Commercializing iDEP, an interactive and reproducible tool for analyzing RNA-Seq data

RNA sequencing (RNA-Seq) is routinely used to survey the expression of tens of thousands of genes. Analyzing such large datasets poses a significant challenge for many biologists, especially those with limited resources. Through an R01 from NHGRI and six years of dedicated work, we developed iDEP (integrated Differential Expression & Pathway analysis), an interactive web app for comprehensive, reproducible bioinformatic analysis of RNA-Seq data. iDEP integrates over 70 R packages for exploratory analysis, clustering, and differential gene expression. Pathway analysis is powered by an extensive database covering gene annotations in 14,000 species, including animals, plants, and microbes. With over 650,000 website visits and 1000 citations, it has garnered widespread usage across many fields, proving particularly invaluable for researchers lacking in-house bioinformatics support. A common issue plaguing many bioinformatics services is their tendency to cease updates or disappear once initial funding runs out. This project seeks to transform iDEP into a commercially viable product through a partnership between RTutor, LLC, and South Dakota State University (SDSU). We plan to reduce the cost of database updates, improve deployment, and enhance access to public RNA- Seq data. Aim 1. Streamline Database Updates: We will create workflows to automate annual updates from Ensembl and STRING. Aim 2. Develop a Desktop Application: We aim to package the iDEP web server as a desktop application to enhance user experience, data security, and reproducibility. Aim 3. Improve access to public RNA-Seq data using AI. We will adopt large language models (LLMs) to facilitate the reuse of public expression data, using multiple LLM agents to find and summarize published data. We will also create a tech support chatbot based on existing iDEP documentation to answer simple user questions, supplementing continued support via emails. The need for a secure, interactive, knowledge-based app for analyzing and interpreting RNA-Seq data clearly exists both in academia and industry. RTutor LLC secured an exclusive license from SDSU for sublicensing. Our business model is to generate revenue through licensing fees and customized databases. This revenue will fund R&D to improve and update iDEP, ensuring free access for non-profit institutions. This STTR project represents a crucial step toward long-term viability of iDEP to amplify its impact on a large, diverse scientific community. Project Number: 1R41HG014101-01A1 | Fiscal Year: 2025 | NIH Institute/Center: National Human Genome Research Institute (NHGRI) | Principal Investigator: Xijin Ge | Institution: RTUTOR, LLC, Brookings, SD | Award Amount: $395,316 | Activity Code: R41 | Study Section: Special Emphasis Panel[ZRG1 MCST-S (14)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11186600