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Table 2 Characteristics of LongSAGE tag frequency distribution

From: Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries

Tag Frequency & Abundance

Tag Count per 100,000t

≤1

2-4

5-9

10-99

100-999

≥1,000

 

Transcript Copies per Cellu

≤5

10-20

25-45

50-495

500-4,995

≥5,000

 

% Transcript Abundance in Cellv

≤0.001

0.002-0.004

0.005-0.009

0.01-0.099

0.1-0.999

≥1

R1881

Total Tags

15,141

13,985

11,055

32,800

21,971

3,029

 

Tag Types

15,141

5,464

1,703

1,417

101

2

Vehicle

Total Tags

16,562

1 0,229

11,633

26,466

18,453

2,518

 

Tag Types

16,562

4,427

2,195

1,313

93

2

% of Tags that Map as Transcription Factorsα, z, δ

9.14

8.94

7.95

6.0

0

0

 

% of Tags that Mapχ, β, δ

29.40

57.82

76.22

83.1

85

100γ

% of Tags Significantly Differentially Expressedε, a, δ

0.4

1.15

16.17

25.38

58.12

100

  1. t Tag count per 100,000 = (observed tag count/total tags in the library) × 100,000
  2. u Transcript copies per cellw= (observed tag count/total tags in the library) × 500,000
  3. v % Transcript abundance in cellw= (transcript copies per cell/500,000) × 100%
  4. w Calculation based on ~500,000 transcripts in a cell [36]
  5. α % of tags that map as transcription factors = (no. of genes with "transcription regulation acivity"/no. of genes with unambiguous sense mappings and GO terms) × 100%
  6. zMapped unambigously sense toRefSeqand subjected to Gene Ontology (GO) analysis
  7. δ Tag types from each tag frequency class of R1881 and vehicle LongSAGE libraries were combined
  8. χ % of tags that map = (no. of genes with sense mappings/combined total tag types) × 1 00%
  9. β Mapped sense (incl. ambiguous) to RefSeq
  10. γ One tag was mapped sense using Ensembl gene
  11. ε % of tags significantly differentially expressed = (no. of significantly differently expressed tag types in class/combined total tag types in class) × 100%
  12. a Statistics according to the Audic and Claverie test statistic (p ≤ 0.001)