植物转录因子数据库构建实例

学术报告

1. 植物转录因子分类、预测和数据库构建[PDF]
2. PlantTFDB简介 [PDF]

相关文章

1. Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J. DATF: a database of Arabidopsis transcription factors. Bioinformatics. 2005 May 15;21(10):2568-9.
2. Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. DRTF: a database of rice transcription factors. Bioinformatics. 2006 May 15;22(10):1286-7.
3. Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang M, Luo J. DPTF: a database of poplar transcription factors. Bioinformatics. 2007 May 15;23(10):1307-8.
4. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res. 2008 Jan;36(Database issue):D966-9.
5. He K, Guo AY, Gao G, Zhu QH, Liu XC, Zhang H, Chen X, Gu X, Luo J. Computational identification of plant transcription factors and the construction of the PlantTFDB database. Methods Mol Biol. 2010;674:351-68.
6. Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J. PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res. 2011 Jan;39(Database issue):D1114-7.
7. Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014 Jan;42(Database issue):D1182-7.
8. Jin J, He K, Tang X, Li Z, Lv L, Zhao Y, Luo J, Gao G. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol Biol Evol. 2015 Jul;32(7):1767-73.
9. 靳进朴,郭安源,何坤,张禾,朱其慧,陈新,高歌,罗静初. 植物转录因子分类、预测和数据库构建. 生物技术通报，2015，Vol.31(11):68-77.
10. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017 Jan 4;45(D1):D1040-D1045.
11. Tian F, Yang DC, Meng YQ, Jin J, Gao G. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res. 2020 Jan 8;48(D1):D1104-D1113.

PHP文档

1. PlantTFDB构建 [PDF]

数据库查询方法

1. 数据库连接 - 修改db_connect.php，将问号“??”改为相应的用户名，如leb20
   $user = 'leb??';
   $db = 'leb??';
   
2. 查询提示信息 - 修改index.html，将Input gene name:改为
   Input Accession (P69905) or Entry Name (HBA_HUMAN) or Gene name (HBA) or Species (Human):
   
3. PHP文件调用 - 修改index.html，将2_para.php改为4_db_query.php
4. 数据库查询 - 修改4_db_query.php，将 "SELECT * FROM globin WHERE id = "$ID"; 改为：
   "SELECT * FROM globin WHERE ac='$ID' OR entry='$ID' OR gene='$ID' OR species='$ID' ";
   注意：若数据库名为globin_new，请同时修改globin为globin_new
   
5. 查询结果表头 - 修改4_db_query.php，将UniProt Entry改为Accession，将Protein Names改为Gene Name：
   
6. 查询结果表格 - 修改4_db_query.php，将while语句中第一行id改为ac，将第二行ac改为entry，将第三行name改为gene，将第四行sp改为species
   

相关网站

1. 植物转录因子数据库PlantTFDB
2. 动物转录因子数据库AnimalTFDB