Mammalian transcription factors can bind to and regulate thousands of sites throughout the genome. The deep complexities of these gene regulatory networks make conventional methods an unsuitable choice for comprehensive analysis. The advent of genomic technologies, in particular DNA microarray profiling and chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIPSeq) or ChIP-on-Chip, has led to the identification of target genes and transcriptional networks on a genome-wide scale.
All these techniques have been used to characterize the gene regulatory networks of a growing number of transcription factors. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active in different cells.
Genomic signature: it refers to the characteristic frequency of oligonucleotides in a genome or sequence. It has been observed that the genomic signature of phylogenetically related genomes is similar,
Gene signature: a condition's gene signature is represented by a group of genes in a type of cell whose combined expression pattern is uniquely characteristic of that condition. Ideally, the gene signature can be used to select a group of patients at a specific state of a disease with accuracy that facilitates selection of treatments.
Interestingly, signature concept was improved to not only as tool to identify possible connection in signaling pathways and their regulation mediated by transcription factors, but also the regulatory networks that result altereted during pathological states. Gene signature profile may function as a prognostic tool, functional to understand the specific state/grade of a disease.