ASCancer Atlas: A Comprehensive Knowledgebase of Alternative Splicing in Human Cancers
Over the past decade, there have been extensive evidences showing that aberrations in mRNA splicing contribute to neoplastic transformation, tumor progression and therapeutic resistance. Splicing dysregulation can alter a multitude of critical cellular processes, covering all cancer hallmarks. With accumulating studies of carcinogenic mis-splicing in cancers, there is an urgent demand to integrate cancer-associated splicing changes to better understand their internal cross-talks and functional consequences from a global view. Unfortunately, there is still a lack of such resources, which serve as not only a collection of computationally putative AS events for correlation-based analysis, but more importantly, a knowledgebase of key functional AS events together with its upstream splicing regulators, downstream oncogenic effects and possible therapeutic strategies.
To fill the gap, researchers from the Beijing Institute of Genomics of Chinese Academy of Sciences (China National Center for Bioinformation) have constructed a comprehensive knowledgebase of alternative splicing in human cancers —— ASCancer Atlas. This work was published in Nucleic Acids Research.
In the current release, a total of 2,006 high-confidence cancer-associated splicing events (CASE) were manually curated from 610 publications. These CASE have a unified curation model, including upstream splicing regulations, splicing event annotations, downstream oncogenic effects, and possible treatments. Meanwhile, ASCancer Atlas houses about 2 million computationally putative splicing events (CPSE), covering 33 TCGA cancer types and 31 GTEx normal tissues. In addition, an interactive splicing visualization tool and a multi-dimensional online analysis toolkit were equipped to further explore the splicing events.
Collectively, ASCancer Atlas provides the first knowledgebase of carcinogenic AS in human cancers, which can help users to investigate the full spectrum of splicing dysregulation in cancers and will become a value-added resource when more and more splicing variants are identified as targets for cancer treatment.
Database contents and organization (Image by NGDC)
Dr. BAO Yiming
Dr. LIU Zhaoqi