BioPAN
Biosynthetic pathway analysis from lipidomics dataset
Description
BioPAN combines lipid profiles (lipidome), with current knowledge of lipid metabolism using a statistical functionality. BioPAN compares two biological conditions to identify systematic changes in lipid pathways at different levels (lipid subclass and lipid molecular species). Lipid pathway changes are presented in an interactive graphical display and results of most likely active or supressed lipid transforming genes modulated by an experiment are provided. BioPAN provides a biological insight of mammalian reaction information to generated hypotheses that can be experimentally tested.
Technical Information
License:
GNU GPL 3.0 (Academic)
GUI:
Yes
CLI:
No
Desktop client:
No
Web platform:
Yes
Input formats:
CSV
Output formats:
SVG,
PNG,
JPEG,
JSON,
For graphs content
TXT
For graphs content and for results tables
Platforms:
MacOS,
Linux,
Windows
Programming languages:
R
Source code repository:
Download / Web-service link:
Documentation and user guide:
Training datasets:
Publications:
PMID:33564392
Tasks
7.3)
Pathway and network solutions
Input style:
Multiple annotations and IDs (automatically converted via LipidLynxX plug-in)
Additional requirements:
Quantitative (absolute/relative) lipidomics data
Available biopathways:
Main lipid biosynthesis and remodelling pathways (e.g. de novo lipogenesis, de novo sphingolipids, and cholesterol biosynthesis).
Covered species:
Mammals (the user can make use of biochemistry and lipid metabolism to check if the obtained genes are conserved across species).
Pathway editing:
NA
Pathway mapping strategy:
Altered pathway reactions are classified as activated/supressed with direction shown; based on a Z-score, which considers the mean and standards deviation of lipid quantities. Z-scores are used to rank the reactions and whether a particular reaction is significantly changed between control and a treated condition.
Links to related genes proteins:
Predicted genes
Links to other databases:
LIPID MAPS LMSD
Data visualization:
Interactive pathway graphs comprising regulated lipids and reactions; available at lipid subclass, lipid molecular species, and fatty acid levels