HPVTIMER: A Shiny web application for tumor immune estimation in human papillomavirus-associated cancers

The tumor immune microenvironment (TIME) is closely associated with tumor formation, particularly linked to the human papillomavirus (HPV), and regulates tumor initiation, proliferation, infiltration, and metastasis. With the rise of immunotherapy, an increasing amount of sample data used for TIME exploration is available in databases. However, no currently available web tool enables a comprehensive exploration of the TIME of HPV‐associated cancers by leveraging these data. We have developed a web tool called HPV‐associated Tumor Immune MicroEnvironment ExploreR (HPVTIMER), which provides a comprehensive analysis platform that integrates over 10,000 genes and 2290 tumor samples from 65 transcriptome data sets across 8 cancer types sourced from the Gene Expression Omnibus (GEO) database. The tool features four built‐in analysis modules, namely, the differential expression analysis module, correlation analysis module, immune infiltration analysis module, and pathway analysis module. These modules enable users to perform systematic and vertical analyses. We expect that HPVTIMER will help users explore the immune microenvironment of HPV‐associated cancers and uncover potential immune regulatory mechanisms and immunotherapeutic targets. HPVTIMER is available at http://www.hpvtimer.com/.

HPVTIMER comprises 65 transcriptomic data sets of HPV‐associated tumors, covering two species (human and mouse) and eight cancer species. The transcriptome data were preprocessed and standardized based on their kind. HPVTIMER provides users with four analysis modules, namely, the differential expression analysis module, correlation analysis module, immune infiltra tion analysis module, and pathway analysis module (Figure 1). These four analysis modules enable users to investigate the properties of signatures of interest in HPV‐associated tumor HPV‐positive/negative samples.