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Table 1 xMAN probe mapping of various Affymetrix tiling arrays to the most recent genome assembly

From: xMAN: extreme MApping of OligoNucleotides

Affymetrix tiling arrays

#UniqSeq

#Seq. MEntries

#Query Entries

#Seq. MGenomeMatches

#Seq.NoGenomeMatch

#Total Entries

Human ENCODE 1.0a

721,043

14,322

756,555

16,444

506

884,634

Human Chr21/22a

979,553

21,930

1,054,324

49,316

75

1,627,746

Human Promoterb

4,220,999

40,099

4,275,079

251,460

2,537

5,706,819

Human Tiling 1.0 & 2.0b

41,370,900

301,947

41,782,720

1,215,226

13,120

48,332,137

Mouse Tiling 1.0 & 2.0c

38,788,060

431,551

39,576,383

993,890

437,877

51,036,801

Mouse Promoterc

4,096,798

30,835

4,154,546

192,119

37,483

5,716,068

Arabidopsis thaliana 1.0d

3,046,178

7,275

3,053,686

164,728

0

3,772,912

  1. Table head line:
  2. #UniqSeq: Number of unique 25-mer in the original BPMAP file
  3. #Seq.MEntries: Number of 25-mer with multiple spots in the array
  4. #QueryEntries: Number of array spots in the original BPMAP file
  5. #Seq.MGenomeMatches: Number of 25-mer with multiple genomic copies
  6. #Seq.NoGenomeMatch: Number of 25-mer with no match in the genome
  7. #TotalEntries: Number of total entries in the xMAN mapping
  8. aThe original Affymetrix probe mapping is from the NCBIv33 human genome. The new xMAN probe mapping is based on NCBIv35 human genome.
  9. bThe original Affymetrix probe mapping is from the NCBIv34 human genome. The new xMAN probe mapping is based on the NCBIv35 human genome.
  10. cThe original Affymetrix probe mapping is from the NCBIv33 mouse genome. The new xMAN probe mapping is based on the NCBIv35 mouse genome.
  11. dBoth the original Affymetrix probe mapping and xMAN probe mapping are based on the TIGRv5 Arabidopsis genome.