Genomics

Dataset Information

43

Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [methylation]


ABSTRACT: Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic profiles of primary tumors, normal tissues, and cell lines Overall design: DNA methylation profiles of 19 T/N pairs

INSTRUMENT(S): Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

SUBMITTER: Aditi Qamra  

PROVIDER: GSE85464 | GEO | 2016-09-28

SECONDARY ACCESSION(S): PRJNA338608

REPOSITORIES: GEO

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Publications

Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.

Ooi Wen Fong WF   Xing Manjie M   Xu Chang C   Yao Xiaosai X   Ramlee Muhammad Khairul MK   Lim Mei Chee MC   Cao Fan F   Lim Kevin K   Babu Deepak D   Poon Lai-Fong LF   Lin Suling Joyce J   Qamra Aditi A   Irwanto Astrid A   Qu Zhengzhong James J   Nandi Tannistha T   Lee-Lim Ai Ping AP   Chan Yang Sun YS   Tay Su Ting ST   Lee Ming Hui MH   Davies James O J JO   Wong Wai Keong WK   Soo Khee Chee KC   Chan Weng Hoong WH   Ong Hock Soo HS   Chow Pierce P   Wong Chow Yin CY   Rha Sun Young SY   Liu Jianjun J   Hillmer Axel M AM   Hughes Jim R JR   Rozen Steve S   Teh Bin Tean BT   Fullwood Melissa Jane MJ   Li Shang S   Tan Patrick P  

Nature communications 20160928


Regulatory enhancer elements in solid tumours remain poorly characterized. Here we apply micro-scale chromatin profiling to survey the distal enhancer landscape of primary gastric adenocarcinoma (GC), a leading cause of global cancer mortality. Integrating 110 epigenomic profiles from primary GCs, normal gastric tissues and cell lines, we highlight 36,973 predicted enhancers and 3,759 predicted super-enhancers respectively. Cell-line-defined super-enhancers can be subclassified by their somatic  ...[more]

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