Wnts are the major ligands responsible for activating Wnt signaling pathway through binding to Frizzled proteins (Fzd) as the receptors. Among these ligands, Wnt2 plays the main role in the tumorigenesis of several human cancers especially colorectal cancer (CRC). Therefore, it can be considered as a potential drug target.The aim of this study was to identify potential drug candidates ...

MOTIVATION Pathway Hunter Tool (PHT), is a fast, robust and user-friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002 Graphs, Network and Algorithm. Springer-Verlag, Berlin)...

Long-term potentiation (LTP) is a biological process of learning and memory after a high-frequency train of electrical stimulations. By binding of brain-derived neurotrophic factor (BDNF) to Tropomyosin receptor kinase B (TrKB) receptors in postsynaptic neurons, tyrosine kinase Fyn is bound to these receptors and hereby plays a mediating role to binding and activation of N-methyl-D-aspartic aci...

PURPOSE PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying featur...

The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, comp...

Human immunodeficiency virus (HIV) affects millions of people across the globe. Despite the introduction of powerful anti-viral therapies, one factor confounding viral elimination is the ability of HIV to remain latent within the host genome. Here, we perform a network analysis of the viral reactivation process using human gene expression profiles and curated databases of both human-human and h...

artemisia annua is still the only commercial source of artemisinin. to date, a number of biochemical and molecular studies about artemisinin’s biosynthetic pathway have been carried out. in metabolic engineering approach, isolation and characterization of promoters leads to an understanding of which cis-acting elements are responsible for the regulation of gene expression. dbr2 is a key enzyme ...

MOTIVATION Pathway or gene set analysis has been widely applied to genomic data. Many current pathway testing methods use univariate test statistics calculated from individual genomic markers, which ignores the correlations and interactions between candidate markers. Random forests-based pathway analysis is a promising approach for incorporating complex correlation and interaction patterns, but...