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JASPAR is a free and open database of transcription factors, in which the mitif information of transcription factors is included, which can be used to predict the binding regions of transcription factors and sequences. The web address is as follows

Http://jaspar.genereg.net/

In this database, the following nine different sources and categories of transcription factor information are provided.

1. JASPAR CORE

Under this category, eukaryotic transcription factor motif information is collected from the literature and supported by experimental evidence, and after manual verification, it is a non-redundant, high-quality transcription factor motif database, so it is also the core of the whole database.

Because of its high quality, non-redundancy and other characteristics, this category of information is usually our first choice. Each motif number begins with MA, as shown below

2. Collection CNE

The data set contains the motif information of 233transcription factors that regulate human non-coding genes, according to Xie et al. (PNAS 2007) the data in the article is collected and sorted out, and the number begins with CN, as shown below

3. Collection FAM

What is saved under this category is the category class information of transcription factors. Multiple transcription factors can have the same regulatory sequence, and transcriptional factors with the same regulatory sequence are grouped into one category. The number of each class begins with MF, as shown below

4. Collection PBM

Under this category, the motif information obtained from the analysis of transcription factors of 104 mice by in vitro technique. Each motif number begins with PB, as shown below.

5. Collection PBM HLH

Similar to PBM, except that under this category is the information of the 19 transcription factors of C. elegans bHLH, different species, the motif number under this category begins with PL, as shown below

6. Collection PBM HOMEO

This category contains mouse transcription factor motif information, which is collated from the literature Berger et al (Cell 2008). Each motif number begins with PH, as shown below.

7. Collection PHYLOFACTS

Under this category, the transcription factor motif information of mammalian evolutionarily conserved genes is analyzed.

Systematic discovery of regulatory motifs in human promoters and 3 'UTRs by comparison of several mammals

The number of each motif begins with PF, as shown below

8. Collection POLII

This category contains the motif sequence of the RNA polymerase binding region, with each motfi number beginning with PL, as shown below

9. Collection SPLICE

This category contains motif sequences of human splice sites, with a small amount of data, only 6 motif in total, each motif number beginning with SA, as shown below

Each collection is a small subset, and core is a non-redundant dataset that integrates all of these subsets. In the core dataset, species are stratified into six categories

Through the retrieval function of the official website, it can be easily searched, as shown in the following diagram

A lot of information is provided on the retrieved motif details page, taking MA0001.1 as an example

1. Basic information

Including name, number, category, corresponding species and other information, as shown below

2. Sequence logo

The distribution of bases on each bp of motif. The size of the bases is proportional to the corresponding frequency. The higher the frequency, the larger the corresponding letters, as shown below.

3. Position frequency matrix

Referred to as PFM, the frequency distribution of four bases on each bp of motif is available for download in various formats, as shown below

4, Binding sites

Red marks the specific sequence corresponding to motif, as shown below

The database provides a download function, mainly the PFM matrix corresponding to motif, as shown below

The JASPAR database is free, but compared with the TRANSFAC database, there are still many shortcomings. The first is the difference in the number of motif, which is much less than the TRANSFAC database. Secondly, in the category of information, JASPAR only provides motif information, and there is no direct transcriptional factor regulatory target gene information.

Through the JASPAR database, we can only obtain the motif information of transcription factors, and then use software to predict the binding site with DNA sequence, namely TFBS.

The above is all the contents of the article "what is the use of JASPAR database". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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