泥炭藓：苔藓植物的基因表达图谱。

PEATmoss: A Gene Expression Atlas for Bryophytes.

机构信息

Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany.

Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Algarrobo-Costa, Málaga, Spain.

出版信息

Methods Mol Biol. 2023;2703:91-107. doi: 10.1007/978-1-0716-3389-2_8.

DOI:10.1007/978-1-0716-3389-2_8

PMID:37646940

Abstract

PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.

摘要

PEATmoss 是一个藓类植物交互式基因表达图谱，它最初将 Physcomitrium patens 的 RNA-seq 和来自多个基因注释版本的微阵列表达数据统一起来。该图谱包含 100 多个 P. patens 的实验，正在扩展以容纳 Anthoceros agrestis 和 Marchantia polymorpha，并计划将来容纳更多物种的数据。PEATmoss 具有多种可视化方法和数据下载工具，并与 Physcomitrium patens Gene Model Lookup DB（PpGML DB）连接，该数据库将 P. patens 基因与来自多个数据库的注释和资源链接起来，并包含用于基因版本查找以及序列和注释提取的工具。PEATmoss 中的新功能包括数据集隐私控制、多物种菜单、交互式颜色范围、共表达网络可视化和重复数据下载。