Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis

BMC Bioinformatics

Table 5 Representation of the spotted probes exhibiting negative correlation coefficients with Affymetrix probes.

Long oligonucleotide sequence 5'-3'	GenBank accession no.	Probe Set ID RAE230A	Correlation coeficient
CACAGAAGATGGAGAAAATCTAAAG-TGAAAGTGCGCGTGACACACATGCA	^cXM_213699 *NM_001011901	^c1388898_at	-0.37107
CAGACCTTCATCGCTCTGTGTGCTACCGA-CTTCAAGTTTGCCATGTACCCGCCATCGA	^cD16308	^c1370810_at	-0.24892
GGACATCTGAGTTGAGACCCAGTTGTTAC-TAACCTTATTGTGAATTGCCTGATCTACA	^a,bM11794	^a,b1371237_A_AT	-0.13854
ATTCTCTGGTCTAATGTCTGGCTGGGGT-TCTCCGTCTGCTTCCTGTATCTATATTCT	^bM15562	^b1370883_AT	-0.43223
ACTTACAAGGACCAAATACCAAACTAGAAG-AAAAGATAGACATGGTGCCTATTGACTTTC	^cM63101	^c1387835_AT	-0.93746
CTAAAATTGGGCTTGCGGTTTTCATTTCTG-ATGTCTCTGGATTGGCACCCTTATGGTTTA	^a,b,dNM_019356	^b,d1367713_at	-0.88595
GTCTGTAAAATAACCATCAGTTCCTTCAC-CCACCCTCTTCCCCTTAACACTCAGC	^bXM_340904 *NM_012809	^b1387897_at	-0.6239
TGTAAATTACACCACGGACTTCATCTACC-AGCTCTACTCAGAGGAAGGGAAAGGAG	^a,bL25387	^b1372182_at	-0.37801
GTCTTGACAATGTTCACAAACAGAGAGT-GGCTGAAGTGCTAAATGACCCTGAGAA	^a,b,dXM_216792 *XM_343114	^a,b1370886_a_at	-0.82769

a. Low signal intensity (signal below mean of all arrays); b. Affymetrix and long oligonucleotide probes mapped to the APOCHIP target mRNA; c. Affymetrix and long oligonucleotide probes mapped partly or not at all to the APOCHIP target mRNA; d. Probes exhibiting variation close to the lower limits shown in Figure 4. *. New annotation obtained by BLAST.

ISSN: 1471-2105