A systematic review of network analyst - Pubrica
                     A SYSTEMATIC REVIEW OF  
NETWORK ANALYST- A WEB  
BASED BIOINFORMATICS TOOL  
FOR INTEGRATIVE 
VISUALIZATION  OF EXPRESSION 
DATA
An Academic presentation by
Dr. Nancy Agens, Head, Technical Operations, 
Pubrica  Group: www.pubrica.com
Email: [email protected]
Today's Discussion
Outline In-Brief  
Introducti
on
Steps 
Involved in 
PPI Analysis
Key Features of the Network 
Analyst  Program Description and 
Methods  Implementation
Limitatio
ns  
Conclusio
n
In-Brief
In a Systematic Review Writing, the network analyst is a bioinformatics tool  
designed to perform efficient PPI network analysis for data generated from gene 
 expression experiments the following contents explain about the network analyst 
 and their methods, in brief, using the help of pubrica blog. Systematic Review
writing Services for network analysis purposes explain you about the integrative 
 visualization of data expression used in health care sectors
Introduction 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 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
Steps  After c onducting a systematic review, there are 
Involved in  three  significant steps involved in PPI analysis
PPI Analysis To identify the gene or protein of interest which
includes differentially expressed genes, the gene with 
 nucleotide polymorphism and gene-targeted by
microRNAs
The input data is to search and find binary information 
 from a systemized PPI database
There are two complementary approaches performed in 
 the third step, Topology analysis and Module 
analysis
Key Features 
 of the  Supports gene or protein list and single or multiple gene 
Network  expression data.
Analyst
Flexible differential expression and analysis for multiple 
 experimental designs.
Multiple options provide the control of network size.
Interactive network visualization with other features 
 such as facile searching, zooming and highlighting by 
 writing a systematic review.
Contd..
Supports topology, module and shortest-path analysis
Functional enrichment analysis on current selection includes GO, KEGG, Reactome 
 Customize options with layout, edge shapes and node size, colour, visibility
Network features including node deletion and module extraction
The output downloads the network files (edge list, graphML), Images (PNG, PDF) 
 and Topology or Functional analysis result
Program  
Descriptio There are three significant steps in working of network 
n  and   analyst based on Systematic Review writing
Methods
Data processing to identify the genes
Network construction for mapping, building and 
 refining networks
 Network analysis and visualization
1. Data  
Processin
g Data processing involves
Data formats and uploading
Data processing and annotation
Data normalization and analysis
2. Network  
Constructio Network analyst will give a detailed, high-quality PPI 
n  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.
Contd..
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
3. 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
Trimming the default network to retain only those 
 significant nodes or edges
Developing better visualization methods to reduce edge 
 and node occlusion
Contd.
.

4. Network 
 Analysis There are five significant panels
Network explorer- shows all networks created from seed 
 proteins
Hub explorer – consist of detailed information of nodes within 
 the current network
Module explorer -permits the user to decompose the current 
 network into condensed modules
F unctional explorer – permits the user to detect the 
shortest  path between two nodes
5. Network  
Visualizatio There are certain events recommended to follow for  
n visualization and these events are carried using the 
 mouse, there are various user-friendly options are  
available such as
Node display option 
 Network option
Node deletion and 
module extraction
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 n etwork analyst takes a test with major
modern browsers with HTML support such as  
Google Chrome, Mozilla Firefox and Microsoft 
 Internet Explorer
Limitations
PPI database may contain false positives
Unable to determine new interactions which are 
 condition-specific
The plans include
Increase its support for more organisms
More updates in the Visualization field
Conclusion
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.
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