Stuart G. Baker, 2014
Introduction
This program fits biologically relevant response curves in comparative analysis of the two gene expression experiments involving same genes but under different scenarios and at least 12 responses. The program outputs gene pairs with biologically relevant response curve shapes including flat, linear, sigmoid, hockey stick, impulse and step curves.
Reference
Baker, S.G. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry. Microarrays 2014, 3, 39-51.
https://www.mdpi.com/2076-3905/3/1/39
Requirement
Mathematica Version 8 or later.
To run example in manuscript
| copy | all files into some folder called "FOLDER" |
|---|---|
| start | a new Mathematica session |
| type | SetDirectory["FOLDER"] |
| type | << mfit.m |
| type | MFit[datasetm1,datasetm2,NewFitQ->True] |
To try on your own data,
| type | MFit[dataset1,dataset2,options] |
|---|
Options
| NewFitQ | TRUE | Fits new data or retrieves data from previous fit |
|---|---|---|
| NewNameCORE | "mfit" | Name prepended to data set name for new fit |
| StoredNameCORE | "mfit" | Name prepended to data set name for retrieving fit (usually the same as NewNameCORE) |
| ModelSetQ | full+poly | full+poly" fits flat, line, sigmoid, double sigmoid, generalized double sigmoid, and polynomial curves of degree 3, 5, 7 (requires 7 fitted points and recommended with at least 14 time points |
| full" fits flat, line, sigmoid, double sigmoid, generalized double sigmoid (requires 7 fitted points and recommended with at least 14 time points). | ||
| "reduced" fits flat, line, sigmoid, double sigmoid curves (requires 6 fitted points and recommended with at least 12 time points) | ||
| SplitType | alternating | "alternating" which fits every other point or "custom" |
| SplitFitSet | {1,4,7,10,13} | Applies only for SplitType->"custom", ranked points for fitting the model |
| ShowPlot | FALSE | Shows plots for gene pairs with biologically relevant curves |
| ShowReport | FALSE | Report on gene pairs with biologically relevant curves |
| ShowSummary | TRUE | Shows summary results |
| ShowRPEAIC | FALSE | Show relationship of RPE to AIC |
dataset={data, geneid, genename, times, xname, yname, plotname, dataname},
| data | matrix of responses, where rows indicate genes and columns indicate times |
|---|---|
| geneid | a list of gene identification numbers corresponding to data rows |
| genename | a list of gene names corresponding to data rows |
| times | list of observation times |
| xname | name of horizontal axis on plot |
| yname | name of vertical axis on plot |
| plotname | name of data set for plot |
| dataname | name of data set for storing files |
File Contents
Download All (ZIP, 7.6 MB)
| File name | Description |
|---|---|
| mfit.m | main program and calls all programs |
| mfitpair.m | compute results for model pairs |
| mfitsupport.m | support functions |
| mfitform.m | compute heterochrony and heterometry |
| mfitkey.m | model selection |
| mfitplot.m | compute plots |
| mfitplotoverlay.m | overlay plot |
| mfitplotside.m | side-by-side plot |
| mfitreport.m | report lists of genes by model pair |
| mfitcore.m | core fitting program |
| mfitdiagnostic.m | plots RPE vesus AIC |
| mfitdata.m | generate data in correct format from following files |
| mfitrawdata1.m | raw data for frog example 1 (X.laevis) |
| mfitrawdata2.m | raw data for frog example 2 (X.tropicalis) |
| mfitgenename.m | gene names for frog examples |
Notes on raw data for example
The files mfitrawdata1.m and mfitrawdata2.m are structured as follows: There 11299 rows correspond to genes. The 126 = 14 x 9 columns are ordered from left to right as 14 times for replicate 1 from sample 1, 14 times for replicate 2 from sample 1, 14 times for replicate 3 from sample 1, 14 times for replicate 1 from sample 2, 14 times for replicate 2 from sample 2, 14 times for replicate 3 from sample 2, 14 times for replicate 1 from sample 3, 14 times for replicate 2 from sample 3, 14 times for replicate 3 from sample 3. The 14 times are 1.5, 5, 7, 9, 13.25, 14.75, 16.25, 18.25, 19.75, 21.75, 24.75, 27.5, 35, 44.5. The file mfitgenename.m is structured as follows. The first 11299 rows correspond to the genes in the raw data (there are extra rows). The 3 columns are row number, gene ID, and gene name (or nothing if no gene name).
Disclaimer
This code is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the NCI or the individual developers be liable for any claim, damages or other liability of any kind. Use of this code by recipient is at recipient's own risk. NCI makes no representations that the use of the code will not infringe any patent or proprietary rights of third parties.
Last updated: March 18, 2014