Shulou(Shulou.com)06/01 Report--

Xiaobian to share with you what is the use of LncBook database, I hope you have something to gain after reading this article, let's discuss it together!

With the development of lncRNA research, the number of lncRNAs is increasing, but only a small part of them have functional annotations. In order to better carry out functional research on lncRNA, scientists collected data related to human lncRNA in the literature, including expression quantity, related diseases, methylation sites, SNP sites, functional descriptions, etc., and organized them into a database LncBook.

http://bigd.big.ac.cn/lncbook/index

The database contains information about eight lncRNAs

1. LncRNAs

A total of 277044 lncRNAs were collected from Gencode, RefSeq, Noncode, Lncipedia, MiTranscriptome, etc. The intersection of CPAT, PLEK, LGC was used to predict lncRNAs.

This section provides basic information such as lncRNA ID, chromosome position, length, exon number, type, etc., as follows

2. Featured LncRNAs

This section contains only lncRNAs with functional comments and literature support from the lncRNAWiki database. The results are as follows

3. Function

This section gives the biological function annotations and biological processes involved in lncRNA, including the following five categories of functions

transcriptional regulation

ceRNA

splicing regulation

protein localization

RNAi

are indicated as follows

4. Diseases

This section gives lncRNA-related disease information, including experimental verification and prediction. The experimental verification data are directly obtained from lncRNADisease and lncRNAwiki databases. The prediction is mainly combined with other omics data, including the following three strategies.

An lncRNA is considered to be associated with a disease if a hypermethylated region is present in the promoter region of the lncRNA in the tumor sample compared to the normal sample;

If an lncRNA region exists at a disease-associated SNP site, the lncRNA is associated with the disease;

An lncRNA is associated with a disease if it interacts with more than 5 disease-associated miRNAs (miRNA-associated disease information from the HMDD database);

the results are indicated as follows

5. Expression

By analyzing transcriptome data of two public programs, HPA and GTEx, FPKM expression values of lncRNA in various tissues are given as follows

By analyzing the expression in different tissues, it can be used to determine whether tissue-specific lncRNA or housekeeping lncRNA is calculated as follows

N represents the number of tissues and x represents the normalized expression in each tissue, where normalization is the expression in each tissue divided by the maximum expression in all tissues.

6. Methylation

By analyzing data from TCGA and ENCODE databases, methylation information associated with lncRNA is given as follows

7. Variation

SNP loci in dbSNP database are mapped to lncRNA, and annotation information from COSMIC and ClinVar database and frequency information in 1000G are provided. The results are shown as follows

8. lncRNA Interactions with miRNAs

tagetScan and miRanda were used to predict the interaction between lncRNA and miRNA, and the intersection was taken as the final result. The experimental evidence mainly came from starbase database. The results are shown as follows

In addition, four tools are provided.

Blast

LGC

Classification

Conversion

Blast is used to align the input sequence with lncRNA sequences in the database, LGC is used to analyze the protein coding potential of the sequence and predict lncRNA, Classification is used to classify genes according to chromosome position, Conversion is used to provide ID conversion in multiple lncRNA databases, and the results are shown as follows

lncBook and lncRNAwiki are the same development team, lncBook can be regarded as an upgraded version of lncRNAwiki.

After reading this article, I believe you have a certain understanding of "what is the use of LncBook database". If you want to know more about relevant knowledge, please pay attention to the industry information channel. Thank you for reading!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.