README.md

mito_dysfunction_PIH

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AUTHOR: CONTESSA A. RICCI, PhD

MANUSCRIPT: DYSREGULATION OF MITOCHONDRIA-MEDIATED MATERNAL-FETAL

INTERACTIONS IN HYPERTENSIVE DISORDERS OF PREGNANCY

DOI:

STUDY PURPOSE: Reanalysis of longitudinal maternal RNAseq data from

peripheral blood plasma and endpoint fetal RNAseq data

from placenta at delivery. Goal is to understand

consequences of mitochondrial gene dysregulation by

examining expression patterns of genes the dysregulated

mitochondrial genes are known to interact with

DATA: GEO accession GSE154377 (maternal longitudinal data)

GEO accession GSE114691 (fetal placental)

Accessible via NCBI GEO datasets

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Each script explains the process it is meant to carry out. This read me outlines the computational process carried out for this study

1. Obtain DEGs from maternal and fetal samples (DESeq2 analysis, mito_dysregulation_Ricci2021.r, R)
2. Identify mtDEGs from maternal and fetal samples (find_mtDEGs.py, Python)
3. Identify interaction genes present in maternal and fetal samples (find_mtDEG-INTXs.py, Python)
4. Write GMT files (actual and null model testing) for TcGSA (find_mtDEG-INTXs.py, Python)
5. Carry out TcGSA (TcGSA, mito_dysregulation_Ricci2021.r, R)
6. Carry out Ingenuity Pathway Analysis and Gene Ontology functional enrichments (externally)