Lauren's Capstone Research

lkelly9 commented 5 years ago

This issue contains updates on Lauren's capstone research

lkelly9 commented 5 years ago

https://github.com/lkelly9/DahlquistLab/blob/master/data/Spring%202019/Edge_deletion_consolidated_data_LK.xlsx

Link to excel sheet containing consolidated data/heatmaps

lkelly9 commented 5 years ago

abstract_2019.docx

Attached is an initial draft of my abstract for the conference at UC Irvine/the research symposium.

lkelly9 commented 5 years ago

Outline_Thesis.docx

Attached is the initial draft of my thesis outline. Please let me know if I need to adjust the formatting/elaborate anywhere.

kdahlquist commented 5 years ago

Got it. I'll have some comments for you on Tuesday.

kdahlquist commented 5 years ago

@lkelly9--congratulations on getting into Baylor!

Here is a summary of what we just talked about:

here is where @bklein7 put the heat map workbook: https://github.com/kdahlquist/DahlquistLab/blob/master/data/Spring2017/15-gene_networks_analysis/Regulatory-Relationships_Six-Networks_BK20170313.xlsx
- when you make the heat map, order the edge deletions in order from smallest LSE:minLSE to largest to highlight quadrants in the heat map that correspond to the smallest and largest errors
create normalized plots of the production rates (which you basically already did)
do an edge-by-edge analysis (brute-force) where you write a summary paragraph about each edge deletion that analyzes the following. This will give you a deep dive into the results and should suggest some overall patterns for you.
- LSE:minLSE
- production rates
- b's
- notable differences in MSE:minMSE (note that displaying the expression vs simulated data on nodes gives a visual about this
- some kind of explanation of why you see what you see. There is likely interplay between production rates and weights, for example.
Maybe some kind of 3D plot of the MSE:minMSE values where the x and y axes are genes and strains and the height of the bars is the MSE:minMSE values. We can ask @bengfitzpatrick about this.

kdahlquist commented 5 years ago

what is the in-degree of the genes that have whacked out production rates? What is the pattern?
What is time course of expression look like for those genes? Are they not expressed or huge change in expression? Is there a big drop in expression?
make a bar chart for the b's; b is a summary of the thresholds
plot production rate vs. b? they might produce close to collinearity, could cancel each other out? leave out for when be is zero because cause problems
order heat map rows by positive to negative weights
fitness landscape

lkelly9 commented 5 years ago

Results_Thesis_LK.docx

Attached is the draft of my results section. I had some trouble finding where to cite references, so there are only a few in-text citations at the moment.

kdahlquist commented 5 years ago

Got it!

Kam D. Dahlquist, Ph.D. Professor of Biology Loyola Marymount University

kdahlquist commented 5 years ago

@lkelly9, I pinned a copy of your results with comments to the bulletin board outside my door. So far so good, I'm going to have to think about the results some more to think about what this means. Maybe we need a tally of results that make sense based on the network structure and results that don't make sense, like when parameter values change for genes not in any way connected to the edge that was deleted.

lkelly9 commented 5 years ago

Discussion_Thesis.docx

Attached is the draft of my discussion section. As I was writing, I realized a need for more literature that relates to MSE:minMSE and optimized expression changes, so for the sake of time, that will be addressed in later drafts.

kdahlquist commented 5 years ago

Hi,

Got it!

Best, Dr. D

At 04:59 PM 3/1/2019, you wrote:

Discussion_Thesis.docxhttps://github.com/kdahlquist/GRNmap/files/2921575/Discussion_Thesis.docx

Attached is the draft of my discussion section. As I was writing, I realized a need for more literature that relates to MSE:minMSE and optimized expression changes, so for the sake of time, that will be addressed in later drafts.

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lkelly9 commented 5 years ago

LK_symposium_2019.pptx Draft of URS talk

lkelly9 commented 5 years ago

LK_symposium_2019.pptx updated version of URS talk

lkelly9 commented 5 years ago

Introduction_Thesis_LK.docx

Draft of thesis introduction section

final version of URS talk following shortly

lkelly9 commented 5 years ago

LK_symposium_2019.pptx

Final version of URS talk