A New Gene Co-expression Networking Technique for In-silico Expression Data

نویسندگان

  • Swarup Roy
  • Dhruba K Bhattacharyya
  • Jugal K Kalita
چکیده

Biological networks may be categorised [1] as metabolic pathways, signal transduction pathways, gene regulatory networks and protein-protein interaction (PPI). A Gene Regulatory Network (GRN) is a collection of genes in a cell which interact with each other and with other molecules in the cell such as proteins or metabolites, thereby governing the rates at which genes in the network are transcribed into mRNA. Unlike GRN, a gene co-expression network (CEN) is an undirected graph, where nodes correspond to genes or gene activities, and undirected edges between genes represent significant co-expression relationships [2,3]. In a co-expression network, two genes are connected by an undirected edge if their activities have significant association considering a series of gene expression measurements. Compared to regulatory networks, a gene co-expression network does not attempt to draw direct causal relationships among the participating genes in the form of directed edges. A co-expression network may contain co-regulated gene clusters that can encode proteins, which interact among themselves and take part in common biological processes. In our work, we capture pair-wise similarity purely based on pattern matching followed by construction of the co-expression network. Unlike available measures, we use a support based approach to compute similarity between two expression patterns to include the case where two genes show similar patterns only under some conditions or dimensions. We use signed edges between the genes to represent positive and negative regulations, an important component in gene regulatory network.

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تاریخ انتشار 2013