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

Website:
https://lipidmaps.org/biopan

Publications:
PMID:33564392

Documentation:
https://lipidmaps.org/biopan/doc/index.html

Download / Web-service:
https://lipidmaps.org/biopan

Source code:
https://osf.io/pkd6b/files

Programming languages:
R

Platforms:
Windows, linux, macOS

Input formats:
CSV

Output formats:
TXT, JSON, JPEG, PNG, SVG

Interface:
Web platform, GUI

Licence:
GNU GPL 3.0 (academic)

Sections

Section 7.3 — Pathway and Network Solutions

Species covered:
Mammals (user can make use of biochemistry and lipid metabolism to check if obtained genes are conserved across species).

Data visualisation:
Interactive pathway graphs comprising regulated lipids and reactions; available at lipid subclass, lipid molecular species, and fatty acid levels

Visualisation export:
Yes

Pathway mapping:
Pathway reactions are classified as activated or suppressed using a Z-score based on the mean and standard deviation of lipid quantities, used to rank reactions and identify significant changes between control and treated conditions.

Pathway mapping strategy:
Pathway reactions are classified as activated or suppressed using a Z-score based on the mean and standard deviation of lipid quantities, used to rank reactions and identify significant changes between control and treated conditions.

Pathway editing:
No

Available biopathways:
Main lipid biosynthesis and remodelling pathways (e.g. de novo lipogenesis, de novo sphingolipids, and cholesterol biosynthesis).

Links to related genes/proteins:
predicted genes

Up/down regulation on maps:
Yes

Direct projection of identification results:
Yes

Additional requirements:
Quantitative (absolute/relative) lipidomics data