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Table 2 Annotation improvement of the less-informative Agilent features

From: Linking microarray reporters with protein functions

Old Annotation

New Annotation

Description Type

#Reporters

#Ens ID

#SP ID

% Annotated

Riken cDNA

9,759

2,937

2,008

50.7%

ESTs

369

173

132

82.7%

Hypothetical

348

173

52

64.7%

CDNA

640

325

200

82.0%

Gene Model

734

271

90

49.2%

Gene Trap Library

48

13

15

58.3%

Intronic

1,408

146

285

30.6%

Similar to

748

273

154

57.0%

Unknowns

7,849

1,156

1,448

33.2%

DNA Segments

270

110

127

87.8%

Clones

213

39

37

35.7%

TOTAL

22,386

5,616

4,548

45.4%

  1. This table categorizes all originally less-informative feature descriptions on the Agilent G2519A Option 2 Mouse Development array (22,386) into several groups. After BLASTing their corresponding sequences against either cEMBL or EnsEMBL, we were able to relate 10,164 (45.4%) features to an improved description. For the "unknown" category more than half of the features now have an improved annotation. Of those, more than half refer to known proteins.
  2. SP, SwissProt/UniProt; Ens, EnsEMBL