You can combine the following four criteria to perform advanced search.
- Cancer Type
26 cancer types are available for search. Multiple choice is supported.
- Clinical Feature
74 clinical features are available for search. Multiple choice is supported.
- Data Type
3 data types are available including mRNA, CNV and miRNA. Mono-choice only.
- Gene Set
Gene/miRNA or gene/miRNA list separated by comma is allowable. Or you can input one gene per
Results that match all of the set conditions will be shown by default.
The column order of the Result Table could be adjusted customized by clicking the ‘config’ button
above the Result Table (right).
Change the order of a specific column by clicking the arrow besides the column title.
You can also filter the cancer types by clicking the 'filter' button, as shown below.
Download the entire table by clicking the 'download' button. The file format is csv.
For convenience, the relationship between the genes/miRNAs and clinical features can be visualized
in two ways including network and heatmap. By clicking the 'network' or 'heatmap' button, a network
or heatmap will be displayed below. Please note, only one cancer type is supported for
visualization. If there are multiple cancer types, you should choose one cancer type for
visualization first and display them one by one!
The network and heatmap are both interactive, for more features please refer to the analysis
As shown above, by clicking the 'network' button above the result table, a network representation of
the genes/miRNAs and clinical features is provided. Please note that it may take minutes
to load the network if the result table contains too many genes. In the Gene-clinico network, the
clinical features are group individually. The edges are differentially
colored according the p value. Edges with p<0 are colored blue, and p>0 are colored red. Edges with
p value have darker color.
Below is an example figure for cancer Adrenocortical carcinoma (ACC).
The left top window is a result display, showing all the pathogen(s) that share(s) the designated
gene(s) as EHF(s) and corresponding numbers.
The following operations are supported in the network window:
- Click a node to select a node and its connections.
When clicking a node, the node and its neighbourhood (edges and nodes connected to the node) are
highlighted. Moreover, a tip which shows the detailed
p value information will be displayed.
- Click an edge to select an edge.
When clicking an edge, the p value information will be displayed in a
- Drag nodes around.
You can drag a single node to the place
you want in the window for better view.
- Zoom and pan the figure.
You can zoom and pan the figure with mouse wheel, or with the buttons on the left top of the
- Search the network.
You can search gene symbol in the network. When an exact match is found,
corresponding node and its neighborhood will be highlighted.
- Save the network as an image.
You can save graph in current viewport or entire graph as an png image.
Please note that single node may not be placed in the visible scope of the network window. You can
zoom in to see all nodes.
You can also change the parameters by clicking the 'Show Parameter
' button at ease.
Gene-clinico Heatmap Analysis displays the genes/miRNAs and clinical features in a heatmap
Below is an example of heatmap representation with the same parameter as show in network visualization. In the heatmap, squares
differentially colored according to the p value (same color scheme as in Gene-clinico Network
the p value is placed in the center of each
square, with the detailed information displayed in the left bottom panel.
By default, the result is generated and ordered by gene and clinical feature name. You can
also change the dominant display order. Now, 4CR supports two orders:
- Gene/miRNA name
- Significant Clinical Feature Number
e.g., abs(p) < 0.05.
What's more, you can search specific gene/miRNA. Results which show the p values of the gene/miRNA and
clinical features are shown below.