iDEP

iDEP performs integrated differential expression and pathway analysis of RNA-Seq transcriptomic data to identify differentially expressed genes and enriched pathways.

Key Features:

• Integration of Bioconductor packages: Integration of 63 R/Bioconductor packages provides a comprehensive framework for RNA-Seq data processing and analysis.
• Web services and annotation databases: Connectivity with two web services and annotation and pathway databases covering 220 plant and animal species enables species-specific pathway and gene annotation.
• Exploratory analysis and quality control: Supports exploratory data analysis, quality control, normalization, and differential expression workflows for transcriptomic datasets.
• Reproducible workflows: Generation of customized R scripts and related pathway files enables reproducibility of analyses.

Scientific Applications:

• Lung fibroblasts with Hoxa1 knockdown: Analysis identified transcription factors SP1 and E2F1 and implicated microRNAs regulating target genes that influence the G1/S transition.
• Mouse B cells and p53 status: In B cells lacking functional p53, ionizing radiation was associated with MYC pathway activation promoting proliferation and ribosome biogenesis, whereas in wildtype B cells radiation triggered p53-mediated apoptosis and DNA repair and inhibited MYC and E2F1 target genes leading to growth arrest.
• p53 regulatory network and microRNAs: Analyses implicated multiple microRNAs, including miR-92a, miR-504, and miR-30a, in p53-associated regulatory mechanisms.

Methodology:

Data input followed by quality control, normalization, differential expression analysis, and pathway enrichment using integrated annotation and pathway databases.