Informative nucleic acid arrays and methods for making same
AssigneeIntegriderm, Inc.
InventorsThomas P. Dooley, Ernest V. Curto, Richard L. Davis, Jr.
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Abstract
The present invention is directed to methods for making and using informative nucleic acid arrays (e.g., DNA including cDNA, RNA, PNA) for research and other applications in various disciplines or areas of interest. Examples of such disciplines include, without limitation, dermatology, pharmacology, toxicology, oncology, gynecology, urology, gastroenterology, as well as studies of sentinel gene discovery, signature gene discovery, mechanism of action, drug screening, drug metabolism, etc. The informative nucleic acid arrays of the present invention may contain only the gene sequences that are of interest in a particular area of interest or application, and may exclude other gene sequences.
Claims30
A method for identifying a plurality of genes that are differentially expressed between dissimilar biological samples for use in an informative array, comprising:
- providing a first set of heterogeneous nucleic acid probes derived from a first biological sample;
- providing a second set of heterogeneous nucleic acid probes derived from a second biological sample;
- hybridizing a nucleic acid array comprising a plurality of sequences derived from genes of a biological process with the first set of probes and determining a first level of expression for sequences of the array;
- hybridizing the array with said second set of probes and determining a second level of expression for sequences of the array;
- identifying a plurality of genes that are differentially expressed in said biological process by comparing the first level of expression with said second level of expression for hybridized sequences;
- and
- establishing a ranking of the identified genes by a step selected from the group of steps consisting of:
- determining an absolute value of the difference between the first level of expression and the second level of expression, and ranking genes having a higher difference over genes having a lower difference;
- and
- determining a standard deviation of the difference between the first level of expression and the second level of expression, and ranking genes having a higher standard deviation over genes having a lower standard deviation.
A method for selecting a plurality of genes for an informative nucleic acid array for a biological process, comprising:
- identifying genes that are differentially expressed in a biological process;
- establishing a ranking of the differentially expressed genes by a step selected from the group of steps consisting of:
- determining an absolute value of the difference between the first level of expression and the second level of expression, and ranking genes having a higher difference over genes having a lower difference;
- and
- determining a standard deviation of the difference between the first level of expression and the second level of expression, and ranking genes having a higher standard deviation over genes having a lower standard deviation;
- and
- placing sequences derived from ranked differentially expressed genes on the informative array.
A method for converting a nucleic acid array into an informative array comprising:
- providing a first set of heterogeneous nucleic acid probes derived from a first biological sample;
- providing a different, second set of heterogeneous nucleic acid probes derived from a second biological sample;
- hybridizing a nucleic acid array comprising a plurality of sequences with the first set of probes and determining a first level of expression for sequences of the array;
- hybridizing the array with said second set of probes and determining a second level of expression for sequences of the array;
- identifying a plurality of genes that are differentially expressed in said biological process based on a difference between the first level of expression and the second level of expression for identified genes, by a step selected from the group of steps consisting of:
- determining an absolute value for the difference between the first level of expression and the second level of expression, and ranking genes having a higher difference over genes having a lower difference;
- and
- determining a standard deviation of the difference between the first level of expression and the second level of expression, and ranking genes having a higher standard deviation over genes having a lower standard deviation;
- and
- selecting genes from the plurality of identified differentially expressed genes for inclusion on the informative array.
Dependencies are inferred from the claim text.