November 27, 2022

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Nature Methods: Disease-oriented Gene Database

Nature Methods: Disease-oriented Gene Database


Nature Methods: Disease-oriented Gene Database. What does the disease-related gene search database published on Nature Methods look like?

As the results of research on disease-related genes increase, we have already found many disease-related genes. Often when studying a disease, we have to understand what genes are related to the disease. This is convenient for us to design our own research direction in the future.

There are still many databases for disease-related gene retrieval. The malacards and GeneShot we introduced earlier can query disease-related genes.

Today, I will introduce a database of disease-related gene retrieval published on Nature Methods: Phenolyzer (

  Nature Methods:  Disease-oriented Gene Database   

Database usage

Data input

For the Phenolyzer database, in the basic test results, we only need data-related disease phenotypes. Here we can enter multiple tables, these phenotypes can only be separated by;.

PS: For the input of diseases, this database supports the input of plain text, OMIM ID number and HPO ID number. Let’s take two English words for stomach cancer as an example

Nature Methods:  Disease-oriented Gene Database

The above is the basic input for the analysis. If we have certain restrictions on genes, for example, we want to see specific genes related to diseases, and we want to see whether there are disease-related genes in a certain position. At this time, further input is required.

Nature Methods:  Disease-oriented Gene Database
After selecting all of the above, click submit.

Interpretation of results

As far as the results of the data are concerned, first of all, it is displayed through a network diagram. In this network, you can see which genes are related to the searched diseases. At the same time, the database also predicts a part of the possible interaction genes, and this part of the genes is also marked on it. We can use the legend of the network diagram to illustrate what diseases we see mean.

Furthermore, we can use the bar graph to know which gene is related to the retrieved disease.

Further, we can see the specific evidence for each gene in the Details to support its interaction with the phenotype.

Database usage scenarios

The above are the main steps to use the database. Regarding the usage scenario of the database, first of all, if your boss gives you a gene, ask you to find out if this gene is related to a certain disease. Then you can use this database to take a look.

What if it doesn’t matter? Then through this database, we have learned about the core genes related to this disease. We can use the protein interaction database to find out whether the target gene is related to these core genes. If so, it can also indicate that the target gene may be related to the target disease.

The above is a simple example of the use of this database. As for other uses, it depends on everyone’s performance.


(source:internet, reference only)

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