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 promoters in plants. The current PlantPAN release (version 2.0) contains 16,960 TFs and 1,143 matrices of TF binding sites among 76 plant species. | |
★★★★★ PlantPAN 2.0 TF position weight matrix download is available. ★★★★★ |
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Citation: Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang "PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants", Nucleic Acids Res. 2015 : gkv1035v1-gkv1035. |
Gene Search |
TF/TFBS Search |
Gene Group Analysis |
Promoter Analysis |
Cross Species |
1. Identification of cis- and trans-elements of input gene. 2. Construction of gene regulatory networks by using coexpression analysis. |
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Gene Search |
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Access TF/TFBS information by ID, matrix, and keyword search (or browse by TF family and species). | ||
TF/TFBS Search |
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1. Determine co-occurrence TF and their binding sites within the promoters of input gene group. 2. Regulatory network construction of co-occurrence TFs based on protein-protein interaction. |
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Gene Group Analysis |
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TFBS scanning in the promoter sequence. | ||
Promoter Analysis |
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Search conserved TFBSs in promoters of similar genes or user-customized promoter pairs. | ||
Cross Species |
Citation:
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✎ |
Chang, W.C., Lee, T.Y., Huang, H.D., Huang, H.Y. and Pan, R.L. (2008) PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC genomics, 9, 561.
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✎ |
Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang "PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants" Nucleic Acids Res. 2015 : gkv1035v1-gkv1035.
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Abstract:
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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 promoters in plants. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between homologous gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16,960 TFs and 1,143 matrices of TF binding sites among 76 plant species. Besides update of the annotation information, adding experimentally verified TF matrices, and improvements in visualization of transcriptional regulatory networks, several new features and functions were first 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 (i.e., environmental stresses, hormone treatments, and developmental stages), (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 first provided in plant resources. The PlantPAN 2.0 is the most systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.
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A comparison of PlantPAN 2.0 with previous version and the similar resources:
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The statistics of TFs and Matrices incorporated in six resources:
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Number of TFs and matrices from top 20 species:
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