v1.26.0 was used during the analysis. Please note that DEG results can vary depending on the DESeq2 version.

Pharmacogenomic network construction:

analysis_with3Meta/network/01_run.sh

analysis_with3Meta/network/02_parse_subnetwork.sh

analysis_with3Meta/network/03_create_pharmacogenomic_network.sh

Other analyses:

PCA

src/statistics/PCA_whole_data.ipynb

Identification of confounding effects

src/statistics/linear_model_variable_significance.ipynb

Pie chart for PANTHER results

src/statistics/panther_pie_chart.ipynb

.fastq file trimming and alignment

/Users/m221138/Aortitis_Public/preprocess/01_trim_rawdata.sh /Users/m221138/Aortitis_Public/preprocess/02_run_alignmnet.sh

Data:

Read counts of 50 samples and 26,475 genes with STAR alignment

data/aortitis.tsv

log2-transformed TPM values of 50 samples and 26,475 genes with RSEM

data/tpm_profile.log2.tsv

Raw data (.fastq) files are available upon request (sung.jaeyun@mayo.edu)