seq2pathway

"seq2pathway" introduces an approach, FAIME (Functional Analysis of Individual Microarray Expression), aimed at enhancing the interpretability and utility of gene expression signatures, particularly in predicting therapeutic responses or prognoses in clinical settings. The traditional challenge in gene expression analysis has been the mechanistic interpretation of expression arrays, and the low gene overlap among distinct, clinically validated expression signatures has limited the adoption of multi-gene signatures compared to single-gene biomarkers.

FAIME addresses these challenges by generating "personal mechanism signatures" representing molecular pathways and functions derived from individual gene expression arrays. This method calculates mechanism scores based on rank-weighted gene expression of a single sample, allowing for a precise and intuitive understanding of deregulated pathways and molecular functions. When applied to head and neck squamous cell carcinoma (HNSCC) samples and compared with non-tumor control tissues, FAIME demonstrates comparable precision and recall to conventional cohort-wide methods, like GSEA, in identifying deregulated mechanisms.

A significant advantage of FAIME is its ability to produce a higher overlap in Oncogenic FAIME Features of HNSCC across different datasets compared to traditional gene overlap, indicating a more consistent identification of relevant biological pathways and functions. Additionally, these Oncogenic FAIME Features can accurately discriminate between tumors and control tissues in separate datasets and stratify recurrence-free survival in patients from independent studies, highlighting its potential for clinical application.