Abstract
BackgroundConstruction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. Numerous high-throughput approaches, including microarray and next-generation sequencing, are extensively adopted to examine transcriptional expression patterns on the whole-genome scale; those data are helpful in reconstructing TRNs. Identifying transcription factor binding sites (TFBSs) in a gene promoter is the initial step in elucidating the transcriptional regulation mechanism. Since transcription factors usually co-regulate a common group of genes by forming regulatory modules with similar TFBSs. Therefore, the combinatorial interactions of transcription factors must be modeled to reconstruct the gene regulatory networks.Description For systems biology applications, this work develops a novel database called Arabidopsis thaliana Promoter Analysis Net (AtPAN), capable of detecting TFBSs and their corresponding transcription factors (TFs) in a promoter or a set of promoters in Arabidopsis. For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN. Additionally, proteins interacting with the co-expressed TFs are also incorporated to reconstruct co-expressed TRNs. Moreover, combinatorial TFs can be detected by the frequency of TFBSs co-occurrence in a group of gene promoters. In addition, TFBSs in the conserved regions between the two input sequences or homologous genes in Arabidopsis and rice are also provided in AtPAN. The output results also suggest conducting wet experiments in the future.ConclusionsThe AtPAN, which has a user-friendly input/output interface and provide graphical view of the TRNs. This novel and creative resource is freely available online at http://AtPAN.itps.ncku.edu.tw/.
Highlights
Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology
Many bioinformatics web servers, including PlantCARE [1], AthaMap [2,3] and PlantPAN [4] have adopted the analysis of transcription factors and their corresponding binding sites in the promoter of genes as their primary strategy
Following the development of whole-genome microarrays and the increased availability of gene expression data in Arabidopsis, significant efforts have been denoted to unraveling the relationships between genes, such as GeneMANIA [6] and ATTED-II [7]
Summary
Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. To our knowledge, none of the resources incorporate microarray co-expression data of TFs and their TGs in promoter analysis system or in TRNs reconstruction system in Arabidopsis. In addition to integrating microarray co-expression data in the promoter analysis system, this work attempts to provide high confident TFs that are coexpressed with their TGs. The databases IntAct [9], BioGRID [10], and BIND [11] help to elucidate protein-protein interactions.
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