Per feedback from recent trainings, we are hosting a training focused on biomarkers and drug target investigation through effectively utilizing high quality curated public proteomics expression data. OmicSoft Lands database is a high-quality curated repository which contains gene and protein expression data derived from a variety of sources such as CPTAC, TCGA, HPA, GTEx and more.
Using OmicSoft Lands APIs, you will learn how to:
- Easily locate proteomics samples and projects (studies) of interest (example can we locate proteomics data related to the breast cancer or specific drug treatment?)
- Check expression of a protein of interest (drug target or biomarkers) across different experimental groups or conditions (diseases, treatments, cell types and more) as well as across samples coming from different collections (example is a protein upregulated in breast cancer samples from TCGA and CPTAC but downregulated in normal samples from TCGA, GTEx and HPA?)
- Correlate protein levels with RNA-seq expression data for the same samples, and compare differential expression results from proteomic and RNA-seq results
- Investigate whether there is correlation in expression between two (or a group/list of proteins) across different experimental groups/conditions (example do two proteins of interest show correlation in expression in TNBC samples? Is protein and gene expression correlated as well?)
- Derive a protein signature from conditions of interest (example are a group of protein upregulated in disease condition but downregulated upon drug treatment)
- Perform Geneset Enrichment for a group of proteins
