Abstract: Methods and systems for detection of HPV mediated cervical or oropharyneal cancer are provided. The methods include contacting a fluid sample from a patient with multiple antibodies to HPV16 early gene proteins and comparing patterns of HPV16 antibody bound to said early gene proteins with a control associated with cervical or oropharyneal cancer (FIG. 1).

Abstract: A method for preserving information about cytosine methylation status in amplified nucleic acid molecules is disclosed. The method includes contacting a sample that contains nucleic acid molecules, such as nucleic acid molecules having or suspected of having methylated cytosines, with a modifying agent that converts the unmethylated cytosines to produce converted nucleic acid molecules. The converted nucleic acid molecule retains information about cytosine methylation. The method further involves contacting the sample with a DNA polymerase to amplify the converted nucleic acid molecules by multiple strand displacement amplification. The sample is not contacted with a nucleic acid ligase or an RNA polymerase. Also disclosed are methods for detecting cytosine methylation in a sample. Such methods include detecting the presence of the signature of cytosine methylation in a bisulfite treated DNA sample that has been amplified by multiple strand displacement.

Abstract: Gene expression data and non-gene data can be integrated. Data so integrated can be analyzed in a variety of ways. For example, queries based on epidemiological data can be processed to generate results. The results can be further refined and analyzed. For example, further queries can be based on gene expression criteria to identify gene expression phenomena within the results. Grouping of data into sets is supported, and analysis tools can determine feature differences between sets or otherwise present the sets in a variety of ways, including visual depiction of gene expression data.