> For the complete documentation index, see [llms.txt](https://docs.owkin.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.owkin.com/what-you-can-do-with-k-pro/indication-prioritization-and-target-validation.md). # Indication prioritization & target validation Use K-Pro to assess whether a target is worth advancing, and to check that biomarkers behave consistently across data modalities. * **Assess target tractability & druggability**: evaluate target tractability, safety profiles, and therapeutic potential using curated knowledge bases (such as Open Targets, ChEMBL, DepMap, and the Human Protein Atlas). * **Validate biomarkers across modalities**: test biomarkers and hypotheses across bulk RNA-seq, mutations, proteomics, single-cell, spatial, and clinical data. ### Find candidates with convergent evidence **What to do:** Combine several data modalities (for example RNA-seq and mutation data) within a cohort to find candidates supported by more than one layer of evidence. Start with a specific comparison between two subgroups rather than "analyze everything": focused questions give clearer, faster results. **Example prompt:** > In the TCGA-LUAD cohort, integrate RNA-seq gene expression and mutation data. Identify genes that are both differentially expressed and frequently mutated in current smokers versus never-smokers. **Expected result:** A differential expression analysis (volcano plot) and a mutation landscape (oncoprint) for the two subgroups, with a summary of the genes that stand out in both. **Follow-up:** > Compare MSigDB DNA repair, oxidative stress, and EMT signature scores between current smokers and never-smokers in TCGA-LUAD, as violin plots with p-values. ### Check the signal at protein level **What to do:** Confirm that a transcript-level signal holds at protein level, using proteomics data from CPTAC. **Example prompt:** > In CPTAC breast cancer, compare ERBB2 protein abundance between tumors with high and low ERBB2 RNA expression, and show how well RNA and protein levels agree. **Expected result:** A protein-level comparison between the two groups, and an RNA-protein concordance plot. ### Validate at single-cell resolution **What to do:** In K-Pro, use MOSAIC single-cell data to check which cell types drive a bulk signal, for example whether a target is expressed by malignant cells rather than by the tumor microenvironment. **Example prompt:** > In MOSAIC bladder cancer, show NECTIN4 expression by cell type, and run a pseudobulk differential expression analysis of malignant cells versus all other cells. **Expected result:** A dot plot of NECTIN4 expression across cell types, and a pseudobulk differential expression result for malignant cells. {% embed url="" %} --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://docs.owkin.com/what-you-can-do-with-k-pro/indication-prioritization-and-target-validation.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.