Mercator - a plant protein annotation tool
Mercator4 is an online tool to assign functional annotations to land plant protein sequences. All Mercator4 protein functional annotations (for example Photosynthesis.photorespiration.phosphoglycolate phosphatase) can be split into a toplevel context (Photosynthesis) one or more biological subcontexts (photorespiration) and a description of the protein family (phosphoglycolate phosphatase). The Mercator4 annotation is based on a framework that arranges plant protein categories (called BINs) embedded in a hierarchical structure of context descriptions. Learn more about the framework (Bolger et al. 2021, Schwacke et al. 2019). The latest version of Mercator4 is release 4 (2021) with 5250 individual protein family categories.
Mercator v.3.6 is an older version of Mercator based on an older version of the Mapman framework (Lohse et al. 2014, Thimm et al. 2004). The Mercator v.3.6 online tool is still available but active maintenance has ended.
Mercator4 job submission
From the Mercator4 website, enter your plant protein sequences in a valid FASTA format. It is also possible to submit nucleotide sequences (specify sequence type 'DNA') which will be internally translated into protein sequences. The validity of the FASTA format can be verified using the online Mercator FASTA validator. After submitting the sequences, the Mercator4 website keeps you informed about the status of your job. In general, the functional annotation of a couple of thousands of plant protein sequences takes only a few minutes.
Mercator4 annotation results
When a Mercator4 job finishes, a bar chart summarising the protein assignments across the 30 currently available top level context descriptions is diplayed. Each bar represents a top level context description and the percentage of its protein categories occupied by at least one protein from the submitted protein sequences. The annotations can be downloaded for further processing on your local computer. Click on 'Mercator4 annotated fasta file' to download a FASTA-formated file that contains the Mercator4 annotation added to the FASTA-formatted sequence which was submitted. The link 'Mercator4 annotation results' provides the functional annotation in a specific tabular format that is required for the Mapman desktop application (see below).
Mercator4 annotation result TreeViewer
The TreeViewer shows the protein categorization visualized as hierarchical tree with annotation context descriptions as branch nodes and protein categories as leaf nodes. Click 'Result Tree Viewer' and select a ‘user job’ to display the results in the tree structure and - optionally - add pre-evaluated protein annotations from one or more of the listed reference plant species. Expanding the tree diagram at a location of interest displays the protein count per species per category. A mouse-over on a count tab pops up the individual names of the categorized proteins.Mercator4 annotation result HeatmapViewer
The HeatmapViewer displays the comparison of two protein sets with protein categories as spots colored according to the comparison outcome. Click on 'Result Heatmap Viewer' and select a comparison ‘proteome A’ data set (user jobs will be displayed at the bottom of the drop down list). Select a ‘proteome B’ from the second drop down list and click on the button to compare the two protein sets. The color of a spot indicates whether the protein category is available in one or both protein sets and whether one of the protein sets has more or less proteins assigned to that protein category. A mouse-over on a spot pops up the description of the protein category and its context. The Heatmap Viewer creates an SVG diagram for each toplevel context that conveniently can be downloaded (with an SVG exporter add-on installed, for example SVG Export).Mapman desktop application
The Mapman desktop application (Thimm et al. 2004) displays the Mercator annotation results combined with gene expression data onto diagrams of metabolic pathways or other processes. This requires an installation of the Mapman desktop application (available for MS Windows, MacOS and Linux) on your local computer.
The installed Mapman desktop application needs:
- Mercator4 or Mercator v.3.6 annotation results
Download the Mercator4 annotation results (see above and example below) or a result file from Mercator v.3.6 of your sequences. - gene expression data (gene expression count table)
Provide a gene expression count table (see example below) of your sequences (generated by RobiNA or any other tool, further details on the format are available in the Mapman desktop application user guide) - a pathway diagram
Provide a pathway diagram (see next section).
Example table from a Mercator4 annotation result file
It is important that protein/gene identifiers are identical (case sensitive) in both the Mercator annotation file and the gene expression file (green columns in example tables).
Example for a gene expression count table
Diagrams for the Mapman desktop application
The Mapman desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (.svg) and an extra protein/gene mapping file (.xml). There are different diagram sets for Mercator4 annotations and for Mercator v.3.6 annotations available.
Diagrams of a certain Mercator4 release version can only be used with Mercator4 annotation results of the same release (for example X4.4 diagrams with Mercator4 release 4 annotation results). Also, diagrams designed for annotation results from Mercator4 are not compatible to results from Mercator v.3.6 and vice versa.
Basic diagrams for annotations from Mercator4 v.4
Download a diagram from the lists below and unzip it (the .zip file contains both the pathway image file and the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.
Custom-made diagrams for annotations
User can create an individual pathway diagram to display their own data. Use your favorite image software to create the background image file. Choose a version of Mercator annotations and generate the extra protein mapping file within the Mapman desktop application by using annotation result files from the chosen Mercator version. Some custom-made diagrams are publicly available.
Diagrams for annotations from Mercator v.3.6
Look up available diagrams at the Mapman Download Site and download the pathway image files and protein mapping files.
Overview
The Mercator/Mapman project (white background, no longer actively maintained) includes the Mercator v.3.6 online annotation tool, the Mapman v.3 framework, v.3 diagrams and the Mapman desktop application. It is described in Thimm et al. (2004) and Lohse et al. (2014).
The current Mercator4/Mapman4 project includes the Mercator4 online annotation tool (including TreeViewer and HeatmapViewer), the Mapman4 framework and X4.. diagrams adopted to the Mapman desktop application. It is described in Schwacke et al. (2019) and Bolger et al. (2021).
References
Bolger et al. (2021), MapMan Visualization of RNA-Seq Data Using Mercator4 Functional Annotations.
Methods Mol Biol. 2021; 2354: 195-212.
Schwacke et al. (2019), MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.
Mol Plant. 2019 Jun 3; 12(6): 879-892.
Lohse et al. (2014), Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.
Plant Cell Environ. 2014 May; 37(5): 1250-1258.
Thimm et al. (2004), MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Plant J. 2004 Mar; 37(6): 914-939.
