Here you can use the Gene search box to search whether a gene comprises part of a cell type
expression profile. You may search its gene ID via its gene symbol or name (e.g. APOA2). A
dropdown box will appear showing related gene symbols and species-specific results to choose from.
You can also specify which species (e.g. Mus musculus) you are interested in. Use the Species
drop down to specify your organism of interest. Once your selection is made, searching for a gene ID
will restrict suggestions to the specified species.
Once you have selected the gene symbol of interest click Search and this will load a new page of
all experiments where your selected gene is expressed.
Search results can be filtered using the selection criteria along the left hand side of the search results
page. Selecting a filter criteria will remove all non-applicable experiments from the search results. For
example: selectingSpecies: Homo sapiens will show only human experiments, similar to searching only
on the human specific gene symbol in the Home page Search bar. You can also select experiments where your
gene of interest is expressed only in a particular Organism partor Inferred cell type by
selecting these from the relevant drop-down menus.
Additionally, by clicking on the "Marker gene" filter you can return search results based on whether
your gene of interest comprises part of the specific expression profile for a cluster.
Featured and Latest Experiments
Here, you can toggle between featured experiments and the latest experiments added to the Single Cell
This is a list of the latest experiments added to the Single Cell Expression Atlas, their title and
upload date. You can click on the Results link or the experiment title to jump directly to the
results page for that dataset. The number of assays is related to the number of sequencing runs. This is
not equivalent to the number of cells as some cells do not pass sequencing file quality checks or you can
have multiple sequencing runs or libraries generated from the same cell (technical replicates).
In order to view the full list of experiments in the Single Cell Expression Atlas click on the Browse
Experiments tab along the top of the page.
This page shows you an updated list of all the experiments currently available in the Single Cell
The table allows you to quickly browse, filter and download experiment data.
Searchable headers: type in your species or a keyword of interest to filter the table results
Download experiments: click on the checkbox next to your datasets of interest and click on the
Download link on the table header to download a bundle (see tooltip) for those experiments
Each experiment in Single Cell Expression Atlas has its own experiment page, just click on the title
of any experiment to view it. At the top of the results page you will see the title of the experiment, the
type of experiment and species information.
Below the experiment information you will find a list of any associated publication(s).
The Experiment page is comprised of four sections:
Results: this is where you can visualise the t-SNE plots (clustering and gene expression) as well as
the marker gene heatmap of the data
Experiment Design: this is where you can find the simplified sample metadata for the experiment
Supplementary Information: here you can find the data analysis pipelines and corresponding
Downloads: links to the raw data files; analysis results and sample metadata files
Here you can view the results of the data analysis. This comprises of two visualisation methods: t-SNE
plots and the marker gene heatmap. The t-SNE plots display subpopulations within the data and on the left
and gene expression variation at single-cell resolution on the right. Each plot can be saved by clicking on
the drop down menu symbol at the top right-hand side of the plot.
t-SNE plot with clusters
These are found in the t-SNE plots tab under Results.
t-SNE plots are a useful way of visualising highly complex
data in a 2D space. Although the size and distance between clusters is not very informative, manipulating
the t-SNE perplexity value allows you to re-display the data in different ways.
The number of clusters (k value) shows the output of the
Scanpy clusters cells into subgroups using the Louvain algorithm.
This also colours the data to allow easier visualisation of different sub-populations within a dataset.
It is also possible to colour the clusters by metadata! The colour legend for each
group of cells is displayed along the bottom of the t-SNE plot.
The metadata used to colour the clusters is derived from different experimental groups described by the
authors. This is displayed in the Experiment Design tab along the top of the results page.
You can hover over a single data point (cell) and a tool-tip will pop up. This displays the single cell
identifier (a unique reference for that cell) and the cluster ID (which other cells share
similar gene expression profiles). Additional information can include cell type: submitted cell type
prior to sequencing analysis and/or the inferred cell type: cell type inferred by sequencing
analysis based on gene expression profile.
t-SNE plots are calculated at a range of perplexities by the analysis pipeline. The central value is
selected by default. Clustering is performed over range of values for resolution in Louvain clustering by
Scanpy (producing variable numbers of clusters), and by default the number of clusters corresponding to the
default resolution of 1 is selected.
t-SNE plot with gene expression
Use the Gene search box to search whether a gene comprises part of a cells' expression profile.
Expression levels are displayed as CPM (counts per million) and broken down into four different,
logarithmic colour ranges:
Grey spot: expression level is below cutoff (0.1 CPM) or undetected
Light blue spot: expression level is low (between 0.1 to 10 CPM)
Medium blue spot: expression level is medium (between 11 to 1000 CPM)
Dark blue spot: expression level is high (more than 1000 CPM)
Marker Gene heatmap
Genes which comprise part of the specific expression profile for a cell population (cluster) are defined as
marker genes. These are displayed - 5 per cluster in the Marker Genes tab under
Results. Along the top of the page, you can specify the number of clusters or to view only a subset
of clusters. As with the t-SNE plots, the heatmap can also be saved either an image or you can also
directly download the data as expression values for each gene per cluster.
Experiment Design tab
This tab displays the Experiment design file – a simplified table of the the sample metadata and
experimental variables. Sample characteristics are generally intrinsic metadata required to
understand each sample. Experimental variables are usually one or several sample characteristics
that describe the experiment groups defined by the study aim. You can browse by row (each row is a single
cell). You can also sort each column by clicking on the header row of your attribute of interest. Traverse
the data by indicating the number of rows to view at the bottom and by clicking on the Previous and
You can download the file either via the Download button or along with the other data and results
files by selecting the Downloads tab (see below).
Supplementary Information tab
Here you can see the Analysis Methods applied to the raw data to obtain the clustering and gene
The Downloads tab contains all the files that you can download: