Gene Expression Graph
This tutorial explains how to use the gene expression graph, which is used in the gene expression comparison and on the gene page.
The use in the gene page (single-gene) is different from that in the expression comparison (multi-gene), so we will first explain the common features and later explain the specific features of both of the former pages.
What the graph shows
The expression graph displays the expression of one or multiple genes in different tissues as a heatmap. The displayed value is the expression score calculated by us. See the main Bgee publications for details.
- x axis: represents the respective gene(s).
- y axis: represents the anatomical entity (tissue, cell type).
- color: represents the expression score, as calculated by Bgee:
- Expression scores of expression calls is based on the rank of a gene in a condition according to its expression levels (non-parametric statistics), normalized using the minimum and maximum Rank of the species. Values of Expression scores are between 0 and 100. Low score means that the gene is lowly expressed in the condition compared to other genes. Scores are normalized and comparable across genes, conditions and species.
- Gray: Gene has been called as "not expressed" in the given condition.
- White: There is no data for that gene in that condition.
How to use the graph
Hover over heatmap cells to reveal a tooltip showing the corresponding value:
Click on heatmap cell to display detail view. From there you can access links to the ontology terms (anatomy, cell type) and source datasets:
Expand a condition term to reveal expression data for child terms:
Export options
- Download graph as SVG or PNG file
- Download underlying data in tabular format as TSV file
Note the download buttons below the graph:
Settings
There are several display and style settings that can be expanded by clicking on the "Settings" button below the graph:
- Graph width: Determines the total graph width.
- Graph height: Determines the total graph height.
- Show legend: Shows / hides the color legend.
- Y label width: Determines the width of the y labels.
- Color palette: Lets the user choose between different color palettes (derived from the 'viridis' R package)
- Adaptive color scale: When selected, the color scale is limited to the max expression value displayed in the graph, otherwise the scale is [0,100].
- Background color: Select a different background color (default is 'white').
Technical details
The displayed top-level anatomical entities contain a curated list of 20 UBERON terms:
- body wall
- central nervous system
- circulatory system
- connective tissue
- digestive system
- endocrine system
- exocrine system
- glandular system
- hemolymphoid system
- immune system
- integumental system
- ligament
- multicellular organism (While this term is technically a parent term of the other ones, some data sets are derived from whole body samples and are therefore annotated as 'multicellular organism'.)
- musculature
- peripheral nervous system
- renal system
- reproductive system
- respiratory system
- sensory system
- skeletal system
The root term of the top-level terms is anatomical entity.
Any data points that are not linked to any of the top-level terms are displayed as children of 'anatomical entity'.
Feedback
If you are missing anything in the graph, please let us know using the feedback form below the graph. We appreciate all kinds of feedback!