Open AccessZokorDB: tissue specific regulatory network annotation for non‐coding elements of plateau zokor
Author(s) -
Xin Jingxue,
Hao Junjun,
Chen Lang,
Zhang Tao,
Li Lei,
Chen Luonan,
Zhao Wenmin,
Lu Xuemei,
Shi Peng,
Wang Yong
Publication year - 2020
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-020-0195-4
Subject(s) - gene , computational biology , transcription factor , annotation , biology , gene regulatory network , regulatory sequence , gene annotation , genome , gene expression , genetics
Background Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai‐Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration. Methods We provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. ZokorDB is based on a high‐quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain, heart, liver, kidney, and lung. The conserved non‐coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites. Results ZokorDB provides a general draft gene regulatory network (GRN), i.e., potential transcription factor (TF) binds to non‐coding regulatory elements and regulates the expression of target genes (TG). Furthermore, we refined the GRN by incorporating matched RNA‐seq and DNase‐seq data from mouse ENCODE project and reconstructed five tissue‐specific regulatory networks. Conclusions A web‐based, open‐access database is developed for easily searching, visualizing, and downloading the annotation and data. The pipeline of non‐coding region annotation for zokor will be useful for other non‐model species. ZokorDB is free available at the website ( bigd.big.ac.cn/zokordb/ ).