Update History
  • Code refactoring for improved performance (01/23/2026)
  • Added batch correction (ComBat) to normalization workflow for removing technical batch effects (01/17/2026);
  • Upgraded R to the latest version 4.5.2 "[Not] Part in a Rumble" (12/15/2025);
  • Added support for gene co-expression network analysis - WGCNA (09/17/2025);
  • Added Median-of-Ratio followed by log2 normalization (08/08/2025);
  • Interactive QC diagnostic graphics (06/18/2025);
  • Added more QC diagnostic graphics to identify outlier samples (05/29/2025);
  • Added William's trend test for dose response module (05/29/2025);
  • Added support for Madagascar Periwinkle (05/15/2025);
  • Added "Sample Exclusion" in Data Normalization page (04/27/2025);
  • Interactive PCA visualization in data processing steps based on user feedback (04/27/2025);
  • Added support for Zhangshugang pepper (01/28/2025);
  • Upgraded Java from version 17 to Java 21 LTS (12/16/2024);
  • Added support to allow users to download all sig. genes in dose response analysis (11/25/2024);
  • Fixed an issue for curve fitting when used together with results from DESeq2 (11/07/2024);
  • Improved interface and documentations for tPOD calculation based on gene-level BMD (10/29/2024);
  • Upgraded to PrimeFaces 13.0.10, and Jakarta EE 10 (09/16/2024);
  • Added support for custom gene set library upload for gene expression analysis module (09/05/2024);
  • Added QC diagnostics quality metrics based on omics data analysis framework for regulatory application (R-ODAF) (07/05/2024);
  • Added QC diagnostics for raw data processing (06/20/2024);
  • Added raw data processing support for Clostridium tyrobutyricum (06/13/2024);
  • Code refactoring for improved performance (04/29/2024);
  • Added KEGG pathway analysis support for Brugia malayi (bmy) (03/13/2024);
  • Added support for WormBase Transcript ID for C. elegans (02/12/2024);
  • Enabled GSEA support for Arabidopsis thaliana (ATH) (01/23/2024);
  • Upgraded to Java 17, R 3.4.2 and PrimeFaces 13.0.1 (12/20/2023);
  • Added support for two species E. andrei and O. nitens (11/26/2023);
  • Added support for significant genes selection based on average fold changes in the feature-level meta-analysis and volcano plots (Meta-analysis module) (11/16/2023);
  • Fixed minor bug in the tPOD (20th gene) calculation method (11/14/2023);
  • Check out our detailed protocols Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms (11/11/2023);
  • Improved graphics and scientific notation handling for dose-response data sets to accommodate many dose groups with very low values (08/24/2023);
  • Minor bug fixes and code refactoring based on user feedback from OmicsForum (08/18/2023);
  • Enhanced support for enrichment analysis with default universe set to all genes measured rather than all genes with functional annotations (08/01/2023);
  • Fixed an bug with dose response curve analysis (07/28/2023);
  • Fixed an bug in metadata Editor when one column left (07/26/2023);
  • Added support for generating high-resolution feature plot (06/18/2023);
  • Added interactive accumulation plots for dose response analysis (06/12/2023);
  • Added support for benchmark dose (BMD) response and time series analysis (05/31/2023);
  • Added missing value imputation and updated the normalization method for proteomics data (05/15/2023);
  • Enhanced support for complex metadata table upload and differential expression analysis with covariate adjustment (03/23/2023);
  • Updated databases and tutorials for RNAseq raw data processing (02/23/2023);
  • Updated H. azteca gene annotation database based on the latest annotation (02/15/2023);
  • Code refactoring for better performance (01/06/2023);
  • Fixed the issue with Upset plot generation (01/03/2023);
  • Upgraded to the latest R version 4.2.2 (12/15/2022);
  • Fixed an issue Seq2Fun ID and JS code refactoring (11/15/2022);
  • Added an example dataset and related tutorial for Seq2Fun/ExpressAnalyst output (10/25/2022);
  • Added R command history and ExpressAnalystR tutorial (10/01/2022);
  • Updated tutorials based on the latest version (09/01/2022);
  • Enhanced support for generic genes based on KO and Seq2Fun IDs (08/22/2022);
  • Fixed ORA heatmap issue and improved Ridgeline chart (07/12/2022);
  • Minor improvements of enrichment network and user interface (07/05/2022);
  • Fixed the issue in data upload for meta-analysis (06/22/2022);
  • Switching from FAQs page to using OmicsForum (06/17/2022);
