Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

BACKGROUND: Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. RESULTS: To study more complex relationships involving multiple biological interaction types, we assembled an integrated Saccharomyces cerevisiae network in which nodes represent genes (or their protein products) and differently colored links represent the aforementioned five biological interaction types. We examined three- and four-node interconnection patterns containing multiple interaction types and found many enriched multi-color network motifs. Furthermore, we showed that most of the motifs form 'network themes' – classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. Network themes can be tied to specific biological phenomena and may represent more fundamental network design principles. Examples of network themes include a pair of protein complexes with many inter-complex genetic interactions – the 'compensatory complexes' theme. Thematic maps – networks rendered in terms of such themes – can simplify an otherwise confusing tangle of biological relationships. We show this by mapping the S. cerevisiae network in terms of two specific network themes. CONCLUSION: Significantly enriched motifs in an integrated S. cerevisiae interaction network are often signatures of network themes, higher-order network structures that correspond to biological phenomena. Representing networks in terms of network themes provides a useful simplification of complex biological relationships

Chemotherapy for Nasopharyngeal Cancer: Neoadjuvant, Concomitant, and/or Adjuvant

© 2015, Springer Science+Business Media New York. Nasopharyngeal cancers are unique among other head and neck cancers, not only in epidemiology and histological characteristics, but also on treatment strategies as well. Radiotherapy is the primary treatment due to its radiosensitivity. In locally advanced stages, concurrent chemoradiation has been established to be effective to eradicate the disease and improve survival, in favor of radiotherapy alone. While increasing studies have explored the potential benefit of adding more chemotherapy to the concurrent regimen, whether adjuvant or neoadjuvant, it is generally agreed that proper patient selection is needed to stratify high-risk groups to intensify treatment and to optimize the disease outcome. Future studies are ongoing, possibly with the addition of biomarkers such as EBV DNA for risk group stratification. Refinement of patient groups that should be selected for combined modality treatment in stage II disease is also warranted.Link_to_subscribed_fulltex