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Introduction:
Long non-coding RNAs (LncRNAs) are involved in numerous biological roles including translation, splicing, nuclear organization and were found to be participated in many kinds of diseases. Moreover, growing evidence suggests that lncRNAs, similar to protein-coding genes, may be a new class of therapeutic target. They could represent signatures of various biological states, including disease, or induced with a variety of chemicals.
The LNCmap (LncRNA Connectivity Map) database, 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, each 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 kinds of lncRNA signatures (drugs and instances with two cutoff (foldchange > 1.5 or 2)).
Currently, users can
- reveal the novel connections between drugs, lncRNAs, or diseases by inputting a lncRNA expression profile or a list of lncRNAs (e.g. differentially expressed lncRNAs related to a special disease).
- search the lncRNA signatures of a specific small molecular drug or an instance.
- download all the correlations between drugs/instances and lncRNAs.
