Transcription factor databases:

• DBD: Transcription factor prediction database
• AnimalTFDB: Animal Transcription Factor Database
• TFdb: Riken Transcription Factor Database
• The Drosophila Transcription factor Database
• TFCat: The curated catalog of mouse and human transcription factors
• PlantTFDB: Plant Transcription Factor Databases

Transcription regulation prediction tools:

• MEME: Motif-based sequence analysis tools
• JASPAR: The high-quality transcription factor binding profile database
• MatInspector: Search for transcription factor binding sites
• ESCAPE: Embryomic Stem Cells Atlas of Pluripotency Evidence
• TRANSFAC: gene transcriptional regulation
• MotifMogulServer
• TRED: Transcriptional Regulatory Element Database
• TESS: Transcription Element Search System
• BTSS: Database of Transcriptional Start Sites
• UCSC ENCODE

Function analysis tools:

• DAVID:The Database for Annotation, Visualization and Integrated Discovery
• GenMAPP: Gnene Map Annotator and Pathway Profiler
• WEGO: Web Gene Ontology Annotation Plotting
• Gene Ontology

Other tools and websites:

• WebLogo: A sequence logo generator
• The Tree of Life Web Project