Welcome to LnCompare

With the rapid growth of high-throughput RNA-seq and other omics data, there is an increasing need for tools to analyse the features of large lncRNA sets, such as for example those differentially expressed between two conditions.

LnCompare is a web server for lncRNA feature analysis. It is based on the GENCODE v24 lncRNA annotation, comprising 15,941 loci, for which >20 useful features have been compiled. It comprises two functonal module.

1) Gene set feature comparison. It compares two sets of lncRNAs, and identifies significantly different features, both categorical and quantitative.

2) Similar gene discovery. It uses user-defined gene(s)-of-interest to query for the set of most similar lncRNAs, based on one or more features.

All analyses are performed at the levels of gene loci (not transcripts). The full feature datasets can also be downloaded in the "Download" page.

Comprehensive usage instructions can be found in the "Help" menu.

Jul 2018: the original LnCompare program is released.
Feb 2019: a stable similar gene discovery module has been established.

Dr. Rory Johnson, Department of Biomedical Research, University of Bern 3008 Bern, Switzerland.
Email: roryjohnson.dkf@gmail.com

Dr. Jianwei Li, school of artificial intelligence, Hebei University of Technology, Tianjin 300401, China
Email: lijianwei@hebut.edu.cn

Dr. Yuan Zhou, Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
Email: soontide6825@163.com

LnCompare works on GENCODE lncRNA gene loci (ENSGxxxxxxxxxxx), not lncRNA transcripts.

This website has been tested by using Chrome, Microsoft Edge and Firefox browsers. Microsoft IE may not work well.

Analysis Wizard

Step 1: Input your LncRNA list through left panel.

Step 2: Input your background LncRNA (format same as step 1).

Step 3: Submit the request by clicking Run button.

Download the entire feature table for LnCompare here: table_feature.

How to use and interpret the Gene Set Feature Comparison function?

How to use and interpret the Similar Gene Discovery function?

1. Input your lncRNA list through left panel.

Note that, since all features are determined for GENCODE annotated lncRNA genes, every lncRNA should be present in GENCODE and should be passed using the corresponding GENCODE identifier, which begins with “ENSG”. The user may also start two kinds of pre-defined lncRNA examples by clickcing the corresponding buttons: a simple lncRNA or Cancer LncRNA Census (CLC), a manually-curated compilation of LncRNAs with causative roles in cancer. https://www.biorxiv.org/content/early/2017/06/20/152769

2. Input your background lncRNA list, also using GENCODE IDs.

Note: If no background list is provided, then by default, LnCompare will use the entire GENCODE annotation set as the background.

3. Submit the request by clicking Run button.

How to interpret the results of Gene Set Feature Comparison

A brief summary of the user's input is provided (indicated by the green lines below).

In this tabular result page, users are provided with two kinds of analysis results: quantitative features and categorical features.

(---For quantitative features---)

1. Toggle the number of displayed results according to the indicated cut-offs: top 10, P-value<0.05, FDR<0.05, All.
2. Barplot depicting the ratio of the average feature values between the input and background lncRNA sets.
3. The feature table shows the mean and standard error (SEM) values for each feature. Click the ❓ icon to see more details about each feature.
4. Click "Plot" in the last column to generate a dedicated boxplot for this feature. Boxplots can be downloaded using the "Download Figure" button.



(---For categorical features---)

5. Toggle the number of displayed results according to the indicated cutoffs: top 10, P-value<0.05, FDR<0.05, All.
6. Bubble plot summarizing the analysis results of categorical features. The bubble position is determined by odds ratio, while the bubble size is proportional to –log10(P-value).
7. Click "Plot" to generate a dedicated barplot for this feature, showing ratio of the number of LncRNAs with the feature between the input LncRNAs versus the background LncRNAs. Barplots can be downloaded using the "Download Figure" button.

How to run Similar Gene Discovery

1. LnCompare can compare the similarity between LncRNAs by using cosine similarity and mutual rank similarity metrics. Here, two ways of comparison are provided: one is the 1-to-N comparison (input one lncRNA and compare it with other GENCODE lncRNAs); the other is M-to-N comparison (input two lists lncRNA and calculate the similarities between them). In addition, a test gene set can also be analysed by clicking the "example" button.
2. Select feature subsets. Users can select the set(s) of features used to calculate similarity
3. Submit the request by clicking the "Submit" button.

Note: If users choose the M-to-N comparison, the maximum size of each set is 100. Due to intensive computational requirements for the mutual rank similarity, when performing 1-to-N comparison, the pre-calculated mutual rank similarity will be retrieved only if all five feature subsets are enabled (default option).

How to interpret results of Similar Gene Discovery

1. Results for cosine similarity analysis. Toggle the number of displayed results according to the indicated cutoffs: top 10, top 20 and top 50.
2. Cosine similarity results are displayed as a table. The lncRNA pairs are sorted according to their cosine similarity, with HIGHER values indicating greater similarity.
3. The full cosine similarity table can be downloaded using the "Download" button below the table.
4. Results for mutual rank similarity analysis. Toggle the number of displayed results according to the indicated cutoffs: top 10, top 20 and top 50.
5. Mutual rank similarity results are displayed as a table. The lncRNA pairs are negatively sorted according to their mutual rank similarity, with LOWER values indicating greater similarity.
6. The full mutual rank similarity table can be downloaded using the "Download" button below the table.

Download

The entire feature table of LnCompare can be found on the download page, user can click 'table_feature' link to download it.