Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
School of Molecular Sciences, Arizona State University, Tempe 85281, USA.
Nucleic Acids Res. 2024 Jan 5;52(D1):D1569-D1578. doi: 10.1093/nar/gkad945.
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
PlantPAN 4.0（http://PlantPAN.itps.ncku.edu.tw/）是一个用于构建不同植物物种转录调控网络的综合资源。在这个版本中，基因注释和启动子序列扩展到覆盖 115 个物种。PlantPAN 4.0 可以帮助用户描述顺式调控元件之间的进化差异和相似性；此外，该系统现在还可以帮助识别同源基因之间保守的非编码序列。更新后的转录因子结合位点库包含了 18305 个转录因子的 3428 个非冗余矩阵；这一扩展有助于探索保守非编码序列中顺式调控元件的组合和核苷酸变体。此外，还手动更新了调控因子的基因组景观，并添加了来自单细胞绿藻（Chlamydomonas reinhardtii）的 ChIP-seq 数据集。此外，还改进了统计审查和图形分析组件，通过 ChIP-seq 数据分析提供易于理解的信息。这些改进包括易于阅读的实验条件聚类、可搜索的基因为中心的界面，用于通过考虑实验条件聚类和所有调控因子的峰可视化来识别启动子区域的结合偏好，以及调控因子的 20 个最显著富集的基因本体功能。因此，PlantPAN 4.0 可以有效地重建基因调控网络，并帮助比较不同植物物种和实验的基因组顺式调控元件。
