dorsal/arxiv
View SchemaBase pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays
| Authors | Hans Binder, Stephan Preibisch, Toralf Kirsten |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501008 |
| URL | https://arxiv.org/abs/q-bio/0501008 |
Abstract
The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of the gene of interest. We analyzed the concentration dependence of the signal intensity of perfect match (PM) and mismatch (MM) probes in terms using a microscopic binding model using a combination of mean hybridization isotherms and single base related affinity terms. The signal intensities of the PM and MM probes and their difference are assessed with regard to their sensitivity, specificity and resolution for gene expression measures. The presented theory implies the refinement of existing algorithms of probe level analysis to correct microarray data for non-specific background intensities.
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"date_created": "2026-03-02T18:01:31.540000Z",
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"abstract": "The lack of specificity in microarray experiments due to non-specific\nhybridization raises a serious problem for the analysis of microarray data\nbecause the residual chemical background intensity is not related to the\nexpression degree of the gene of interest. We analyzed the concentration\ndependence of the signal intensity of perfect match (PM) and mismatch (MM)\nprobes in terms using a microscopic binding model using a combination of mean\nhybridization isotherms and single base related affinity terms. The signal\nintensities of the PM and MM probes and their difference are assessed with\nregard to their sensitivity, specificity and resolution for gene expression\nmeasures. The presented theory implies the refinement of existing algorithms of\nprobe level analysis to correct microarray data for non-specific background\nintensities.",
"arxiv_id": "q-bio/0501008",
"authors": [
"Hans Binder",
"Stephan Preibisch",
"Toralf Kirsten"
],
"categories": [
"q-bio.BM"
],
"title": "Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays",
"url": "https://arxiv.org/abs/q-bio/0501008"
},
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