GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.

BACKGROUND: Biomedical researchers often want to explore pathogenesis and pathways regulated by abnormally expressed genes, such as those identified by microarray analyses. Literature mining is an important way to assist in this task. Many literature mining tools are now available. However, few of them allows the user to make manual adjustments to zero in on what he/she wants to know in particular. RESULTS: We present our software program, GenCLiP (Gene Cluster with Literature Profiles), which is based on the methods presented by Chaussabel and Sher (Genome Biol 2002, 3(10):RESEARCH0055) that search gene lists to identify functional clusters of genes based on up-to-date literature profiling. Four features were added to this previously described method: the ability to 1) manually curate keywords extracted from the literature, 2) search genes and gene co-occurrence networks related to custom keywords, 3) compare analyzed gene results with negative and positive controls generated by GenCLiP, and 4) calculate probabilities that the resulting genes and gene networks are randomly related. In this paper, we show with a set of differentially expressed genes between keloids and normal control, how implementation of functions in GenCLiP successfully identified keywords related to the pathogenesis of keloids and unknown gene pathways involved in the pathogenesis of keloids. CONCLUSION: With regard to the identification of disease-susceptibility genes, GenCLiP allows one to quickly acquire a primary pathogenesis profile and identify pathways involving abnormally expressed genes not previously associated with the disease.

Mathematical model of phosphatidylinositol-4,5-bisphosphate hydrolysis mediated by epidermal growth factor receptor generating diacylglycerol.

Phosphatidylinositol-4,5-bisphosphate (PIP2) is hydrolyzed in response to the tyrosine phosphorylation of the epidermal growth factor receptor (EGFR) and plays an important role in regulating cell proliferation and differentiation through the generation of second messengers diacylglycerol (DAG) and trisphosphate inositol (IP3) which lead to the activation of protein kinase C (PKC) and increased levels of intracellular calcium, respectively. In the paper, a mathematical model was established to simulate the accumulation of DAG due to PIP2 hydrolysis mediated by EGFR. Molecular mechanisms between DAG, PIP2, EGFR and phosphatidylinositol transfer protein (PITP) were explained successfully, and positive cooperativity which existed between phospholipase C-gamma1 (PLC-gamma1) and PIP2 was also explained. In the model the effects of parameters on simulation of PIP2 hydrolysis were analyzed and the efficacies of some molecular intervention strategies were predicted. To test the coherence between the model and the biological response to epidermal growth factor (EGF) in cells, the levels of DAG and the tyrosine phosphorylation-EGFRs in NIH3T3 mouse embryonic fibroblast (MEF) were determined by biochemical experiments which showed that the accumulation of DAG was a sigmoidal function of phosphorylation-EGFR concentration, and the consistency between the mathematical model and experimental results was confirmed. In brief, this mathematical model provided a new idea for the further study of the dynamic change of biological characteristics in inositol phospholipid hydrolysis, predicting the efficacy of molecular intervention and the relationship between the metabolisms of inositol phospholipid and other signal transduction pathways.

Validation of the TRANSTEK TMB-988 wrist blood pressure monitor for home blood pressure monitoring according to the International protocol.

OBJECTIVE: To evaluate the accuracy of the TRANSTEK TMB-988 for home blood pressure monitoring according to the International Protocol of the Working Group on Blood Pressure Monitoring of the European Society of Hypertension. METHOD: Device evaluation was done in 33 participants (16 men and 17 women) with a mean±SD age of 58.2±11.8 years (range 32-80 years). Blood pressures [systolic blood pressure (SBP) and diastolic blood pressure (DBP)] were sequentially measured using mercury sphygmomanometer (by two trained observers) and alternately measured by the test device (by one supervisor). RESULTS: In phase 1, a total of 33, 42, and 44 of SBP differences and 40, 43 and 45 of DBP differences were within 5, 10 and 15 mmHg, respectively. In phase 2.1, 68, 93, and 97 of SBP differences and 75, 92 and 98 of DBP differences were within 5, 10 and 15 mmHg. The difference between the device and the mean of two observers was -0.6±5.0 mmHg for SBP and 0.2±5.8 mmHg for DBP, respectively. In phase 2.2, for SBP and DBP, respectively, 27 and 26 participants had at least two of their three differences with 5 mmHg, and there were two participants who did not have any difference within 5 mmHg for both SBP and DBP. CONCLUSION: The TRANSTEK TMB-988 successfully passed all the phases and is recommended for home use in adults.