Input and output files of the case studies included in the manuscript "MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration".

This repository contains the input and output files necessary to reproduce the case studies reported in the manuscript "MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration". MUUMI is an R package implementing network-based data integration and statistical meta-analysis within a single analytical framework. MUUMI allows the identification of robust molecular signatures through multiple meta-analytic methods, inference and analysis of molecular interactomes and the integration of multiple omics layers. The functionalities of MUUMI are showcased in two case studies in which we analysed 17 transcriptomic datasets on idiopathic pulmonary fibrosis (IPF) from both microarray and RNA-Seq platforms and multi-omics data of THP-1 macrophages exposed to different polarising stimuli. Part of the data reported in this repository derive from the Zenodo entry https://doi.org/10.5281/zenodo.10692129 (Curated and harmonised transcriptomics datasets of interstitial lung disease patients). Other data derive from the following publication: Migliaccio G, Morikka J, del Giudice G, Vaani M, Möbus L, Serra A, Federico A, Greco D. Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages, Comp and Struct Biotech J, 2024(25), 143-152. doi: 10.1016/j.csbj.2024.08.018.本仓库包含用于复现论文《MUUMI：用于多组学数据整合的统计与基于网络的meta分析R包》中报道的案例研究所需的输入与输出文件。MUUMI是一款在统一分析框架内实现基于网络的数据整合与统计meta分析的R包。该工具可通过多种meta分析方法识别稳健的分子特征，可对分子互作组进行推断与分析，并可整合多组学层面的数据。本研究通过两项案例研究展示了MUUMI的功能：其一为分析17组针对特发性肺纤维化（idiopathic pulmonary fibrosis, IPF）的转录组数据集，涵盖微阵列（microarray）与RNA测序（RNA-Seq）平台；其二为分析暴露于不同极化刺激的THP-1巨噬细胞的多组学数据。本仓库中的部分数据源自Zenodo收录条目https://doi.org/10.5281/zenodo.10692129（经整理与标准化的间质性肺病患者转录组数据集）。其余数据源自下述刊载于《计算与结构生物技术期刊》的论文：Migliaccio G、Morikka J、del Giudice G、Vaani M、Möbus L、Serra A、Federico A、Greco D所著的《甲基化与转录组分析揭示极化巨噬细胞的短期与长期调控应答》，该论文刊载于2024年第25期，页码范围为143-152，DOI为10.1016/j.csbj.2024.08.018。