A comparative analysis of ENCODE and Cistrome in the context of TF binding signal.

ABSTRACT:

Background

With the rise of publicly available genomic data repositories, it is now common for scientists to rely on computational models and preprocessed data, either as control or to discover new knowledge. However, different repositories adhere to the different principles and guidelines, and data processing plays a significant role in the quality of the resulting datasets. Two popular repositories for transcription factor binding sites data - ENCODE and Cistrome - process the same biological samples in alternative ways, and their results are not always consistent. Moreover, the output format of the processing (BED narrowPeak) exposes a feature, the signalValue, which is seldom used in consistency checks, but can offer valuable insight on the quality of the data.

Results

W

SUBMITTER: Perna S 

PROVIDER: S-EPMC11363379 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature