Update History

  • Minor fixes and reduced naming conflicts in R functions (01/13/2026);
  • Code refactoring and modernization for Jakarta EE 11 (12/24/2025);
  • Upgraded R to the latest version 4.5.2 "[Not] Part in a Rumble" (12/15/2025);
  • Code cleaning and consolidated P.value to Pval for consistency (05/02/2025);
  • Bug fix for empty error message issue (02/19/2025);
  • Added mature miR to precursor function and default layout fix (01/20/2025);
  • Updated database and functions to distinguish mature vs pre-miR (01/15/2025);
  • Upgraded to PrimeFaces 13.0.10 and Java version 21 (12/16/2024);
  • Migrated from Java EE to Jakarta EE (09/21/2024);
  • For miRNetR users, the path to sqlite database is updated to: https://www.xialab.ca/rest/sqlite/mir2gene.sqlite (10/08/2024);
  • Harmonized curation from different TF databases (ENCODE, ReMap, Enrichr, GTEx, ARCHS4), and updated the CHEA TF-target database to version 3 (06/27/2024);
  • Updated the microRNA and gene targets databases - Tarbase 8.0 to 9.0; and miRTarBase 8.0 to 9.0. (06/27/2024);
  • Updated the Human microRNA Disease Database (HMDD 3.2 to 4.0) (06/27/2024);
  • Enhanced network layout based on latest updates in igraph (04/18/2024);
  • Upgraded to R 4.3.2, Java 17 and PrimeFaces 13.0.1 (12/20/2023);
  • The gene expression analysis is now migrated to ExpressAnalyst; and q-PCR analysis is now migrated to EcoToxXplorer (10/20/2023);
  • Fixed the bug on miRNA gene target analysis for Schistosoma (10/17/2023);
  • Minor text updates and interface improvements (08/18/2023);
  • Removed support for searching predicted xeno-miRs based on the retraction notice for the original paper (05/13/2023);
  • Upgraded R to version 4.2.2 (01/13/2023);
  • Check out our new book chapter on MicroRNA Regulatory Network Analysis Using miRNet 2.0 (11/08/2022);
  • Upgraded to Primefaces 12.0.0 (10/12/2022);
  • Added the FDR column to the download table of enrichment analysis result (08/02/2022);
  • Upgraded R to version 4.1.3 and code refactoring (05/13/2022);
  • Upgraded to Primefaces 11 (12/20/2021);
  • Added topology distribution measures for Network Topology filter (07/04/2021);
  • Fixed error when no hits found for miRNA queries (05/04/2021);
  • Upgraded to Primefaces 10 (03/30/2021);
  • Enhanced support for PNG export - up to 3X larger (01/29/2021);
  • Fixed the issue with network export (01/29/2021);
  • Fixed the issue with tissue mapping in gene, TF and ncRNA modules (01/28/2021);
  • Fixed the issue with empirical sampling when microservice failed (12/22/2020);
  • Fixed the issue with Steiner Forest algorithm (11/24/2020);
  • Check out our video tutorials for intuitive network visual analytics (10/15/2020);
  • Updated R from 3.6.2 to 4.0.2 and code refactoring (09/15/2020);
  • Added support for gradient background (09/14/2020);
  • Added support for piechart nodes with multiple annotations (i.e. lncRNA and Gene, TF and Gene) (07/30/2020);
  • Users can now select the original database for miRNA gene target analysis (07/06/2020);
  • Our miRNet 2.0 paper is now accepted by NAR 2020 web server issue (05/21/2020);
  • Added support for the Human Reference Interactome (HuRI) map (05/14/2020);
  • Added detailed online tutorials (04/24/2020);
  • Updated Java (from Java8 to Java11) and Primefaces (from PF7 to PF8) (04/08/2020);
  • Added support for edge bundling to reduce edge crossing in large networks (03/28/2020);
  • Added support for p-value adjustment in Function Explorer (03/28/2020);
  • Users can easily update colors and sizes for different node types using Global Node Styles pane (03/19/2020);
  • Updated FAQs and the miRNet Overview tutorial (03/13/2020);
  • Added the "Module Explorer" panel for better network visual analytics (03/08/2020);
  • Fixed performance issue of several algorithms for large network layout (03/02/2020);
  • Added two layout algorithms (Concentric and Backbone) for multipartite networks (02/24/2020);
  • Code cleaning and refactoring (02/14/2020);
  • Added support for the latest miRBase ID (v22) (02/09/2020);
  • Added six miRNA set libraries (Function, Disease, Transcription Factor, Cluster, Family, Tissue specificity) for enrichment analysis based on TAM 2.0 (02/09/2020);
  • Added support for computing minimum subnetworks (02/01/2020);
  • Added support for highlighting seed nodes (01/31/2020);
  • Optimized workflow (01/28/2020);
  • Code cleaning and refactoring (01/24/2020);
