Yuhan Fei1, Rui Wang1, Haoyuan Li2, Shu Liu1, Hongsheng Zhang1, Ji Huang1. 1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture. 2. College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
Abstract
Motivation: MicroRNAs (miRNAs) play essential roles in plant growth, development and stress responses through post-transcriptionally regulating the expression levels of their target mRNAs. Although some tools and databases were developed for predicting the relationships between miRNAs and their targets (miR-Tar), most of them were dependent on computational methods without experimental validations. With the development of degradome sequencing techniques, researchers can identify potential interactions based on degradome sequencing data. The validations with specific degradome data are useful to identify the miR-Tar interactions (MTIs) occurring in/under some specific tissues or treatments. Degradome-based plant miRNA-target interaction and network database (DPMIND) collected almost all available plant degradome data and built a retrieval and analysis platform of miRNA-target interactions and miRNA regulatory networks (MRNs). Results: DPMIND contains the recently updated 3794 miRNAs and 28 666 verified MTIs with 69 degradomes from 10 plant species. Not only the verified MTIs but also the degradome-based MRNs can be retrieved from DPMIND. Users can search for the verified MTIs and build degradome-based MRNs for the specific miRNAs or targets. DPMIND can build the MRNs based on all degradomes or specific degradomes, which helps to identify all possible connections among specific miR-Tar and compare the miRNA-mediated networks among various tissues or treatments. It can also build the networks mediated by all known miRNAs based on specific degradomes. Furthermore, DPMIND can be used to study the conservation and specificity of MTIs and sub-networks across different plant tissues or species. Availability and implementation: http://202.195.246.60/DPMIND/. Contact: huangji@njau.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: MicroRNAs (miRNAs) play essential roles in plant growth, development and stress responses through post-transcriptionally regulating the expression levels of their target mRNAs. Although some tools and databases were developed for predicting the relationships between miRNAs and their targets (miR-Tar), most of them were dependent on computational methods without experimental validations. With the development of degradome sequencing techniques, researchers can identify potential interactions based on degradome sequencing data. The validations with specific degradome data are useful to identify the miR-Tar interactions (MTIs) occurring in/under some specific tissues or treatments. Degradome-based plant miRNA-target interaction and network database (DPMIND) collected almost all available plant degradome data and built a retrieval and analysis platform of miRNA-target interactions and miRNA regulatory networks (MRNs). Results:DPMIND contains the recently updated 3794 miRNAs and 28 666 verified MTIs with 69 degradomes from 10 plant species. Not only the verified MTIs but also the degradome-based MRNs can be retrieved from DPMIND. Users can search for the verified MTIs and build degradome-based MRNs for the specific miRNAs or targets. DPMIND can build the MRNs based on all degradomes or specific degradomes, which helps to identify all possible connections among specific miR-Tar and compare the miRNA-mediated networks among various tissues or treatments. It can also build the networks mediated by all known miRNAs based on specific degradomes. Furthermore, DPMIND can be used to study the conservation and specificity of MTIs and sub-networks across different plant tissues or species. Availability and implementation: http://202.195.246.60/DPMIND/. Contact: huangji@njau.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.