Exploring annotated networks¶
Exploring annotated nodes and edges¶
Note
INPUT FILES USED IN THIS TUTORIAL
We will use the microbetag-annogated network of the network-based example-case;
you can get directly its corresponding microbetag - annotated network from here.
Once an annotated network is returned (or loaded) on your Cytoscape main panel, you have all Cytoscape features (e.g., annotation, filtering, selecting etc.) plus those coming from the MGG App facilitating a user-friendly way to go through the annotations returned.
Important
Remember that to access the MGG panels, you need to click
Apps > MGG > Show Results panel > Show results panel
Remember that you can always use the Cytoscape core features on a microbetag-annotated network. That means for example, in case you would prefer a different style than the one provided, you can always change node and edges colors and shapes etc. You can do this always for groups of nodes/edges. Anything you could do with a network on Cytoscape is still an option for a microbetag-annotated network.
Visual style¶
Nodes¶
The color-coding of the nodes (taxa) indicate the taxonomic level to which each sequence was assigned by microbetag.
đźź© node was mapped to a genome (i.e. species/strain) and annotations are available for it
node was mapped to the genus level; annotations limited to literature-oriented (FAPROTAX)🟪 node was mapped to the family level; likewise, only FAPROTAX annotations occasionaly
🟥 node was mapped to higher taxonomic level and no annotations were returned
MGG uses the microbetag::ncbi-tax-level column of the microbetag-annotated network returned to apply its visual style
one the network’s edges.
This column indicates the lowest taxonomic level (e.g., species, genus, family, etc.) at which the taxonomy of the sequence
could be matched to the reference taxonomy scheme.
The assigned NCBI Taxonomy ID corresponds to this matched level.
Important
We introduce the term “mspecies” to refer to the taxonomic level at which a node is directly mapped to a genome.
In case you have metadata variables in you analysis, those would be shown as hexagons having a
microbetag::ncbi-tax-level column on the Nodes table as [metavar].
Edges¶
Color-coding of the edges (taxa relationships) indicate the edge type, where undirected edges represent the co-occurrence score of the network and its color whether the two taxa cooccur or exclude one another, while directed edges represent potential metabolic complementarities.
🟦 undirected co-occurrence edge with positive score \(\ge 0.1\)
🟥 undirected co-occurrence edge with negative score \(\ge 0.1\)
⬛ undirected co-occurrence edge with \(0.1\ge\) score \(\ge 0.1\)
→ directed complementarity edge; source being the potential donor and target the beneficiary
🟨 selected edge
If you edit the style of your microbetag-annotated network, you can always bring back its original style through the MGG main menu.
Investigating nodes’ annotations¶
Once your microbetag-annotated model is imported and the MGG results panel opened, you can now browse the network along with its annotations using both Cytoscape core features and those of MGG.
Notice that the MGG results panel on its bottom has two options: the Nodes and the Edges panels. By default, the Nodes panel is selected. Let’s start with that then!
By clicking on the Show Species button, all nodes that were not mapped to a genome will be masked,
i.e. only nodes with a microbetag::ncbi-tax-level equal to mspecies will be shown.
You can choose/click directly any node on the network and check the Nodes Panel
or several at the same time
For more about how the phenotrex-oriented traits are assigned in each node you may have a look
here and for a thorough list of all the traits supported,
you may check the corresponding table.
In addition, for the FAPROTAX-based annotations, you may have a look here for how it works, and you can go through the whole list of potential traits supported in this table.
Filter for traits¶
You may select among a list of annotations under the PhenDb/FAPROTAX filters with AND and OR relationships.
For example, I was curious about the Nitrite-oxidizing bacteria (NOB) on my network
Likewise, you may go through the annotations on the edges of the network.
Investigating edges’ annotations¶
Now, you can click on the Edges button on the bottom of the MGG panel to jump to the Edges annotations.
Potential seed complementarities¶
Like in the case of the pathway complementarities, a new panel is displayed when seed complements are available for an edge. Here is an example:
Seed scores between the two genomes are also shown here. Remember that like the edge under study, seed scores have also directionality;
Important
Seed score for competition between \(genome_A\) and \(genome_B\) is not necessarily the same with the one between \(genome_B\) and \(genome_A\). Those scores are only indicative, and they should not be considered as fact of observed cooperation/competition.
In cases where more than one GTDB genomes were mapped to a node, then microbetag ends up with several seed scores on an edge.
Thus, on the Edge panel we display their average and their corresponding standard deviation:
Seed complements are then shown on a collapsible table, where each row corresponds to the seeds related to a KEGG PATHWAY map. More specifically, each seed complement entry consists of:
The metabolism Category the pathway is part of
A KEGG PATHWAY and its corresponding map
The seed compounds related to KEGG modules involved in the PATHWAY in the ModelSEED namespace
Their corresponding terms in the KEGG COMPOUNDS namespace
A colored URL highlighting the (PATHWAY-related) compounds that the beneficiary species can produce on its own (blue) and the complements that could potentially get from the donor
Each KEGG PATHWAY map belongs to a metabolism category in KEGG’s hierarchy, with apparently, several maps to belong to the same category.
microbetag returns all seed compounds related to such a map that the beneficiary could potentially get from the donor.
For the on-the-fly version, since metabolic networks used in microbetag have been reconstructed with ModelSEEDpy, it’s the ModelSEED namespace in which the seeds complements are predicted, which are then mapped to their corresponding KEGG COMPOUND IDs.
Note
In case you are using microbetag locally, and you reconstruct networks using carveme or provide models in the BiGG namespace, current version of microbetag will still first map them to the ModelSEED namespace.
Important
The returned complements in the seed complementarity module of microbetag are KEGG COMPOUNDs,
each of which may participate in multiple metabolic pathways and thus, appear in more than one KEGG MAP.
As a result, a single seed complement may be listed in multiple rows within the collapsible table — one for each KEGG map it is involved in.
Potential pathway complementarities¶
By clicking on a potential metabolic interaction edge, the donor and the beneficiary species, along with their corresponding sequence identifiers will be displayed.
Then, for cases where pathway complementarities have been returned for this association, a panel will be available for each pair of genomes that were mapped to those two taxa. For each pair of genomes, a list with the potential metabolic complementarities is then returned. In the first column the KEGG MODULE ID of the corresponding complementarity is provided, and in the second and third column their description and metabolism category. In the fourth column, called “Complement” the KO that need to be provided to the beneficiary species to support the module are given and in the next column, the complete alternative that would then facilitate the module is shown; i.e., assuming the complement is provided.
In the final column a link to a related KEGG map is provided where KO available in the beneficiary species are colored with pink and those provided by the donor in the scenario of the potential metabolic interaction with green. The screenshot below illustrates the highlighted complementarity in the biosynthesis of methionine.
Save your work¶
The best approach is to save your entire session, as you will likely apply various filters, annotations, and other modifications to your microbetag-annotated network. Simply click on File > Save Session As..., assign a name to your session, and Cytoscape will generate a .cys file. This allows you to reload the session later and resume exactly where you left off.
You can also export your network by using the rest of Cytoscape options.