Methods and systems for identifying target genes

Abstract

The present disclosure provides methods and systems for identification of genomic regions for therapeutic targeting. A method for identifying one or more genomic regions for therapeutic targeting, which may facilitate re-programming of a cell from one phenotypic state to another, may comprise: providing single-cell RNA-seq data for a plurality of diseased cells and a plurality of normal cells of a cell type; mapping the single-cell RNA-seq data for the plurality of diseased cells and the plurality of normal cells into a latent space corresponding to a plurality of phenotypic states of the cell type; identifying, based at least in part on a topology of the latent space, the one or more genomic regions for therapeutic targeting; and electronically outputting the one or more genomic regions for therapeutic targeting.

1 - 38 . (canceled) 
     
     
         39 . A method for identifying one or more genomic regions for therapeutic targeting, said method comprising:
 providing single-cell ribonucleic acid (RNA) sequence data for a plurality of diseased cells and a plurality of normal cells of a cell type;   mapping said single-cell RNA sequence data for said plurality of diseased cells and said plurality of normal cells into a latent space;   identifying, based at least in part on a topology of said latent space, said one or more genomic regions for therapeutic targeting; and   electronically outputting said one or more genomic regions for identifying therapeutic targets.   
     
     
         40 . The method of  claim 39 , wherein said mapping comprises using a dimensionality reduction algorithm. 
     
     
         41 . The method of  claim 40 , wherein said dimensionality reduction algorithm comprises a uniform manifold approximation and projection (UMAP) algorithm.