FASPAD: fast signaling pathway detection
نویسندگان
چکیده
UNLABELLED Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown. AVAILABILITY Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.
منابع مشابه
Interaction of viral oncogenic proteins with the Wnt signaling pathway
It is estimated that up to 20% of all types of human cancers worldwide are attributed to viruses. The genome of oncogenic viruses carries genes that have protein products that act as oncoproteins in cell proliferation and transformation. The modulation of cell cycle control mechanisms, cellular regulatory and signaling pathways by oncogenic viruses, plays an important role in viral carcinogenes...
متن کاملThe Role of Wnt/β-catenin Signaling Pathway in Rat Primordial Germ Cells Reprogramming and Induction into Pluripotent State
Primordial Germ Cells (PGCs) are unipotent precursors of the gametes. PGCs can give rise to a type of pluripotent stem cells in vitro that are called embryonic germ (EG) cells. PGCs can also acquire such pluripotency in vivo and generate teratomas. Under specific culture conditions, PGCs can be reprogrammed to embryonic germ cells which are capable of expression of key pluripotency marker...
متن کاملآنالیز بیان افتراقی ژن ها در پاسخ به عصاره لیپوپلی ساکاریدی ازباکتری اشیرشیاکولای در سلول های اپی تلیال اندومتریوم گاوی
Lipopolysaccharide is a component of outer membrane of gram-negative bacteria involved in the pathogenic process leading to mastitis and metritis in dairy cattle. Additionally, LPS could be caused endometrium inflammation and implantation failure in many animal species. Based on economic importance of these diseases in dairy cattle industry, analysis of differential gene expression (DGE) and al...
متن کاملEupafolin ameliorates lipopolysaccharide-induced cardiomyocyte autophagy via PI3K/AKT/mTOR signaling pathway
Objective(s): Eupafolin, a major active component of Eupatorium perfoliatum L., has anti-inflammatory and anti-oxidant properties. Lipopolysaccharide (LPS) is responsible for myocardial depression. A line of evidences revealed that LPS induces autophagy in cardiomyocytes injury. This study aims to evaluate the effects of eupafolin on LPS-induced cardiomyocyte autophagy...
متن کاملP22: The Association between TrkB Signaling Pathway and NMDARs in LTP Induction
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...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 23 13 شماره
صفحات -
تاریخ انتشار 2007