Fractal genomics modeling: a new approach to genomic analysis and biomarker discovery

Abstract

Reverse engineering of genetic networks generally requires establishing correlative behavior within and between a very large number of genes. This becomes a difficult analytical problem for even a few hundred genes and the difficulty tends to grow exponentially as more genes are examined. Using a hybrid data analysis method known as Fractal Genomics Modeling (FGM), this problem is reduced to examining correlative behavior within small gene groups that can then be compared and integrated to produce a picture of larger networks using a type of shotgun approach. We have applied FGM toward examining genetic networks involved in HIV infection in the brain. These networks have relevance both to processes related to HIV infection and neurodegenerative disorders. Our preliminary findings have produced conjectures of related pathways and networks as well new candidates for genetic markers in HIV brain infection. Evidence has also been produced which appears to show the presence of a hierarchical network structure within the genes studied. We will discuss the background and methodology of FGM as well as our recent findings.

Self-organization of developing embryo using scale-invariant approach

“…Vélez et al reported the possible use of multifractals in the measurement of local variations in DNA sequence in order to define the structure-function relationship in chromosomes [ 41 ], and Mathur et al used fractal analysis of gene expression in studying the hair growth cycle. Moreover [ 42 ], fractal genomics modeling has been used to predict new factors in signaling pathways and the networks operating in neurodegenerative disorders [ 43 ]. At the cellular level, fractal dimension was used in evaluating the morphological diversity of neurons and discriminating them on the basis of the neuronal extensions [ 44 ]; fractals can also explain higher orders of organization in biological materials such as the organization of tissues [ 45 ] and branching of tubular systems such as the respiratory and the vascular systems [ 46 - 49 ].…”