Some studies have also compared expression signatures from primary tissue paired with matched metastatic tissue and showed similarities in the patterns of expression observed (Roepman et al, 2006; Mendez et al, 2007; Colella et al, 2008; Liu et al, 2008).
Many microarrays studies aim to detect "gene expression signatures" specific to various human diseases by comparing expression levels between two distinct groups.
The "DNA damage" signature was identified by comparing expression programs in S. cerevisiae that were modulated by a range of environmental stresses including heat shock, oxidative stress, reductive stress, osmotic shock and amino acid starvation to those elicited specifically by DNA damage induced by the alkylating agent methylmethane sulfonate (MMS) and ionizing radiation (γ-radiation) [ 1, 15].
We next examined gene networks shared between NR2E3 and ESR1 by comparing gene expression signatures specific to silencing expression of each gene in MCF-7 cells.
We started by comparing gene expression signatures of 19 osteosarcoma cell lines, 12 MSC, and 3 osteoblast cultures using unsupervised hierarchical clustering.
By comparing the gene expression signatures of drugs, diseased samples, and mutants, cMap was able to connect compounds, diseases, and genes through gene expression profiles.
As an alternative, single sample-based gene expression signatures can be obtained by comparing the expression levels of each feature in each sample against a set of reference samples by any suitable method, including for example Students t-test, Z-score transformation or fold change; or relative to the average expression level across all samples when clear reference samples are not available.
A similarity measure was developed to compare gene expression signatures associated with different contrasts.
GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data.
"We identified a COPD-specific signature by comparing gene expression changes in COPD-derived chips exposed or not exposed to smoke and subtracting the changes that we see in chips made from healthy lung chips.
