October 4, 2022

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Knowledge of RNA binding protein

Knowledge of RNA binding protein


Knowledge of RNA binding protein.  RNA-protein complexes have become core participants in many key cellular processes, which are critically linked to health and disease. RNA-protein complexes have become an important part of our understanding of many cellular pathways and related diseases.

With the increasing awareness of their importance, the protein that directly interacts with RNA, RNA-binding protein (RBP) has attracted more and more attention, and many published SCIs also conduct follow-up analysis on RBP. So I have a protein in my hand. How do I know if it is RBP? What if I want to write an article about RBP?

Well, since it is so important, let me introduce to you today a database that recognizes RBP: RBP2GO (https://rbp2go.dkfz.de/), a database that contains all currently available RBPs proteome data sets. Covering information on 13 species ranging from humans to bacteria, including 53 studies and 105 basic data sets, a total of 22552 RBP candidates were identified, dedicated to the analysis of RNA-binding proteins, their interactions and functions.

     Knowledge of RNA binding protein

Knowledge of RNA binding protein   

RBP2GO provides three search options for each species, which can be accessed through the sidebar under SEARCH SPECIES. It can be retrieved from the following three aspects, and the output results of each project are as follows.

Knowledge of RNA binding protein

From the sidebar menu of the RBP2GO homepage, you can access search engines for specific species. For each species, three search options “Protein Search”, “GO Search” and “Advanced Search” are available, each of which contains a query field for entering search terms and other options, depending on the data available for that species Types of.

1. Protein Search

Here supports the input of a single protein.

For example, we enter the gene HNRNPC here, and after submission, the score of the input protein will be given (reflecting the possibility of the protein becoming RBP). Click the blue area in the figure below to get 5 aspects of information.

The RBP2GO score is calculated based on the frequency at which the protein is listed as RBP in all data sets of the species and the average number of frequencies at which the top 10 interacting proteins (based on the STRING score) that interact with the protein are listed as RBP. There is a positive correlation between the frequency at which a protein is listed as RBP and the frequency at which its highest interacting protein is listed as RBP, that is, the protein itself that interacts with multiple RBPs is often RBP.

The search results can be downloaded as CSV or TXT files according to the content for further processing.

2. Go Search

This project can screen RBP candidates associated with a specific GO term. You can enter GO term, such as’GO:0003723′ or just enter ‘0003723’, or you can enter a keyword search, such as’RNA binding’. But the accuracy of keyword search is not as good as GO term direct search, and it may retrieve more entries corresponding to multiple different matching GO terms. In short, the universal search module therefore enables users to specifically search for RBPs linked to any function or process of interest.
Here we enter GO:0003723 and submit.

The result includes three parts: “biological process”, “molecular function” and “cell composition”, and displays the corresponding matching number. Because we enter a specific GO entry here, only the RBP of molecular function is displayed. Click GO Molecular Function, the detailed information of RBP will be displayed on the right, including Entry name, Uniport ID, RBP2GO score, amino acid length, protein molecular weight, etc. We can select the target protein in the “Protein Search” section to obtain specific information.

When we input’RNA binding’, the results are as follows, we can find that there are 12 RBPs in biological processes.

 

 

3. Advanced Search

The project can manage and combine different options at the same time, and perform batch searches to filter proteins and GO terms. We can enter the protein of interest or GO term into the corresponding field (you can enter more than one).

The “GO List” field includes the “AND / OR” option to allow the GO list to be run in two different modes, while CGC limits the range of RBP to known cancer-related genes. The two sliders below can select specific for pI and RBP2GO range. After entering as shown in the figure, submit.

The result returns two protein lists, one corresponding to the RBP candidate protein and one corresponding to the unlisted protein (other proteins) for comparative analysis. The results can be downloaded as a TXT file for further analysis by users.


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