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How to analyze ENCODE transcription factor target gene database? in order to solve this problem, this article introduces the corresponding analysis and answer in detail, hoping to help more partners who want to solve this problem to find a more simple and feasible method.

The ENCODE database contains the chip-seq data of many transcription factors. By analyzing the chip-seq data, the target gene data corresponding to the transcription factor can be predicted.

By integrating the analysis results of multiple transcription factors, a database of transcription factor target genes can be constructed at the following website

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

The database contains target gene data of 181 transcription factors, and the target genes of each transcription factor correspond to a data set, as shown below

Taking the transcription factor ARID3A as an example, the results are as follows

It can also be seen from the screenshot that although the chip-seq data are supported by experimental evidence, due to the false positive of peak-calling and other problems, the final number of target genes is very large, which is self-evident.

The data on this site can not only be browsed, but also downloaded. Target gene data for a single transcription factor can be downloaded from the following API

Http://amp.pharm.mssm.edu/Harmonizome/api/1.0/gene_set/ARID3A/ENCODE+Transcription+Factor+Targets

The above link can download the target gene data corresponding to the transcription factor ARID3A. For other transcription factors, you only need to replace the name of the corresponding TF. API returns data in JSON format, and it takes some programming skills to get a file form similar to excel.

For the entire database, you can get a link to the data corresponding to all transcription factors through the following API

Http://amp.pharm.mssm.edu/Harmonizome/api/1.0/dataset/ENCODE+Transcription+Factor+Targets

Then you can download it to the entire database. The information in the whole database is simple and direct, but the disadvantage is that the false positive rate is high. The function of online retrieval is very convenient, but downloading the database requires some programming skills.

This is the answer to the question about how to analyze the ENCODE transcription factor target gene database. I hope the above content can be of some help to you. If you still have a lot of doubts to be solved, you can follow the industry information channel for more related knowledge.

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