Method for identifying biomarkers using Fractal Genomics Modeling
First Claim
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1. A method for modeling gene expression of a small group of genes in a genetic network of a subject comprising:
- (a) providing a dataset of gene expression values of the small group of genes from the subject;
(b) providing a surface wherein each point on the surface can serve as a domain for an iterative algorithm;
(c) selecting a point on the surface;
(d) generating a comparison string from the selected point using the iterative algorithm;
(e) scoring the comparison string against the gene expression values in the dataset;
(f) determining if the score of the comparison string meets a pre-determined condition or property; and
(g) marking the point if the score meets the pre-determined condition or property to generate a fractal genomics modeling (FGM) model of the target string on the surface.
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Abstract
This present invention relates to methods of manipulation, storage, modeling, visualization and quantification of datasets. One application of the present invention is related to developing FGM models of datasets represented by the various points in a multi-dimensional map. The invention can be adapted to genomic analysis by Fractal Genomics Modeling (FGM) which can be used to identify biomarkers to develop treatments, diagnoses or prognoses of disease by exploiting the map of interactions and causality—pathway conjecture—rendered by this technology.
43 Citations
60 Claims
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1. A method for modeling gene expression of a small group of genes in a genetic network of a subject comprising:
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(a) providing a dataset of gene expression values of the small group of genes from the subject;
(b) providing a surface wherein each point on the surface can serve as a domain for an iterative algorithm;
(c) selecting a point on the surface;
(d) generating a comparison string from the selected point using the iterative algorithm;
(e) scoring the comparison string against the gene expression values in the dataset;
(f) determining if the score of the comparison string meets a pre-determined condition or property; and
(g) marking the point if the score meets the pre-determined condition or property to generate a fractal genomics modeling (FGM) model of the target string on the surface. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
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39. A method for identifying a biomarker for a phenotype comprising:
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(a) providing a plurality of datasets of gene expression values wherein each dataset is from a small group of genes, and the plurality of datasets is from one or more subjects having the phenotype;
(b) providing a surface wherein each point on the surface can be served as a domain for an iterative algorithm;
(c) selecting a point on the surface;
(d) generating a comparison string from the selected point using the iterative algorithm;
(e) scoring the comparison string against the gene expression values in the dataset;
(f) determining if the score of the comparison string meets a pre-determined Pearson correlation value;
(g) marking the point if the score meets the pre-determined Pearson correlation value to generate a FGM model of the target string on the surface;
(h) repeating steps (c) through (g) for a plurality of the datasets to generate FGM models for said plurality of datasets;
(i) identifying clusters containing FGM models of the same small group of genes corresponding to the phenotype;
(j) individually testing each of the small group of genes across all datasets to verify that the Pearson correlation between the small groups of genes is markedly different with regard to the phenotype; and
(k) selecting the small group of genes that produces the most marked difference in the Pearson correlation as a biomarker for the particular phenotype. - View Dependent Claims (40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58)
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59. A biomarker for ALL comprising a small gene-group or its FGM model, the small gene-group is selected from a first group of genes, a second group of genes, and both the first group of genes and the second group of genes wherein the first group of genes is GATA2 GATA-binding protein 2, Alcohol dehydrogenase 6 gene, GB DEF=Protein-tyrosine phosphatase mRNA, Globin gene, Pre-mRNA splicing factor SF2, P32 subunit precursor, Major histocompatibility complex enhancer-binding protein, and MSN Moesin;
- and the second group of genes is Onconeural ventral antigen-1 (Nova-1) mRNA, Ini1 mRNA, RORA RAR-related orphan receptor A, FUSE biding protein mRNA, Rar protein mRNA, Fetal ALZ-50-reactive clone 1 (FAC1) mRNA, and MB-1 gene.
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60. A biomarker for differentiating T-Cell ALL from B-Cell ALL comprising a small gene-group of 7 genes or its FMG model, the small gene-group consists of:
- Onconeural ventral antigen-1 (Nova-1) mRNA, Ini1 mRNA, RORA RAR-related orphan receptor A, FUSE biding protein mRNA, Rar protein mRNA, Fetal ALZ-50-reactive clone 1 (FAC1) mRNA, and MB-1 gene.
Specification