LncSEA 2.0 is a powerful platform that provides a variety of types of lncRNA sets for users and perform annotation and enrichment analysis of lncRNA sets based on lncRNA lists submitted by users. We collected lncRNA sets from more than 30 associated lncRNA databases. We not only collected lncRNA sets based on downstream regulatory data sources but also calculated a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data associated with hundreds of human cell types. Importantly, LncSEA 2.0 provides annotation and enrichment analysis functions of lncRNA sets. In addition, LncSEA 2.0 can simultaneously perform enrichment analysis of lncRNA sets related to upstream regulators and downstream targets of lncRNA when selecting upstream and downstream reference categories. LncSEA 2.0 also provides a user-friendly interface to search, browse and visualize detailed information about these lncRNA sets.
The construction of LncSEA 2.0 uses the most advanced process tool Snakemake, which is very convenient for maintenance and update. We also provide the Snakemake file of database construction for reference. Jump to.
Gene Set Enrichment Analysis
I. Input: Allow the user to input an interesting lncRNA name list or a text file.II. Options: Select class and subclass of reference sets and optional parameters for analysis.
III. Analysis: Annotate the input into the reference collections selected by the user, and calculate the significance of enrichment analysis by hypergeometric test according to the number of lncRNA intersecting.
IV. Output: LncSEA 2.0 will return all significant collections of information related to the input to provide users with download and visualization.
GSEA
I. Input: Users are required to input a list of lncRNA names along with corresponding significance statistics (such as Fold Change or -logp). Input in tab-separated format or file format is allowed.II. Options: Select class and subclass of reference sets and optional parameters for analysis.
III. Analysis & Output: LncSEA 2.0 will return all significant collections of information related to the input to provide users with download and visualization.
GSVA
I. Input: Users need to input a matrix where rows represent lncRNAs and columns represent samples, including both row and column names. Input in tab-separated format or file format is allowed.II. Options: Select class and subclass of reference sets and optional parameters for analysis.
III. Analysis & Output: LncSEA 2.0 will return rnrichment score matrix related to the input to provide users with download and visualization.
