Table of contents
This page contains answers to several frequently asked questions regarding usage of The Proteome Browser. The user guide includes detailed information about the system, including descriptions of the display, functionality, parsing rules, etc.
How do I view a chromosome report?
From the home page, select the chromosome of interest in the drop down list and select Explore. The maximal list of data sources and the most recent version is selected to be the default. On the traffic light report additional filters may be applied by selecting the “more options” link near the Explore button. These filters include: specific chromosome regions, specific genes or genes with specific levels of evidence.
How do I filter the chromosome report:
For missing proteins?
View the traffic light report for a chromosome and view the advanced filter options by selecting “more options” near the Explore button. Select the PE (Protein Expression) data type from the TPB data type drop down, select the black and red data level check boxes and select Explore. Note that while red traffic lights show the presence of some data, it is far from definitive and therefore should be considered in the missing proteins.
For specific levels of evidence?
Similar to searching for missing proteins, any combination of data type and colour level may be used as criteria to filter the traffic light report. Under “more options” on the traffic light report, numerous TPB data types and any combination of colour levels for each data type may be used as the filter criteria. Note that the criteria are analysed as an OR within a data type and as an AND between data types, for example, if the colours green and yellow are selected for PE MS and the colour black is selected for PE ANTI, then the criteria will filter genes that have either green OR yellow Mass Spectrometry evidence AND black Antibody evidence. If all or no colour levels are selected for a data type, that filter criteria is ignored. Data types may be removed from the filter criteria by selecting the small red x to the right of the colour criteria.
For a list of specific genes?
A list of gene symbols or accessions may be typed or pasted into the Gene List box, by ensuring the drop box is appropriately selected. Note that currently the system does not look for gene synonyms; therefore the symbols used must correspond to the displayed gene name. Also, currently the system only recognises Ensembl gene accessions (i.e. starting with ENSG). If a single entry is provided in the Gene List it is treated as a (pre and post) wild card. For example, filtering for a gene symbol of “TMEM” will return all genes with TMEM in the name. This can be useful to find members of gene families.
For a chromosome region?
By inserting start and end base pair indexes into the relevant boxes, specific regions of the chromosome can be filtered. These indexes are inclusive; meaning an index of 750000 will pick up a gene that spans the 750000th base pair. Leaving the start or end index as 0 will filter from the start or end of the chromosome respectively.
How can I get a summary of all the traffic light evidence?
On the right hand side, directly below the traffic light report is a link to "view summary report". Selecting this will open the summary report pane, that displays a table summarizing the number of genes with each level of evidence for each data type. A pie chart is provided to visually represent the proportion of genes with each evidence level for the highlighted data type. Selecting any row in the table will update the pie chart to the selected data type.
What data sources are used to generate the report and how often are they updated?
A full list of current data sources is available on the Data Sources tab. Currently, data from neXtProt, GPM, Human Protein Atlas and the Gene Expression Barcode are used to compile the evidence. Each source is updated as soon as a new version is detected by the system and the most recent version and import date for each data source is viewable on the Data Sources tab. Additionally the different versions from each database can be viewed on the traffic light report page by selecting a single data source of interest and viewing the versions available in the drop box. Note that for combinations of data sources, a version of the traffic light is created each time one or more of the data sources is updated, thus if multiple data sources are selected, there will be versions corresponding to the versions of each selected data source.
What do each of the data types and colours refer to in the traffic light report?
A pop-up with a description of the data type and a brief definition of the colour coding is available by selecting the data type name on the traffic light report. For detailed information of the parsing rules from the data sources to TPB data types, please refer to the data types and mapping information on the Documentation tab.
How are the colour levels determined for parent data types?
Currently all data types inherit the highest level evidence from child data types. For example if a gene has red Mass spectrometry evidence (PE MS) and green Antibody evidence (PE ANTI), the Protein Expression traffic light (PE) will be green.
Why are some tracks not visible when I expand the traffic light display?
Due to the size of the database and the large number of genes in some queries, the tracks may take some time to load. A progress wheel shows when data is still being loaded. If some tracks do not appear, please wait and they will render. If they don’t appear after a reasonable time (up to a minute), try collapsing and reopening any sub tracks. Do not refresh the screen, except as a last resort, as this will restart the loading.
Why some genes are named “Unknown”?

Some evidence from the data sources do not cross reference a known gene or don’t include a gene name. At this stage full sequence comparison is not performed to identify identical gene sequences and therefore these data are assigned to an unknown gene and placed at the end of the chromosome if the chromosome is known but no gene location is available. Genes that aren't assigned to a chromosome are placed in a "chromosome Other" until an assignment can be made.

These data are often compiled into known genes (with correct locations) with updates of the underlying data sources. We will endeavour to assign a sensible gene name to these entries in the near future, probably based on an accession or name from the data source that generated the data in TPB.

Can I download the traffic light data?

Yes. The data representing the traffic light can be downloaded from the "export traffic lights" link below the traffic light. This will provide a csv file that contains all genes visible in the traffic light with Ensembl gene accessions and the colour level for each data type. Additionally, the file contains a header section describing any filters applied and the version of the traffic light.

To view this file in Excel, open the document, select column A and select "Text to Columns..." from the data menu. Select "Delimited" on the first page of the wizard. Select "Tab" and ensure that double quotes are used as the text qualifier on the second page. On the final page, select "Text" as the format for column A to ensure gene names are not converted to dates.

The data may also be viewed as the traffic lights by selecting all the data cells (those with values 1-4) and using conditional formatting from the format menu. If there is at least one 1 and one 4 in the data matrix, Excel's in-built "4 Traffic Lights" icon set will correctly apply icons to each cell.

Note that the layout is transposed compared to the original traffic light. This can be altered in Excel by selecting all the data (including gene names and accessions and the column titles), copying it and using "Paste Special" with "Transpose" selected.

If you have a question, please click Contact Us.

If you make use of TPB in your research, please cite: Goode, et al. "The proteome browser web portal", Journal of Proteome Research 2013, 12(1):172-8. (PMID:23215242)
This site is provided 'as is' by Monash University for use by researchers. This site is for research purposes only. Services are provided to 3rd parties on an 'all care no responsibility' basis. Use of this site indicates your acceptance of the Terms Of Use.
This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.