Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature

Background: Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis. Results: We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality. Conclusions: CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/.Statistic

Heart Failure Due to Severe Hypertrophic Cardiomyopathy Reversed by Low Calorie, High Protein Dietary Adjustments in a Glycogen Storage Disease Type IIIa Patient

In glycogen storage disease type III (GSD III), deficiency of the debranching enzyme causes storage of an intermediate glycogen molecule (limit dextrin) in the affected tissues. In subtype IIIa hepatic tissue, skeletal- and cardiac muscle tissue is affected, while in subtype IIIb only hepatic tissue is affected. Cardiac storage of limit dextrin causes a form of cardiomyopathy, which resembles primary hypertrophic cardiomyopathy on cardiac ultrasound. We present a 32-year-old GSD IIIa patient with severe left ventricular hypertrophy (LVH) first diagnosed at the age of 8 years. LVH remained stable and symptomless until the patient presented at age 25 years with increasing dyspnea, fatigue, obesity, and NYHA (New York Heart Association) functional classification two out of four. Dyspnea, fatigue, and obesity progressed, and at age 28 years she was severely symptomatic with NYHA classification 3+ out of 4. On echocardiogram and electrocardiogram, the LVH had progressed as well. Initially, she was rejected for cardiac transplantation because of severe obesity. Therefore, a 900 cal, high protein diet providing 37% of total energy was prescribed during 4 months on which 10 kg weight loss was achieved. However, her symptoms as well as the electrocardiographic and echocardiographic LVH indices had improved dramatically – ultimately deferring cardiac transplantation. Thereafter, the caloric intake was increased to 1,370 cal per day, and the high protein intake was continued providing 43% of total energy. After 3 years of follow-up, the patient remains satisfied with reasonable exercise tolerance and minor symptoms in daily life