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The editor would like to share with you what is the target gene database of transcription factors. I hope you will gain something after reading this article. Let's discuss it together.

As far as transcription factors are concerned, the information we most want to know is their corresponding target genes. There are many transcription factor related databases, some databases directly provide target gene information, such as TRANSFAC, some databases only provide motif information, such as JASPAR, we can only use software to predict whether there is a corresponding motif in the gene promoter sequence, so as to identify the target genes of transcription factors.

TRANSFAC charges, and JASPAR's target gene prediction requires certain information skills. Is there any database that is free and directly provides target gene data?

This kind of database certainly exists, such as TRRUST and other databases introduced earlier, but the protagonist of this article is another database, Harmonizonme.

Sort out the original information in each Resource source database to get a more intuitive and convenient dataset Datasets, and then store all the sorted information in the same database to get the Harmonizonme database at the following URL

Http://amp.pharm.mssm.edu/Harmonizome/

At present, the database contains 66 Resources databases, 114datasets datasets, a total of 57620 genes, 295496 attributes, 71927784 interaction relationships. The classification is as follows

You can see that there are many types of information. This article only introduces the target gene data sets of transcription factors. On the home page of the official website, search the relevant data sets according to keywords, as shown below.

Finally, the following six target gene data sets of transcription factors can be retrieved.

Taking the TRANSFAC Curated Transcription Factor Targets dataset as an example, the link is as follows

Http://amp.pharm.mssm.edu/Harmonizome/dataset/TRANSFAC+Curated+Transcription+Factor+Targets

This data set is a manually collected data set of transcription factor target genes, as shown below.

A total of 201 transcription factors are included in the target gene information. Click on each transcription factor to see the relevant target genes, as shown below

In addition to browsing the target genes of specific transcription factors online, you can also easily download the dataset by clicking on the file identified in the red box below to download.

The file has a large number of columns, and the first few columns are shown below

Sourcesource_descsource_idtargettarget_desctarget_idSLC16A9na220963ALX1na8092SLC26A3na1811ALX1na8092ABHD17Bna51104ALX1na8092

The id here refers to the Entrez Id corresponding to the gene, the source value refers to the target gene, and the `target value refers to the transcription factor. The regulatory relationship between the transcription factor and the target gene can be easily obtained through this database.

After reading this article, I believe you have a certain understanding of "what is the target gene database of transcription factors". If you want to know more about it, you are welcome to follow the industry information channel. Thank you for reading!

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