Comparative Analysis of Functional Profiling Tools

Table 1 shows the comparisons between NetworkAnalyst 3.0 and several other well-known web-based tools dedicated to functional profiling of transcriptomics data, including WebGestalt (29 (link)), g:Profiler (30 (link)) and Enrichr (31 (link)). The WebGestalt web application, first released in 2005, provides comprehensive enrichment analysis for 12 selected organisms and also supports user-supplied functional enrichment categories. The g:Profiler tool suite, first released in 2007, provides the broadest species coverage by supporting >200 species and corresponding gene ID conversions. Additional features include mapping human single nucleotide polymorphism (SNP) to gene name as well as ortholog search. The Enrichr web server, first released in 2013, provides the broadest functional coverage by supporting enrichment analysis against >100 gene set libraries. A key contribution of Enrichr is its curation effort, and allowing users to download their curated gene sets. Another unique feature of Enrichr is its support for BED file as input for enrichment analysis. These three tools are powerful web-based platforms that offer rich annotations for a given gene list. In contrast, NetworkAnalyst distinguishes itself from other web-based tool by providing cutting-edge network visualization, versatile visual analytics, comprehensive support for gene expression profiling, meta-analysis and multi-list comparisons. NetworkAnalyst 3.0 offers an end-to-end solution for RNAseq analysis - from raw reads mapping to differential expression analysis and identification of important pathways and functions.