  • Replaced gene-level box plot with violin plot (06/01/2022);
  • Added support for interactive ridge line plot (05/31/2022);
  • Added support to show meta-analysis result in Volcano plot (05/25/2022);
  • Replaced Chord diagram with Upset plot for summarizing meta-analysis results (05/15/2022);
  • Added support for Mongolian gerbil (M. unguiculatus) (04/13/2022);
  • Official launch of ExpressAnalyst dedicated for gene expression profiling and meta-analysis. NetworkAnalyst is reserved for knowledge-driven network analysis from a gene list (03/25/2022);
  • Code cleaning and interface enhancement (03/14/2022);
  • Fixed the issue associated with empty columns in the abundance table (01/28/2022);
  • Users can now perform GO analysis for any non-model species profiled by Seq2Fun (01/20/2022);
  • Added support for Seq2Fun output to enable streamlined analysis of gene expression data from any species (01/19/2022);
  • Migrating raw RNAseq processing from Galaxy to ExpressAnalyst for better interface and support (01/07/2022);
  • Upgraded to PrimeFaces 11 (12/14/2021);
  • Added support for Hyalella azteca (12/09/2021);
  • Fixed issue for gene symbols display for fruit fly (11/18/2021);
  • Enhanced meta-analysis result table download based on user feedback (11/12/2021);
  • Fixed the issue with host-parasite and host-microbiome interaction dialog (10/12/2021);
  • Updated rainbow trout annotation based on the new release (08/15/2021);
  • Added common network topology measures in the Network Builder page (07/01/2021);
  • Fixed node size issue for enrichment networks (06/07/2021);
  • Added support for KEGG ortholog IDs (05/03/2021);
  • Added NCBI annotation support for fathead minnow (04/22/2021);
  • Fixed several issues with tools for network customization (04/16/2021);
  • Upgraded to PrimeFaces 10! (03/27/2021);
  • Fixed SVG export issue for enrichment network analysis (03/06/2021);
  • Enhanced support for enrichment network visualization (02/18/2021);
  • Enhanced support for several important species in ecology (rainbow trout, fathead minnow, Japanese quail, African clawed frog, and northern leopard frog) (02/12/2021);
  • Enhanced network and volcano plot visualization (01/20/2021);
  • Fixed issue with PNG export for networks (12/29/2020);
  • Fixed the issue with uploading data with unspecified ID in the meta-analysis module (12/10/2020);
  • Users can now create integrated networks by selecting several types of network databases during network creation (10/08/2020);
  • Users can now apply reduce node overlap on a selected region of interest (09/15/2020);
  • Added support for gradient background and bi/tripartite network layout (09/03/2020);
  • Consolidated the interface for network selection and network tools (08/20/2020);
  • Added cross-species PPI support between host and 15 parasites as well as host and microbiome(08/07/2020);
  • Added support for page sharing - click the to share interactive visual analytics results with your collaborators! (05/18/2020);
  • Added support for the Human Reference Interactome (HuRI) map (05/13/2020);
  • Added support for edge bundling in 2D network view (04/09/2020);
  • Added support for functional analysis for users upload network files (02/22/2020);
  • Fixed the issue with InnateDB ID mapping (02/17/2020);
  • Code cleaning and refactoring (02/03/2020);
  • Added support for colorblind-friendly schema in network and heatmap visualization (01/10/2020);
  • Updated all gene ID annotation files based on the latest database (NCBI, Uniprot, StringDB and Biomart) (12/16/2019);
  • The Current Selection panel in Network View page show Fold Change (FC) values for genes selected (11/29/2019);
  • Fixed broken link for project management (save/delete) (11/20/2019);
  • Updated R from 3.5.1 to the latest version (3.6.1) (10/16/2019);
  • Volcano plot now supports enrichment analysis against user defined gene sets (10/07/2019);
  • Fixed the broken link in meta-analysis result download page (09/18/2019);
  • Bug fixes - GSEA and uploading multiple list files are working now (06/24/2019);
  • Enhanced graphML parsing for network file upload (05/31/2019);
  • Updated web framework to PrimeFaces 7.0 (05/18/2019);
  • Updated KEGG pathways for all 17 species (04/30/2019);
  • Fixed the issue with PCA 3D visual analytics (04/05/2019);
  • Fixed the issue with DE analysis for species not in the list of 17 organisms (03/28/2019);
  • Our NetworkAnalyst 3.0 manuscript is accepted by Nucleic Acids Research! (03/23/2019);
