VisANT Features

VisANT is a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways. It features:

• Network Module Enrichment Analysis (NMEA) to detect phenotypic difference between two data sets (e.g. gene expression of disease v.s. normal), try out NMEA for cell cycle pathway in P53 mutant data. NMEA is deigned to find functional modules that inform phenotypic differences. For the current release, such differences are usually transcriptional activity. NMEA by default will be performed for all non-embedded metanodes. The function is available under the Expression menu and requires the input of expression data (sample expression data). When execution of NMEA is complete, the nodes in the modules will be colored according to their enrichment scores 

• GO Term Enrichment Analysis (GOTEA) to find the over-represented GO terms in network modules. The function is available under the Metagraph menu and requires genes in the modules being annotated. A quick example can be tried here. An example with the step-by-step macros is illustrated here to predict the function of KEGG cell cycle pathway using both hyper-geometry test and GOTEA. The macro file can be downloaded here. each step is explained in detail in the comments.

• Batch mode automates database queries for interactions, name resolutions, and GO annotations, more ...

• Batch mode to automate batch processes in the background and to handle large-scale networks with millions nodes and edges. A test case has been carried out with 15,447 nodes and 1,722,708 edges as shown below,  more information can be found here