We describe PrimerSelect, a program capable of transcriptome-wide design of primer pairs for optimal performance in kinetic reverse-transcriptase polymerase chain reaction (RT-PCR). For the yeast Saccharomyces cerevisiae, PrimerSelect designs primer pairs for 86% of genomic open reading frames (ORFs) using design criteria we previously established to be optimal for kinetic RT-PCR (kRT-PCR)-based transcript quantitation. Primer pairs designed by PrimerSelect for 230 yeast ORFs were evaluated for primer dimer potential, PCR cyclewise yield, and cross-priming. Performance of 95% of these primer pairs is optimal with respect to primer dimer potential and PCR cyclewise yield for quantitating even the rarest yeast transcript. All of the primer pairs produced a single amplicon of the expected size from yeast genomic DNA template. The utility of PrimerSelect for designing primer pairs complementary to ORF sequences defined for multiple isolates of the human bacterial pathogens Helicobacter pylori and Staphylococcus aureus is also demonstrated.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.
| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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