  • Added support for WormBase ID for C. elegans (03/22/2019);
  • Users can now upload one or more gene list file(s) in addition to direct copy-and-paste (03/18/2019);
  • Fixed issue with box plot display when clicking a data point in volcano plot (03/12/2019);
  • Fixed issue with meta-data upload and table display (03/06/2019);
  • Updated FAQs and Tutorials based on new features (02/01/2019);
  • Added support for heatmap visual analytics for gene lists (01/23/2019);
  • Added GSEA support for gene expression meta-analysis (01/15/2018);
  • Added support for enrichment network visual analytics (01/07/2019);
  • Added support for multiple gene lists upload (12/21/2018);
  • Updated FAQs and added 6 new tutorials for NetworkAnalyst (12/18/2018);
  • Added support for different gene ranking options for GSEA (12/12/2018);
  • Added GSEA support for gene expression analysis (12/08/2018);
  • Code refactoring to improve speed and memory efficiency (12/05/2018);
  • Added support for PANTHER GO slim libraries for all enrichment analysis moduels (11/22/2018);
  • Added project management support to allow registered users to resume their data analysis later! (11/15/2018);
  • Added support for uploading common graph files from R or Cytoscape (10/22/2018);
  • Added support for network visualization in 3D space (10/18/2018);
  • Added support for raw RNAseq analysis using our Galaxy server (10/15/2018);
  • Fixed the annotation file for Illumina HumanRef-8 V3 BeadArray (07/06/2018);
  • See Resources on local installation option (06/11/2018);
  • See Resources on API for programmatic access (05/06/2018);
  • Fixed the issue with M. tuberculosis PPI network generation (05/03/2018);
  • Added support for P. aeruginosa (02/13/2018);
  • Minor bug fix for subnetwork rendering (02/07/2018);
  • Added support for M. tuberculosis (12/05/2017);
  • Added support for gene expression analysis for Japanese quail (11/09/2017);
  • Added support to reduce node overlaps in network layout (09/15/2017);
  • Updated the method for computing minimum network - which can obtain similar minimum network from large-scale network in a short time (07/10/2017);
  • Enhanced heatmap resolutions and network node highlighting (06/01/2017);
  • Fixed name mapping issue with A. thaliana (02/27/2017);
  • Fixed node name display issue for fruitfly and C. elegans (02/06/2017);
  • Fixed ID mapping issue with STRING database (01/23/2017);
  • Fixed the issue with SIF file generation (01/16/2017);
  • Fixed issue with PPI mapping for fruitfly (01/10/2017);
  • Added support for Venn diagram visual analytics (12/9/2016);
  • Added support for gene-TF interactions based on ENCODE, JASPAR and ChEA (12/9/2016);
  • Added support for gene-chemical interactions (12/8/2016);
  • Added support for data filtering step in differential expression analysis (12/6/2016)
  • Added support for protein-drug interactions (12/5/2016)
  • Added VSN normalization support for microarray data (11/25/2016)
  • Both Network and Heatmap now support Retina display (11/20/2016)
  • Enhanced clustering analysis for heatmap visualization (11/18/2016);
  • Added support for miRNA-target gene interaction network. (11/15/2016);
  • Added support for t-SNE clustering 3D visualization. (11/10/2016);
  • Detailed DE result table is now available for single gene expression data. (11/05/2016);
  • Enhanced interface for differential expression analysis. (11/05/2016);
  • NetworkAnalyst now supports limma, edgeR and DEseq2 for RNAseq data analysis. (10/28/2016);
  • Added support for two community detection algorithms (Infomap & Label Propagation) (09/28/2016);
  • Added support for eight new species including three animals (zebrafish, cow & chicken), two bacteria (E. coli & B. subtilis), two parasites (T. brucei & P. falciparum) and one plant (A. thaliana) (09/22/2016);
  • Added support for PPI data from STRING (09/12/2016);
  • Added support for node edge coloring (08/16/2016);
  • Updated major data I/O functions for better performance (08/05/2016);
  • Minor bug fix and code refactoring for memory efficiency (07/20/2016);
  • Enhanced support for network color gradient to reflect expression level (07/18/2016);
  • Updated FAQs (#25) on how to generate a high-resolution network image (07/15/2016);
  • Updated SVG Export to fully capture the network view (07/12/2016);
  • Updated network view and layout features for better visualization (07/8/2016);
