FINAL DATA

1. Dataset 22SIN3set: 22 genes from SIN3set

• Identifiers
  

• Promoters (Fasta, 2000 bps upstream the TSS)

2. Running MEME in the 22SIN3set

• MEME interesting motif
  

  TTTAAATATTATAAAAAAAATATAAATATATAAAATTTATTATAATATTT
  E-value = 8.0e-018
  In 21 out of 22 sequences (CG12505, FBgn0033926)
  

• Log matrix

3. Running the matrix with different thresholds in 22SIN3set

Results sorted by matrix similarity score
MAXSCORE: 5136.0

T = 50%	T = 25%	T = 0%
16 SITES (14 genes, 63%)	53 SITES (21 genes, 95%)	256 SITES (21 genes, 95%)
Genomic annotation

4. Running the matrix with different thresholds in the whole genome (13728 genes)

Results sorted by matrix similarity score
MAXSCORE: 5136.0

T = 50%	T = 25%	T = 0%
862 SITES (330 genes, 2%)	15386 SITES (4923 genes, 35%)	115910 SITES (11590 genes, 84%)

5. Genes whose putative sites (T=50%) are in positions [1500-2000]:

Dataset	sites [1500-2000]	genes [1500-2000]	total Genes	%
SIN3set	8	7	22	31%
Whole genome	288	137	13729	0.9%

6. Functional annotation of 7 and 137 interesting genes:

-- 7 genes from SIN3set with the target site in 1500-2000 --

• Gene identifiers
• GO definitions
• GO definitions (tabular)
• STATS

---

-- 137 genes from whole genome with the target site in 1500-2000 --

• Gene identifiers
• GO definitions
• GO definitions (tabular)
• STATS

---

-- THE WHOLE GENOME --

• Gene identifiers
• GO definitions
• GO definitions (tabular)
• STATS

7. Recomputing the matrices from results sets (T=0.5)

Multiple alignment of sites and matrices obtained using MEME

1. SIN3 set:
   
   • SIN3set 16 aligned sites
   • SIN3set new matrix (16 sites)
     

     Predictions with T=0.5:
     

   • Trying again in SIN3 set (17 sites)
   • Trying again in the whole genome
   
   

2. Whole genome:
   
   • 862 aligned sites
   • Removing repeats: 521 aligned sites
   • New matrix (521 sites)
     

   • Predictions on the whole genome