Document

1. Overview

Welcome to LncMod! Here is a step to step introduction about how to use the web to search the transcription factors (TF) and gene regulations that are mediated by lncRNAs in cancer. The users can search the lncRNA-TF-gene triplets identified in glioma in this web. In addtion, the program code can be downloaded for users to analyze their own datasets.

2. Search

The LncMod provides an interface to retrieve the information about the lncRNA-TF-gene triplets in cancer. The current release of LncMod mainly contains the results in glioma. Users can search by individual lncRNA or by individual TF or by individual genes to view the lncRNA-TF-gene associations.

3. Results

Users can input a lncRNA of interest (e.g. HOTAIR) or choose one TF (e.g. E2F1) or one gene (e.g. APC) to view the lncRNA-TF-gene associations in glioma. The official lncRNA gene name or ensemble ID is expected as the keyword. In addition, the users can search by TF/gene name or Entrez gene IDs. The search result list includes the lncRNAs IDs, lncRNA symbols, the TF IDs, TF symbols, gene IDs, gene symbols, the correlation of TF-gene in lncRNA low expression groups, the correlation of TF-gene in lncRNA high expression groups, the lncRNA action mode of each triplet.

4. Download

The LncMod is implemented as a freely available R-based tool: LncMod.

The available resource of LncMod can be downloaded as follows:

The available resource of R can be downloaded as follows:

To run the example you can use R code as follows: Rcode.R