Noncoding“junk DNA”,which constitutes 98%of our genome,is now generally considered to play a fundamental role in the precise regulation of coding genes to establish cell identity.One feature of functional“junk DNA...Noncoding“junk DNA”,which constitutes 98%of our genome,is now generally considered to play a fundamental role in the precise regulation of coding genes to establish cell identity.One feature of functional“junk DNA”is its accessibility.In cancer cells,aberrant chromatin accessibility is recognized as one of the major hallmarks.Understanding such events requires high-throughput screening,such as Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq),which generates large-scale data that are puzzling for biologists.However,existing web tools only support cell line data and lack high-quality clinical phenotypes or matched transcriptomes.Here,we developed Shiny Pan-cancer Accessible Chromatin Explorer(SPACE)as an all-in-one web server encompassing 562,709 regulatory elements in 404 patients across 23 cancer types.展开更多
基金supported by the National Natural Science Foundation of China(31770935,81873531,31970616)the Distinguished Professorship Program of Jiangsu Province to YF+2 种基金the Distinguished Professorship Program of Jiangsu Province to RMthe National Undergraduate Training Programs for Innovation(201710304030Z)the National Undergraduate Training Programs for Innovation(201810304026Z).
文摘Noncoding“junk DNA”,which constitutes 98%of our genome,is now generally considered to play a fundamental role in the precise regulation of coding genes to establish cell identity.One feature of functional“junk DNA”is its accessibility.In cancer cells,aberrant chromatin accessibility is recognized as one of the major hallmarks.Understanding such events requires high-throughput screening,such as Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq),which generates large-scale data that are puzzling for biologists.However,existing web tools only support cell line data and lack high-quality clinical phenotypes or matched transcriptomes.Here,we developed Shiny Pan-cancer Accessible Chromatin Explorer(SPACE)as an all-in-one web server encompassing 562,709 regulatory elements in 404 patients across 23 cancer types.
