Comparison of gene regulatory networks to identify pathogenic genes for lymphoma.

Lymphoma is the most complicated cancer that can be divided into several tens of subtypes. It may occur in any part of body that has lymphocytes, and is closely correlated with diverse environmental factors such as the ionizing radiation, chemocarcinogenesis, and virus infection. All the environmental factors affect the lymphoma through genes. Identifying pathogenic genes for lymphoma is consequently an essential task to understand its complexity in a unified framework. In this paper, we propose a new method to expose high-confident edges in gene regulatory networks (GRNs) for a total of 32 organs, called Filtered GRNs (f-GRNs), comparison of which gives us a proper reference for the Lymphoma, i.e. the B-lymphocytes cells, whose f-GRN is closest with that for the Lymphoma. By using the Gene Ontology and Biological Process analysis we display the differences of the two networks' hubs in biological functions. Matching with the Genecards shows that most of the hubs take part in the genetic information transmission and expression, except a specific gene of Retinoic Acid Receptor Alpha (RARA) that encodes the retinoic acid receptor. In the lymphoma, the genes in the RARA ego-network are involved in two cancer pathways, and the RARA is present only in these cancer pathways. For the lymphoid B cells, however, the genes in the RARA ego-network do not participate in cancer-related pathways.