Skip to main content

Table 1 Oligonucleotide probes were designed separately from three different sets of ESTs.

From: Spotted cotton oligonucleotide microarrays for gene expression analysis

Types of probes

1st oligo set1

2nd oligo set2

3rd oligo set3

Totals4

Arabidopsis matches5

866

7,419

4,031

12,316

Singletons

na

5,280

3,852

9,132

Transcription factors (TF)6

230

2,223

677

3,130

   GO Biological Process7

46

464

126

636

   GO Molecular Function8

184

1,759

551

2,494

   PFAM9

na

471

na

471

Total number of oligos

1,154

12,006

9,629

22,789

  1. 1Oligonucleotides (oligos) were designed at Texas A&M University in the former lab of Dr. Chen [17]. 2Oligos designed at Iowa State University from a global assembly of ESTs [10]. 3Oligos designed by The Institute for Genomic Research (TIGR) from the Cotton Gene Index 8 [11]. 4Column totals are close approximations since each oligo set was designed separately. 5Arabidopsis matches are based on oligo WUBLASTX hits to the TAIR Arabidopsis protein dataset and parsed for 50 aa length and 50% percent identity. 6Transcription factor sub-total may be an over-estimate as Biological Processes and Molecular Function are not mutually exclusive categories. 7Biological Process = transcription. 8Molecular Function = nucleic acid binding activity, nucleotide binding activity, RNA and DNA binding activity, and transcription factor activity. 9Putative PFAM TF identified in the 2nd oligo set were in addition to those annotated by gene ontology.