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Table 1 S3T Default Rule Set.

From: A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Score Source Condition
-4 Linker (*)  
-3 mRNAs internally primed f(x) = 1
-2   f(x) < 5 and (N(x) ∩ T) ≠ Ø
10 FL cDNAs, 3'most, poly(A) f(x) ≥ 10
9 FL cDNAs, 3'most, poly(A) 1 ≤ f(x) < 10
8 FL cDNAs, 3'most f(x) ≥ 5
7 FL cDNAs, 3'most 1 ≤ f(x) < 5
6 Consensus, 3'most, poly(A) f(x) ≥ 5
5 Consensus, 3'most, poly(A) 1 ≤ f(x) < 5
4 Alt. poly(A)/splicing, > 1 est f(x) > 1
3 Consensus, 3'most f(x) ≥ 1
2 Alt. poly(A)/splicing, 1 est f(x) ≥ 1
1 FL cDNAs, internal Tags  
0   m(x) > f(x)
-1   f(x) = 1
-5 Mitochondrion genome  
-7 Nuclear genome  
-6 Vector pZErO-1 (*)  
-8   
  1. Rule set used in S3T classification process of public SAGE data. The f(x) represents the absolute frequency for tag x and m(x) the average frequency for tag x, considering all libraries in our gene expression database, the set N(x) represents the tag x neighbor tags (that differ from it by a single nucleotide), the T set represents the highest frequency tags of the library (top 20%). (* – This is applicable only for SAGE data)