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. 2016 Jan 4;44(D1):D1154-60.
doi: 10.1093/nar/gkv1035. Epub 2015 Oct 17.

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

Chi-Nga Chow  1 , Han-Qin Zheng  1 , Nai-Yun Wu  1 , Chia-Hung Chien  1 , Hsien-Da Huang  2 , Tzong-Yi Lee  3 , Yi-Fan Chiang-Hsieh  1 , Ping-Fu Hou  4 , Tien-Yi Yang  1 , Wen-Chi Chang  5
Affiliations

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

Chi-Nga Chow et al. Nucleic Acids Res. .

Abstract

Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.

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Figures

Figure 1.
Figure 1.
System flow of PlantPAN 2.0. Five major functions (Gene Group Analysis, Gene Search, Cross Species, Promoter Analysis and TF/TFBS Search) are provided in PlantPAN 2.0. The analysis processes (arrowhead) of five functions are marked by different colors. In TF/TFBS Search, the orange dotted arrowheads represent similar TFBSs identified by the input TFBS motifs, whereas the orange arrowheads refer to the regulatory information obtained by searching TF Name/Locus.
Figure 2.
Figure 2.
An example of the output in TF search.
See this image and copyright information in PMC

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