CosinorJ

A software tool to quantifying the circadian oscillatory profiles

Olivia Mariani, Daniel Schmitter and Daniel Sage at the Biomedical Image Group (BIG), EPFL, Switzerland
Tiphaine Mannic and Charna Dibner at the Division of Endocrinology, Diabetes, Nutrition and Hypertension, University Hospital of Geneva, Switzerland

Outline

CosinorJ is a Java software tool to quantify circadian oscillatory gene expression profiles. It fits a cycling function to accurate estimate of the period, mesor, accrophase and amplitude of any rhythm signals of chronobiology.

Reference

T. Mannic, P. Meyer, F. Triponez, M. Pusztaszeri, G. Le Martelot, O. Mariani, D. Schmitter, D. Sage, J. Philippe, C. Dibner, "Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules," The Journal of Clinical Endocrinology & Metabolism, vol. 98, no. 11, pp. 4446-4456, November 2013.

Software

Requirements

The software package CosinorJ is written in Java. It run on any platform supporting Java. First, check if your machine can run Java applications, if not visit the page https://www.java.com/ to get a free copy of Java.

Download

CosinorJ.jar

Current Version: 30.06.2015

How to use

Start the application by double-clicking on Cosinor.jar
Open a file: File »: Open. The file format is defined below. It is allowed to open several files-
Select the file to analyze by enabling the checkbox
Click on the button "Fit All" to search a good fit for all the data (It could take few minutes)
Click on the button "Fit One" to fit the curve selected in the file droplist
Save the two resulting files see below: File »: Save...

Fitted parameters

Resulting files

1. PROJECT_NAME_Result.csv, contains the parameters of the fitted curve:

Amplitude constant (A)
Amplitude slope [h] (D)
Amplitude slope [rad] (D)
Mesor (C)
Period [h] (T)
Period [rad] (T)
Phase [h] (p)
Phase [rad] (p)
Acrophase
Root Mean Square Error (RMSE): Measure of the difference between the measured data and the fitted curve. sqrt((y-y')^2/n_y)
Mean Relative Error (MRE): Represents the relative difference between the measured data and fitted curve. |y-y'|/y
Chi2: Minimized error in the least-square sense. Chi2 = 0 if the fitted curve perfectly matches the measured data
Chi2 goodness: Goodness of the chi2 fit. Will be smaller with an increasing number of measures
Relative chi2: Cummulative chi2 error over all the time points
Std error amplitude: Standard error of the amplitude parameter
Std error amplitude slope: Standard error of the amplitude slope parameter
Std error mesor: Standard error of the mesor parameter
Std error period: Standard error of the period parameter
Std error phase: Standard error of the phase parameter

2. PROJECT_NAME_ResultData.csv contains the measurements and fitted data values per time point per gene.

Data format

CosinorJ requires a CSV file as input, with the first column being the time in hours, the first row the gene names, and the corresponding data filling the corresponding columns and rows. See examples below.

Bmal.csv

	Time,H,NB,NPTC3,NFTC2,NPDTC,PTC multi
0h,0.808975472,0.839571028,0.948669802,0.615649355,0.509257889,0.956714925
6h,0.644775107,0.69432057,0.624755471,0.516721767,1.206765754,0.858759793
12h,1.274946404,0.900825581,0.915069881,0.871767294,1.083236922,1.185963492
18h,1.34939565,1.242463635,1.083275185,1.042510097,0.80567264,1.022979865
24h,0.989792218,0.884714588,0.901657542,0.665246354,0.454604671,0.689041368
30h,0.606840597,0.630371977,0.54279673,0.449548068,0.937613236,0.478928073
36h,0.679723814,0.5560416,0.857372815,0.441549712,1.443084022,0.642948828

Cry1.csv

	Time,H,NB,NPTC3,NFTC2,NPDTC,PTC multi
0h,0.808975472,0.839571028,0.948669802,0.615649355,0.509257889,0.956714925
6h,0.644775107,0.69432057,0.624755471,0.516721767,1.206765754,0.858759793
12h,1.274946404,0.900825581,0.915069881,0.871767294,1.083236922,1.185963492
18h,1.34939565,1.242463635,1.083275185,1.042510097,0.80567264,1.022979865
24h,0.989792218,0.884714588,0.901657542,0.665246354,0.454604671,0.689041368
30h,0.606840597,0.630371977,0.54279673,0.449548068,0.937613236,0.478928073
36h,0.679723814,0.5560416,0.857372815,0.441549712,1.443084022,0.642948828

Conditions of use

You are free to use this software for research purposes, but you should not redistribute it without our consent.
In addition, we expect you to include adequate citations and acknowledgments whenever you present or publish results that are based on it.