321
edits
EdwardRyanTalatala Week 6: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
→Methods: added last part of methods
(→Results: uploaded new GRNmap workbook) |
(→Methods: added last part of methods) |
||
| Line 114: | Line 114: | ||
=== Dynamical Systems Modeling of your Gene Regulatory Network === | |||
Now you are ready to run the model and analyze the results. The software we will use is called GRNmap, which stands for Gene Regulatory Network Modeling and Parameter Estimation. It is written in MATLAB and can be run from code or run as a stand-alone executable if you don't have MATLAB installed. However, it can only be run in Windows, not on Macs. | |||
* To run GRNmap from code, you must have MATLAB R2014b installed on your computer. | |||
*# Download the GRNmap v1.10 code from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page]. | |||
*#* [https://github.com/kdahlquist/GRNmap/archive/v1.10.zip This is a direct link to start downloading (81 MB).] | |||
*# Unzip the file. (Right-click, 7-zip > Extract here) | |||
*# Launch MATLAB R2014b. | |||
*# Open GRNmodel.m, which will be in the directory that you unzipped GRNmap-1.10 > matlab | |||
*# Click the Run button (green "play" arrow). | |||
*# You will be prompted to select your input workbook. | |||
<!--* To run the GRNmap executable, you must have administrator rights on your computer for installing software. | |||
** Download the GRNmap v1.10 executable from the [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap Downloads page]. | |||
** [https://github.com/kdahlquist/GRNmap/releases/download/v1.10/GRNmap-v1.10.zip This is a direct link to start downloading (688 MB)]--> | |||
*# You will see an optimization diagnostics graphic that shows the progress of the estimation. | |||
*# When the run is over, expression plots will display. | |||
*# Output .xlsx and .mat files will be saved in the same folder as your input folder, along with .jpg files containing the optimization diagnostic and individual expression plots. Save these files. | |||
*# Note that if you need to run GRNmap again, you should not use the same directory for the input file. Currently, GRNmap will overwrite previous output. | |||
* You can upload your output .xlsx file into [http://dondi.github.io/GRNsight/ GRNsight] to visualize the results! | |||
=== Analyzing the Modeling Results === | |||
In class on February 28/March 5, we will take a look at the modeling results and discuss how to analyze them. We will discuss: | |||
* LSE/minLSE ratio | |||
* MSE's and expression plots for individual genes in relation to their ANOVA p values | |||
* Visualization of the weighted graph with GRNsight | |||
* Making bar charts to give a graphical representation of the parameter values. | |||
Based on these analyses, you will propose a some additional ''in silico'' experiments that you can do with the model. You will report out your results in a research presentation in Week 9. Some ideas are: | |||
* For our initial runs, we estimated all three parameters w, P, and b. | |||
** How do the modeling results change if P is instead fixed and w and b are estimated? | |||
** How do the modeling results change if b is fixed and w and P are estimated? | |||
** How do the modeling results change if P ''and'' b are fixed, and only w is estimated? | |||
* For our initial runs, we included all three microarray datasets, wt, ''Δgln3'', and ''Δhap4''. | |||
** What happens to the results if we base the estimation on just two strains (wt + one deletion strain)? | |||
** What happens to the results if we base the estimation on just the wt strain data? | |||
* When viewing the modeling results in GRNsight, you may determine that one or more genes in the network does not appear to be doing much. | |||
** What happens to the modeling results if you delete this gene from the network and re-run the model (remember you will have to delete references to this gene in all worksheets of the input file). | |||
* You also might think that a particular edge (regulatory relationship) is not needed. What happens if you delete that edge? | |||
* What happens if you include the t90 and t120 expression data? | |||
==Results== | ==Results== | ||
