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. 2019 Apr 18;9(4):76. doi: 10.3390/metabo9040076

Table 2.

Summary of multi-omics integration software tools and web applications (adapted from Fondi and Liò [90] and Beale et al. [112]).

Software Tool Omics Integrated Domain Functionality Type of license Reference
3Omics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Medical (human)
  • -

    Correlation network analysis

  • -

    Co-expression analysis

  • -

    Phenotype generation

  • -

    KEGG/HumanCyc pathway enrichment

  • -

    GO enrichment

  • -

    Name to ID conversion

 Open [41]
BiofOmics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Biofilm
  • -

    Experiment library

  • -

    Data depository

 Open [113]
BioCyc/MetaCyc

  • Genomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Online encyclopedia of metabolism

  • -

    Predicted metabolic pathways in sequenced genomes

  • -

    Enzyme data set

  • -

    Metabolite database

 Open [111]
Cell Illustrator 5.0

  • Genomic

  • Transcriptomics

  • Proteomics

 Unspecified
  • -

    Draw biological pathway models and simulations

  • -

    Run biological cellular simulations and graphical display results

 Licensed [74]
CellML
(Open source XML language)

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Open source language for biological cellular models

 Open [73]
COBRA

  • Transcriptomics

  • Proteomics

  • Metabolomics

  • Fluxomics

 Unspecified
  • -

    Genome scale integrated modeling of cell metabolism and macro-molecular expression

 Open [12,79]
Cytoscape with MODAM, and;
Cytoscape with OmicsAnalyzer

  • Transcriptomics

  • Proteomics

  • Metabolomics

  • Fluxomics

 Unspecified
  • -

    Multi-Omic Data Miner and OmicsAnalyzer were designed as an accessible and handy Cytoscape plugin that facilitates omics analysis

  • -

    Compile all biologically-relevant information regarding the model system through web link associationMap the network components with multi-omics data

  • -

    Model omics data

 Open [114,115]
E-Cell

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified (Cells)
  • -

    Modeling, simulation, and analysis of complex, heterogeneous and multi-scale cellular systems

 Open [63]
Escher

  • Genomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Web application for visualizing data on biological pathways.

  • -

    Rapidly design new pathway maps based on user data and genome-scale models

  • -

    Visualize data related to genes or proteins on the associated reactions and pathways

  • -

    Identify trends in common genomic data types

 Open (MIT license) [116]
Gaggle Variety of omics platform bioinformatics solutions Unspecified
  • -

    Inoperability of the following tools:

  • -

    Bioinformatics resource manager

  • -

    Cytoscape

  • -

    DataMatrixViewer

  • -

    KEGG

  • -

    Genome Browser

  • -

    MeV

  • -

    PIPE

  • -

    BioTapestry

  • -

    N-Browse

 Open [117]
GIM3E
(Gene Inactivation Moderated by Metabolism, Metabolomics and Expression)

  • Transcriptomics

  • Metabolomics

 Unspecified
  • -

    Establishes metabolite use requirements with metabolomics data

  • -

    Model-paired transcriptomics data to find experimentally supported solutions

  • -

    Calculates the turnover (production/consumption) flux of metabolites

 Open; Phython based and requires COBRApy 0.2.x. [118]
INMEX
(Integrative meta-analysis of expression data)

  • Transcriptomics

  • Metabolomics

 Medical and Clinical
  • -

    Meta and integrative analysis of data

  • -

    Pathway analysis

 Open [119]
IMPaLA
(Integrated Molecular Pathway Level Analysis)

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Medical and clinical
  • -

    Enrichment analysis

  • -

    Pathway analysis

 Academic only [120]
Ingenuity Pathway Analysis

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Medical (human) and clinical.
  • -

    Metabolic pathway analysis

  • -

    Network visualization

  • -

    Data integration

  • -

    Upstream regulator analysis

  • -

    Mechanistic networks

  • -

    Causal network analysis

  • -

    Downstream effects analysis

 Commercial [121]
IOMA
(Integrative Omics-Metabolic Analysis)

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Integrates proteomics and metabolomics data to predict flux distributions

