Network analyst is a web based visual analytics tool for comprehensive profiling, Meta analysis and system-level interpretation of gene expression data which is based on PPI (protein-protein interaction) network analysis and visualization. The first version of Network analyst was launched in 2014; there are various updates attached afterwards based on the community feedback and technology progress. In the latest version users able to perform gene expression for 17 different species and other benefits such as creating cell or tissue-specific PPI networks, gene regulatory networks, gene co-expression networks using systematic review services
After conducting a systematic review, there are three significant steps involved in PPI analysis
Network analyst combines all three steps and provides result via a robust online network visualization framework, the key features of the network analyst from a systematic review paper are
The current version allows analysis and rapid visualization of resulting PPI networks from small to large size (100-1000s nodes)
Program description and methods
There are three significant steps in working of network analyst based on Systematic Review writing
Data processing
Data processing involves
Network construction
Network analyst will give a detailed, high-quality PPI database obtained from InnateDB in the International Molecular Exchange (IME) Consortium. The experimental PPI database is from IntAct, MINT, DIP, BING, and BioGRID. The database consists of 14,775 proteins, 1, 45,995 experimentally confirmed interaction for humans and 5657 proteins, 14,491 interactions for mouse
For every individual protein, a search algorithm is created, which is capable of direct interaction with seed protein. The results utilize to build the default networks. The users advise controlling the number of nodes within 200 to 2000 for practical reasons because larger systems lead to Hairball effect
Hairball effect
When the network becomes large and complex, it suffers from the hairball effect, which significantly affects the practical utilities and uptake. Two steps follow to resolve this issue
Network analysis
There are five significant panels
Network visualization
There are certain events recommended to follow for visualization and these events are carried using the mouse, there are various user-friendly options are available such as
Implementation
The construction of Network analyst interface using java server faces 2.0 technology relies based on visualization is sigma. Js Java script library, backend statistical computation was implemented using R program language, construction of the layout algorithm based on Gephi tool kit, PPI database are stored in Neo4j graph database. The network analyst takes a test with major modern browsers with HTML support such as Google Chrome, Mozilla Firefox and Microsoft Internet Explorer
Limitations
The plans include
Biological network analysis is difficult to get insight into complex diseases or biological systems, network analyst easy to use web based tool assist bench researchers and clinicians to perform various tasks and highly user friendly. Pubrica helps you to know about the workflow of network analyst in a detailed manner with writing a systematic literature review for future purposes.