Abstract: An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM-score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS-score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer.
Type:
Grant
Filed:
March 23, 2015
Date of Patent:
April 10, 2018
Assignee:
MEDISAPIENS OY
Inventors:
Sami Kilpinen, Kalle Ojala, Timo Ahopelto, Tommi Pisto
Abstract: An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM-score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS-score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer.
Type:
Grant
Filed:
March 11, 2011
Date of Patent:
April 28, 2015
Assignee:
Medisapiens Oy
Inventors:
Sami Kilpinen, Kalle Ojala, Timo Ahopelto, Tommi Pisto
Abstract: An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM-score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS-score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer.
Type:
Application
Filed:
March 11, 2011
Publication date:
March 14, 2013
Applicant:
MEDISAPIENS OY
Inventors:
Sami Kilpinen, Kalle Ojala, Timo Ahopelto, Tommi Pisto
Abstract: A computer-implemented method and apparatus for correcting data sets from microarray measurements of gene expression values made with several different microarray versions. The method comprises obtaining data sets (210) of expression values of several genes of biological samples (202), made with several different microarray versions; normalizing (212) the data sets; determining a first gene-specific distribution parameter (220) for each microarray version and a second gene-specific distribution parameter (222) for a combination of microarray versions; determining a gene-specific correction element (226) for each microarray version based on the discrepancy (224) between the first and second gene-specific distribution parameters; correcting a gene's expression value with the gene-specific correction element (226) for the microarray version on which the gene's expression value is based; and storing (118) the gene's corrected expression value (228) in a physical memory (230).
Type:
Application
Filed:
April 8, 2009
Publication date:
February 10, 2011
Applicant:
MEDISAPIENS OY
Inventors:
Sami Kilpinen, Reija Autio, Matti Saarela