 Open [20]
KaPPA-View

  • Transcriptomics

  • Metabolomics

 Plants
  • -

    Integrates transcriptomics and metabolomics data to map pathways

 Open [122]
MADMAX
(Management and analysis database for multiple omics experiments)

  • Metagenomics

  • Transcriptomics

  • Metabolomics

 Plants, Medical and Clinical
  • -

    Integrates omics data

  • -

    Statistical analysis and pathway mapping

 Open [123]
MapMan

  • Metagenomics

  • Transcriptomics

  • Metabolomics

 Plants (developed for use with Arabidopsis. Includes more species)
  • -

    Compare data across these two species

  • -

    KEGG classification

  • -

    Classification into KOG clusters

  • -

    Mapping expression responses

 Open [124,125]
MarVis-Pathway
(Marker Visualization Pathway)

  • Metagenomics

  • Transcriptomics

  • Metabolomics

 Unspecified
  • -

    Toolbox for interactive ranking, filtering, combination, clustering, visualization, and functional analysis of data sets containing intensity-based profile vectors

 Academic only [126]
MassTrix

  • Transcriptomics

  • Metabolomics

 Unspecified
  • -

    Integration of data

  • -

    Generation of colored pathway maps KEGG data analysis

 Open [127]
MetaboAnalyst

  • Genomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Plants, Microbial, Microbiome, Medical and Clinical
  • -

    Data processing and statistical analysis

  • -

    Pathway analysis

  • -

    Multi-omics integration

 Open [53]
MetaboLights

  • Metabolomics

 Unspecified
  • -

    Database for storing metabolomics experiments and derived information

  • -

    Database for cross-species and cross omics technique

 Open [106]
MetScape 2

  • Transcriptomics

  • Metabolomics

 Medical and Clinical
  • -

    Integrates data from KEGG and EHMN databases

 Open [128]
mixOmics
(R package)

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Integration of data

  • -

    Chemometric analysis (similarity/difference)

 Open [129]
OmicsPLS

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Integration of data

  • -

    Chemometric analysis (similarity/difference)

  • -

    R-package with an open-source implementation of two-way orthogonal PLS

 Open [130]
Omickriging
(R package)

  • Transcriptomics

  • Proteomics

  • Metabolomics

  • Fluxomics

 Unspecified
  • -

    Integration and visualization of omics data

 Open [131]
Omix visualization tool

  • Transcriptomics

  • Proteomics

  • Metabolomics

  • Fluxomics

 Unspecified
  • -

    Integration and visualization of omics data

 Annual license fee [132]
PaintOmics

  • Transcriptomics

  • Metabolomics

 100 top species of different biological kingdoms
  • -

    Integration and visualization of transcriptomics and metabolomics data

 Open [133]
PathVisio 3

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Integration of omics data

  • -

    Visualize omics data based on common data nodes and interactions in the pathway

 Open (Apache) [134]
ProMeTra

  • Transcriptomics

  • Metabolomics

 Medical and Clinical
  • -

    Interactive visualizations of metabolite concentrations together with transcript measurements mapped on the pathways and GenomeMaps

 Open [135]
Reactome

  • Genomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Multi-omics data visualization

  • -

    Metabolic map of known biological processes and pathways

 Open [110]
Recon3D

  • Genomics

  • Proteomics

  • Metabolomics

 Human
  • -

    Computation resource and comprehensive human metabolic network model

 Open [80]
SimCell

  • Genomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Graphical modeling tool

 Open [56]
SIMCA

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Integration of data

  • -

    Chemometric analysis (similarity/difference)

 Commercial [136]
VANTED
(Visualization and Analysis of Networks with related Experimental Data)

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Unspecified
  • -

    Comparison of multiple omics data sets

  • -

    Visualization of metabolic maps

  • -

    Correlation networks analysis

 Open [137]
VitisNet

  • Metagenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

 Grapes
  • -

    Integration of data

  • -

    Visualization of connectivity

 Open [138]
xCellerator

  • Proteins

  • Metabolomics

 Unspecified
  • -

    Mathematica package designed to aid biological modeling

 Open [55]