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This article introduces the relevant knowledge of "what is an Oncomine database". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

Introduction to Oncomine database

Oncomine is a large tumor gene chip database, covering 65 gene chip data sets, 4700 chips and 480 million gene expression data. It can be used to analyze gene expression differences, find outliers and predict co-expression genes. It can also be classified according to clinical information such as tumor stage, grade and tissue type. It can also find possible molecular markers and therapeutic targets based on known gene-drug analysis.

Application Direction of Oncomine Database

If you have obtained a tumor differentially expressed gene and want to study whether it can be used as a potential marker and target for a certain tumor, and you are afraid that doing experiments will get negative results, wasting time and money, you should think of the Oncomine database.

Oncomine is also a classic sample database in the field of oncology, which can help us to screen some target molecules worth studying or predict phenotypes. Why do you say "also"? Because like the TCGA we discussed before, it is a widely used database in the field of oncology.

However, the advantage of Oncomine compared with TCGA is that in addition to data, it also provides some simple and easy-to-operate analysis tools, such as differential expression analysis, co-expression analysis and so on. In addition, it integrates some data from TCGA and GEO. The disadvantage is that the free version of the data can not be downloaded, the charge is sky-high. However, there are ways to get it in bulk from the web page by writing scripts.

The advantage of TCGA is that it has a high dimension and rich levels, but its disadvantage is that it does not provide analysis tools and has to find or learn something else. Let's not say so much here, we can choose according to our own situation. Today we will only talk about Oncomine.

Application scenarios of Oncomine

When it comes to application, it is similar to TCGA, there are two main aspects.

On the one hand, when there is no basis for previous work, mining and screening candidate molecules from the database as the future research direction. It is used to open a topic for a doctor, or to deceive a fund.

On the other hand, when you have done high-throughput screening to get the target molecules, we use the database to analyze their expression in tumors and their correlation with clinical survival and prognosis, so as to provide more evidence for your own research; at the same time, it is also to do more evaluation for future mechanism research. if the molecules that differ in your experiments are also different in other people's experiments, the risk is relatively small.

Technically, the main functions of Oncomine are gene expression difference analysis, gene expression and clinical correlation, multi-gene co-expression analysis and so on.

Data mining tricks:

The first step is to see which tumors have high expression of the target gene.

The second step is to prove that the target gene is highly expressed in a tumor.

The third step is to find co-expressed genes.

The fourth step is to determine whether the target gene is highly expressed in the cell line.

Fifth, the correlation between gene expression and survival.

This is the end of the content of "what is the Oncomine database". Thank you for reading. If you want to know more about the industry, you can follow the website, the editor will output more high-quality practical articles for you!

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