HELP
The LNCmap aims to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics, by attempting to describe all biological states in terms of lncRNA signatures. We provided four datasets (drugs, instances, 1.5 and 2, see HOME page) for users to compare with.
Therefore, we firstly obtained the lncRNA signatures of drugs or instances. To do this, we re-annotated the microarray data in the CMap database to interrogate lncRNA expression after drug treatment. In the CMap database, Every drug (bioactive small molecule) has several perturbation experiments (instances) under different conditions. We used fold-change analysis to identify differentially expressed lncRNAs for every instance with foldchange > 1.5 or 2 from the corresponding treatment and control re-annotated expression profiles. These lncRNAs were considered as signatures of the corresponding instance.
Furthermore, the differentially expressed lncRNAs were merged if the corresponding experiments belonged to the same drug and these lncRNAs were considered to be signatures for this drug.
By this way, we generated a total of four datasets of lncRNA signatures (drugs and instances with two cutoff (foldchange > 1.5 or 2)).
ANALYSIS HELP
In the analysis part, users could reveal the novel connections between drugs, lncRNAs, or diseases by inputting a lncRNA expression profile or a list of lncRNAs, then comparing them with the lncRNA signatures of drugs or instances.
LSEA
Step1. Upload files
As shown in Figure 1, users need to upload lncRNA profile file and
profile label file. The profile should contain two kinds of samples -
"case" and "control" and the label file should describe the kind of
samples. Users could see details of profile file and label file in
corresponding "Example" files. The suffixes of profile file and label
file should be ". gct" and ".cls", respectively.
Figure 1. Upload files
Step2. Setting Parameters
After uploading the lncRNA profiles, users need to setting parameter. As
shown in Figure 2, users could select comparing the uploading file with
drugs or instances. The "Expression parameter" means that the lncRNA signatures
were calculated in 1.5 or 2 fold change value. Furthermore, authors could
select random times and P-value.
Figure 2. Setting Parameters
Step3. Result display
After step 1 and 2, users could click the "submit" to submit the uploading
files and the results are displayed as a table (Figure 3).
Figure 3. LSEA Results
Details of drug information could be got by clicking the link of the drug name (ellipse 1). Users could click the signature number (ellipse 2) to see the overlapped lncRNAs between the lncRNAs in the profile and the signatures of the corresponding drugs (Figure 4). Users could also click the hyperlink of "view" (ellipse 3) to see the overview of compare results (Figure 5).
Figure 4. Overlapped LncRNAs
Figure 5. Overview of Results
2. ORA
Step1. Upload files
As shown in Figure 6, users need to upload a list of lncRNAs (differentially
expressed lncRNAs related to a special disease are suggested). Users could
see format of lncRNA list by clicking "LncRNAs Example" button.
Figure 6. Upload files
Step2. Setting Parameters
After input the lncRNA list, users need to setting parameter. As
shown in Figure 7, users could select comparing the lncRNA list with
drugs or instances. The "Expression parameter" means that the lncRNA signatures
were calculated in 1.5 or 2 fold change value. Furthermore, authors could
select P-value.
Figure 7. Setting Parameters
Step3. Result display
After step 1 and 2, users could click the "submit" to submit the input lncRNA list
and the results are displayed as a table (Figure 8).
Figure 8. ORA Results
Details of drug information could be got by clicking the link of the drug name (ellipse 1). Users could also click the signature (ellipse 2) to see the details of lncRNAs.
BROWSE HELP
Users could browse all the connections between lncRNAs and drugs. This page also contained the information of drugs and lncRNAs. Users could click the link in the red rectangle to see the details of drugs or lncRNAs (Figure 9). Users could download the drug-lncRNA connections in the HOME page.
Figure 9. Browse Page
SEARCH HELP
The search page allows users to input a lncRNA name or drug name to query the association between them.
Figure 10. Search Page