The molecular mechanisms underlying tumor development are highly intricate. For gastrointestinal tumors, comprehending and controlling the heterogeneous molecular mechanisms may unveil novel therapeutic targets. In recent years, the cancer field, including gastrointestinal tumors, has generated an abundance of molecular and phenotypic data. Facilitated by high-throughput technologies, a vast amount of genomic data has rapidly accumulated, giving rise to the era of cancer “big data.” These cancer datasets continue to expand globally, fueled by investments in the research community. The utilization and development of extensive databases play a pivotal role in establishing a sturdy framework for deciphering the molecular mechanisms involved in tumor initiation and progression, while concurrently exploring innovative approaches to diagnosis and treatment.