Example 1: Changing ids

A common problem when integrating data from different biological sources (analysis, databases, etc) is finding the correspondences between genes and proteins identifiers. CellMaps takes advantage of CellBase database to address this frequent problem. CellBase supports 16 types of IDs from the most commonly used sources.

Here we will describe how to change IDs by using as example a network with UniProtKB/Swiss-Prot Accession IDs. This example can be found as the third example in the Example section at the menu bar.

Step 1: Upload your network

Go to File > Import > Network from sift and load the network example

Step 2: Open the node attribute editor

Once the network is loaded, you will see that nodes are Uniprot IDs. If you open Attributes > Edit node attributes you will see that there is only one attribute called Name that contains Uniprot IDs.

Step 3: Import gene symbols

Tom retrieve Gene Symbols (that is HGNC Symbols), go to Attributes > Import attributes from CellBase. First choose the specie you are working with (Human in this example), then select the attribute that contains the IDs you want to translate and select the ID you want to get from CellBase, which are HGNC Symbols in this case. Click GO to retrieve the data.

Step 4: Check that gene symbols are imported in the node attribute editor

Once the IDs are retrieved, they are loaded as a new attribute. If you go to Attributes > Edit node attributes you will see a new attribute called HGNC Symbol.

Step 5: Use gene symbols as node name

Now can use the data you have retrieve! For example, changing the node labels to visualize the Gene Symbols instead of the Uniprot IDs. Go to Node Visualization Settings and click at the Label attr button. A list with all the available attributes will be displayed. Just choose HGNC Symbol and they will appear as nodes names.