  • Fixed issue with data filtering in the Network Tools (01/23/2020);
  • Updated tutorials and FAQs (01/02/2020);
  • Enhanced network visualization & customization. Users can now customize background color, node shape & label, edge color & opacity (01/02/2020);
  • Users can now download all the results from the Download page (12/20/2019);
  • Added support for bipartite and tripartite network layout building and visualization (12/19/2019);
  • Added a new module to support integrating multiple types of molecules (miRNAs, TFs, genes, lncRNAs) for system-level visual analytics (12/18/2019);
  • Added a new module to support miRNA SNP annotation and targets interactions (12/13/2019);
  • Added a new module to support miRNA and transcription factor interactions (12/03/2019);
  • Updated miRNA-disease interaction data based on new release of HMDD v3.2 (11/08/2019);
  • Updated R from 3.5.1 to the latest version (3.6.1) (10/16/2019);
  • Added support for pig (429 miRNAs and 8353 genes targets) (10/09/2019);
  • Code refactoring for better performance (06/06/2019);
  • Upgraded the web framework to PrimeFaces 7.0 (05/29/2019);
  • Added two modules to support analysis of xeno-miRNAs (xenomiRs) and their potential targets in different hosts (02/25/2019);
  • Updated the interface for improved performance and better user experience (02/20/2019);
  • A detailed protocol on using miRNet is now available (11/20/2018);
  • Updated the framework for better performance (08/19/2018);
  • Code refactoring for performance enhancement (05/16/2018);
  • Added exosomal miRNA annotation for human miRNAs (01/05/2018);
  • Added tissue-specific miRNA annotation for human miRNAs (12/26/2017);
  • miRNet can now automatically recognize and correct pre-miRNAs to their mature forms (12/16/2017);
  • Updated miRNA gene targets based on new releases of miRTarbase and TarBase (11/16/2017);
  • Code refactoring for performance improvement (10/25/2017);
  • Fixed issue for miRBase links (09/25/2017);
  • Added support for reducing node overlap for large network layout (09/22/2017);
  • Added Force Atlas layout algorithm to support large network visualization (09/21/2017);
  • Fixed broken links for downloading the mir target data files (08/25/2017);
  • Enhanced data IO for improved performance (06/01/2017);
  • Added support for miRNA family mapping and enrichment analysis (05/09/2017);
  • Fixed bug with lncRNA mapping (05/03/2017);
  • Minor bug fix and performance improvement (03/14/2017);
  • Added support for chicken (943 miRNAs and 8160 genes targets) as predicted by miRanda (09/15/2016);
  • Added support for cow (643 miRNAs and 8160 genes targets) as predicted by miRanda (08/25/2016);
  • Added support for dynamic network editing (07/18/2016);
  • Updated FAQs (#12) on how to generate a high-resolution network image (07/15/2016);
  • Updated SVG Export to fully capture the current network view (07/14/2016);
  • Added batch filtering support (under Network Tools) to refine network on given miRNAs or targets (07/8/2016);
  • miRNet paper is now published (04/21/2016);
  • Updated tutorials and FAQs (04/01/2016);
  • miRNet now supports old miRBase IDs from v15 to v21 (03/30/2016);
  • Added support to compute unions or intersections of selected miRNA targets (02/28/2016);
  • Differential analysis now allows gene selection based on fold change directions (02/25/2016);
  • miRNet database updates (03/20/2016);
  • Updated miRNet tutorials (02/02/2016);
  • Minor bug fix in network filtering (02/01/2016);
  • Updated color scheme for expression (01/28/2016);
  • Updated data filter for predicted miRNA targets (01/25/2016);
  • Bug fixes and feature enhancement (01/20/2016);
  • Bug fixes for S. mansoni data (12/28/2015);
  • Enrichment analysis for miRNA target genes now supports both hypergeometric tests and unbiased random sampling (12/22/2015);
  • Improved support for filtering miRNA-target interaction (12/21/2015);
  • Network visualization now supports high-resolution retina display (12/15/2015);
  • Manually cleaned diseases and small molecule annotations (11/28/2015);
  • Added support for miRNA and epigenetic modification analysis (11/15/2015);
  • Added support for miRNA disease association analysis (11/05/2015);
  • Added support for miRNA and small molecule interactions (11/01/2015);
  • miRNet interface upgrade (10/25/2015);
  • miRNet 1.0 test release (10/1/2015);
  • Set up miRNet domain and website prototyes (08/15/2015);