The functional lncRNA database verified by low-throughput experiments

The functional lncRNA database verified by low-throughput experiments. 

Speaking of lncRNA, everyone is familiar with it. As a key role in different biological processes, it plays an important function and is related to many human diseases, such as cancer, cardiovascular disease and neurodegenerative diseases.

However, not all expressed lncRNAs are functional. So today we will introduce to you a database of manually selected lncRNAs: EVLncRNAs 2.0 (https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/).

This database is the only comprehensive database of functional lncRNAs verified by low-throughput experiments (such as qRT-PCR, knockdown, Northern blotting and luciferase reporter gene detection), which contains the integration of experimentally verified lncRNAs from all species Sequence, structure, function and phenotypic information.

According to the main page, we can find that the database contains 8 parts: “Species”, “Disease”, “Interaction”, “Structure”, “Peptide Code”, “CircRNA”, “Exosomal lncRNAs”, “Resistance” lncRNAs”.

We can search based on these 8 parts. Of course, you can also click “Browse” in the menu bar. At this time, 8 drop-down menus are displayed, which are consistent with the 8 parts of the main page.

We can browse the relevant items in EVLncRNA by clicking the drop-down menu, and then the page will move to the relevant page.

On each page, there are drop-down boxes for us to choose and browse the corresponding categories.

1.Browse

Here we take species as an example to briefly introduce the brief use of this database.

When we click Species, the related information of lncRNA of all species will be displayed. In the drop-down box, we can select or fill in the corresponding conditions as needed to further refine the screening.

Click “Detail” to jump to the corresponding detailed page of lncRNA, here we focus on the detailed information of the target lncRNA.

Click “Detail” in the column of 1500026H17Rik, and more detailed information will be displayed.

It mainly includes basic information of lncRNA (such as ID, name, alias, species, whether it is a cyclic lncRNA, peptide information, structure information, etc.), disease information (based on the experimental support between lncRNA and disease, the functional types are divided into expression, Mutation, interaction, locus and epigenetics) and interaction information.

The interaction level can be divided into RNA-DNA, RNA-RNA, RNA-TF and RNA-protein, etc.; according to the way of molecular interaction, the interaction type can be divided into binding, regulation and co-expression.

2. Interaction Network

Constructed a comprehensive lncRNA interaction network, which can help us explore the potential relationships between lncRNA, miRNA, proteins, genes and other functional elements.

The entire interactive network includes interaction types of combination, regulation, and co-expression.

“Co-expression” means that the expression of lncRNA and other molecules in the same physiological process is positively or negatively correlated.

“Regulation” indicates that lncRNA can regulate the expression of other biomolecules in the same physiological process.

“Binding” indicates that lncRNA is in direct physical contact with other biological molecules.

Note: There are two networks to choose from: one is the total network; the other is the binding network, which are lncRNAs that have direct contact and interaction with other functional elements.

Here we click on Total network, we can find that there will be a very large network, which dazzles us.

At this time, we can display the item by clicking the item that needs to be displayed according to the option settings in the upper left corner. For example, we just want to see all the interaction networks between LncRNA and protein.

Of course, we can also use the search box in the upper left corner to search for lncRNA or the interaction target of interest by directly typing, and then a small interaction network of search keywords will be displayed.

For example, if we enter LncRNA XIST, only XIST-related networks will be displayed. When the mouse is placed on these targets, the detailed information of the targets will be displayed.

3. Search

In the “Search” page, we can search for specific lncRNA, disease or molecules that interact with lncRNA by lncRNA name, disease name, interaction, etc. Here we enter lncRNA H19 and click search.

It can be found that the returned structure page not only includes H19, but also 91H. This is because EVLncRNA provides a “fuzzy” search function and returns all matching records.

Of course, EVLncRNA provides reliable and usable lncRNA prediction and lncRNA function prediction tools on the “Tools” page, and database data can be downloaded on the “Download” page.

Users are also very welcome to submit experimentally verified novel lncRNAs and related diseases or related ingredients on the “Submit” page.

These editors will not introduce them one by one. If you are interested, you can click a few more to understand~

The functional lncRNA database verified by low-throughput experiments

(source:internet, reference only)

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