Step 1: Load a data file


Tip

It is possible to try BioPAN using a demonstration file. Select the small dataset to understand how BioPAN works and the complete one to perform a more complex analysis 1.


How to prepare your data

BioPAN takes an input file in CSV (Comma-Separated Values) format containing quantitative data. The file structure should be as follows:

  • The first row contains sample labels (examples: ‘wild_type_1’, ‘wild_type_2’, ‘control_1’, ‘control_2’). The file must contain at least two conditions and two samples per condition.

  • The first column contains lipid species and must include two parts: the abbreviation of the lipid class and the structure (examples: ‘DG 30:0’, ‘DG 30:1’, ‘TG 38:0’, ‘TG 40:0’). The lipid abbreviations are provided in the table below.

  • Columns 2 to n contain molecular concentration quantification.

Abbreviation

Name

MG

Monoacylglycerols

DG

Diradylglycerols

TG

Triradylglycerols

PA

Phosphatidic acid

PS

Glycerophosphoserines

PE

Glycerophosphoethanolamines

PC

Glycerophosphocholines

PG

Glycerophosphoglycerols

S1P

Sphingosine-1-phosphate

SG

Sphingosine

Cer

Ceramide

SM

Sphingomyelin

dhCer

Dihydroceramide

PI

Glycerophosphoinositols

PIP

Glycerophosphoinositol monophosphates

PIP2

Glycerophosphoinositol bis-phosphates

PIP3

Glycerophosphoinositol tris-phosphates

LPA

Lysophosphatidic acid

LPC

Lyso-glycerophosphocholines

LPE

Lyso-glycerophosphoethanolamines

LPI

Lyso-glycerophosphoinositols

LPS

Lyso-glycerophosphoserines

LPG

Lyso-glycerophosphoglycerols

dhSM

Dihydrosphingomyelin

LysoSM

Sphingosylphosphorycholine

CL

Glycerophosphoglycerophosphoglycerols (Cardiolipins)

FA

Fatty acid

FaCoA

Fatty acyl CoA

Note

The class term is used to refer to the lipid names in the above table and the species one will be used to refer to the complex abbreviation/structure. The structure corresponds to the number of carbons and bonds separated by a colon. For example the ‘DG’ class and the ‘DG 30:0’ species.


Following is an example of an input file:

sample,condition1_1,condition1_2,condition2_1,condition2_2
FaCoA 16:1,87.86,146.49,1041.98,1082.65
FaCoA 17:1,71.98,132.04,354.17,399.86
FA 16:0,25006.43,25477.98,32934.67,33290.69
FA 18:0,19293.23,21057.76,19763.06,20423.42
MG 16:0,28.27,29.62,68.35,66.21
MG 16:1,2.19,2.77,5.00,4.78
MG 18:0,61.31,66.28,92.66,94.77
MG 18:1,67.79,60.46,86.52,91.67
MG 18:2,26.96,24.59,36.34,30.88
MG 20:4,0.53,0.84,2.59,4.95
MG 22:6,0.17,0.49,0.53,0.15
DG 30:0,206.01,159.52,497.23,550.29
DG 30:1,109.54,93.64,246.66,228.54
DG 32:0,1539.57,1764.44,3237.65,3941.12
DG 32:1,1954.26,1976.83,2972.57,2845.93
DG 32:2,575.92,632.22,1216.70,1114.80
DG 34:0,98.05,118.36,649.18,910.87
DG 38:3,161.00,234.27,336.16,281.77
DG 38:4,267.23,423.90,240.93,265.23
DG 38:5,263.92,366.24,123.76,92.20
DG 38:6,281.14,340.46,80.82,72.85
DG 40:6,51.70,55.08,19.81,16.89
DG 40:7,70.78,94.36,15.53,27.21
TG 46:1,5.84,11.08,6.90,3.61
TG 46:2,4.65,10.42,4.90,2.87
TG 46:3,1.69,4.28,1.77,0.85
TG 46:4,0.19,0.52,0.27,0.16
TG 48:0,4.72,16.70,11.85,4.09
TG 48:1,30.94,65.80,40.25,21.59
TG 48:2,36.42,79.39,40.63,19.11
TG 48:3,16.73,41.24,14.45,6.31

It is also possible to download the demonstration files 1 to understand the required structure.




Data summary

The data summary table summarises the data extracted from the imported file:

  • Unrecognised species: species whose class is not recognised by BioPAN. The recognised lipid classes are available in the table from the section How to prepare your data.


  • Processed species: species (for fatty acids) or species whose class (for lipids) are recognised by BioPAN and can be involved in reactions. For the fatty acids, it means that there exists in BioPAN at least one reaction involving this species (as a reactant or product) and the other involved species is also present in the input file. For the lipids, it means that there exists in BioPAN at least one reaction involving this class of lipid (as a reactant or produced) and the other involved lipid class is also present in the input file. Be careful, this does not mean that all lipid species will be involved in a reaction (read more: Which lipids and reactions appeared on the graph?).


  • Unprocessed species: species (for fatty acids) or species whose class (for lipids) are recognised by BioPAN but can’t be involved in reactions.

It is possible to see the list of species “un-recognised”, “processed” and “un-processed” by clicking on the associated numbers.

Note

A distinction is made between fatty acids and lipids because BioPAN stores reactions in a different way. It stores the reactions at the level of the species for FA (example FA (16: 0) -> FA (16: 1)) and at the level of the class for lipids (example DG -> PA).




1(1,2)

Oliver Hahn, Lisa F. Drews, An Nguyen et al. A nutritional memory effect counteracts the benefits of dietary restriction in old mice. Nat Metab 1, 1059–1073 (2019).