Shulou(Shulou.com)06/01 Report--

Editor to share with you what is the use of footprintDB database, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

As far as transcription factors are concerned, the relevant information is as follows

Transcription factors

DNA motifs

DNA binding sites

Target genes

Transcription factors represents the name, corresponding gene, family, sequence and other basic information of the transcription factor, DNA motifs represents the conservative pattern of the binding region of the transcription factor, DNA binding sites represents the actual binding region of the transcription factor, and target genes represents the target gene regulated by the transcription factor.

FootprintDB is a comprehensive transcription factor database. By integrating multiple transcription factor-related databases, a non-redundant data set is finally constructed, in which transcription factors, DNA motifs and DNA binding sites3 information are stored. The URL is as follows

Http://floresta.eead.csic.es/footprintdb/index.php

The database integrates information from the following 19 databases

JASPAR

CISBP

3D-footprint

HT-SELEX2

UniPROBE

HOCOMOCO

AthalianaCistrome

HumanTF

HumanTF2

AthaMYB

FlyZinFinger

SMILE-seq

ArabidopsisPBM

Athamap

DBTBS

RegulonDB

DrosophilaTF

HumanC2H2ZF-Chip

EEADannot

For more information about the version of each database, the number of transcription factors and other statistics, please see the link below.

Http://floresta.eead.csic.es/footprintdb/index.php?databases

All the information in the database is as follows

The data provides a retrieval function to retrieve the information of transcription factors, DNA binding Motifs and DNA binding sites, as shown below

Taking the transcription factor FOXP2_HUMAN as an example, the results are as follows

1. Transcription Factor

It contains the corresponding genes, species, protein numbers, protein sequences, motif, binding sites and other information.

2. DNA Binding Motif

Contains the number of motif, corresponding species, consistency sequence, sequence logo, PSSM matrix, binding sites and other information.

3. DNA binding Sites

Contains the binding site number, sequence, corresponding motif and transcription factors and other information.

In addition to the retrieval function, the database also provides the function of motif compare. By entering a PSSM matrix of motif or a sequence of binding regions, you can compare the motif with the existing motif in the database to determine whether it is a known motif, as shown below

This function will take a long time to run, so it is recommended to provide a mailbox, and the results will be sent to the mailbox after running.

Through the integrated database such as footprinDB, we can save the trouble of cross-retrieval among multiple databases and improve the retrieval efficiency. This type of database is also a popular trend.

The above is all the contents of the article "what is the use of footprintDB 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!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.