Research about biological macromolecular

For any biological macromolecular, such as a gene or a protein, let us study its following characters:

• Consequence
• Its sequence.
• Its subcellular location(GO do it).
• Teamwork
• Complex it attends(GO do it).
• Pathway it attends(GO do it).
  
• The function which it plays(GO do it).
• The ways by which it performs its functions.
• The phenotype related with it.
• Who is co-expressed with it (neighborhood analysis)
  
• Who have similar function with it .
  
• Cause
• How does it evolve?
  
• Who regulate it (from nucleosome, transcription level, post-transcription level, translation level, post-translation level)?
• How does it travel in cell?

Methods used to figure out functions of a gene:

1. Physical interaction (PMID: 15242642).
2. Synthetic genetics analysis (PMID: 11743205).
3. Differentially expression in specifical environment.
4. Co-expression at a variety of environment.
5. Tissue-specific (or other phenotype/environment-specific) expression.
   
6. Mutant (Delete or modification in code region or promoter region)
7. RNA interface.
8. Sequence analysis (PMID: 11904358)
1. Pfam
2. promoter region analysis
3. sequence similarity
4. genome comparison parathog
9. eQTL
10. evolution of gene expression pattern (PMID: 15175431, PMID: 15195092)
11. genetic lineage analysis
    

Evolving ...