  • Updated the web framework for better performance (07/07/2016);
  • Added support for motif (transcriptional factor binding sites, miRNA target sites, etc) enrichment analysis for human and mouse (02/11/2016);
  • Added support for batch selection-and-dragging nodes using mouse (01/05/2016);
  • Enhanced network visualization for retina display (12/21/2015);
  • Enhanced features for heatmap analysis support (10/26/2015);
  • Added EdgeR support for analysis of single RNAseq count data (10/15/2015)
  • Added support for downloading coordinates file in 3D PCA visualization (09/15/2015)
  • Added support for batch effect adjustment (Combat) (07/28/2015)
  • Added support for interactive 3D PCA visualization (07/27/2015)
  • NetworkAnalyst now allows statisitcal gene expression analysis or meta-analysis for any organism (07/24/2015)
  • Added recovery messages to allow user to switch to a different server (07/24/2015)
  • Users can now download and then re-upload the merged data in meta-analysis module (07/23/2015)
  • Updated the normalization interface with more options (07/08/2015)
  • Added support for gene symbols in all modules (07/06/2015)
  • Minor bug fixes for heatmap rendering issue (06/25/2015)
  • Added support for two microarray platforms Affymetrix Mouse Gene 1.0 ST Array and Affymetrix GeneChip Mouse Genome 430 2.0 (06/21/2015)
  • We are testing our mirror site (mirror.NetworkAnalyst.ca) on Google Cloud. Traffics will be distributed between the two websites. Let us know if you experience any issue (06/11/2015)
  • Upgraded the network visualization framework for better performance (06/05/2015);
  • Fixed the chord diagram rendering bug (06/04/2015);
  • Nature Protocols on NetworkAnalyst is now released (05/07/2015);
  • Added more data normalization options and updated FAQs (05/06/2015);
  • Now supports drag-and-drop current highlighted nodes (03/16/2015);
  • Added gene search support for the meta-analysis result table (03/12/2015);
  • Added support for new human interactome data by Rolland T. et al (02/20/2015);
  • NetworkAnalyst now supports data from Yeast (S. cerevisiae) (02/18/2015);
  • Added KEGG pathway analysis support for C. elegans and Fruitfly (02/16/2015);
  • You can download network as SVG image (02/02/2015);
  • Users can now control the order in specific comparison (01/27/2015);
  • Added a toggle highlight function for chord diagram (01/09/2015);
  • Added support for batch selection in network view (12/08/2014);
  • Updated tutorials and FAQs (12/01/2014);
  • Added support for computing the difference and intersection in Chord diagram (11/25/2014);
  • Users can now drag a node and its dependant nodes simultaneously (11/18/2014);
  • Added support to Select all from Overview to Focus view in heatmap view (11/10/2014);
  • Added support to resume analysis from a saved session file; (11/05/2014)
  • Added support to save SVG image for chord diagram;(11/03/2014)
  • You can now manually drag-and-drop individual nodes in network view; (10/15/2014)
  • NetworkAnalyst now supports data from D. melanogaster (fruit fly); (10/3/2014)
  • Users can now compute intersections of any datasets in Chord diagram; (09/25/2014)
  • NetworkAnalyst now supports data from C. elegans; (09/15/2014)
  • Enhanced support for single gene network analysis; (09/10/2014)
  • Added interactive chord diagram support for comparison of multiple datasets; (09/02/2014)
  • Updated the Neo4j graph database; (08/28/2014)
  • Updated interface for network visualzation; (08/25/2014)
  • Added interactive heatmap support for visualizing expression profiles of single or multiple datasets; (08/20/2014)
  • Fixed a minor bug for network visualization; (08/15/2014)
  • Added statistical methods for meta-analysis; (08/10/2014)
  • Users can now use NetworkAnalyst from InnateDB; (07/20/2014)
  • Merged interface for processing single and multiple expression datasets; (06/30/2014)
  • Updated tutorials and FAQs; (06/15/2014)
  • Added support for multiple gene lists; (06/14/2014)
  • Improved interface for Network Builder and performance optimization; (06/12/2014)
  • Added support for white background and edge thickness adjustment (05/20/2014)
  • Updated interface for network builder (04/30/2014)
  • Added Trim function to compute minimum network connecting all seed proteins (04/15/2014)
  • Added support for official gene symbol lists (02/20/2014)
  • NetworkAnalyst official release (01/30/2014)
  • NetworkAnalyst website is ready for testing (12/10/2013)