Lauren's Capstone Research

[lkelly9]

This issue contains updates on Lauren's capstone research

[lkelly9]

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]

abstract_2019.docx

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

[lkelly9]

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]

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

[kdahlquist]

@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]

• 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]

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]

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

[kdahlquist]

@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]

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]

Hi, Got it! Best, Dr. D At 04:59 PM 3/1/2019, you wrote: Discussion_Thesis.docx<https://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. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub<#420 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AGKhe25QYTIiet7OReFvggRHNoJ-aKt_ks5vSczZgaJpZM4aZFwX>.

[lkelly9]

LK_symposium_2019.pptx
Draft of URS talk

[lkelly9]

LK_symposium_2019.pptx
updated version of URS talk

[lkelly9]

Introduction_Thesis_LK.docx

Draft of thesis introduction section

final version of URS talk following shortly

[lkelly9]

LK_symposium_2019.pptx

Final version of URS talk

[lkelly9]

LK_symposium_2019.pptx
found a typo

[lkelly9]

Materials&Methods_Thesis.docx

Appendix_Thesis.docx

Draft of materials and methods section, as well as the appendix with all of the networks

[lkelly9]

FinalDraft1_Thesis.docx

[lkelly9]

Appendix_Thesis.docx
updated appendix with adjusted networks

[lkelly9]

Abstract_Thesis.docx

Abstract draft

[kdahlquist]

I have made comments on a hard copy of your thesis draft. I've put it in an envelope pinned to the bulletin board outside my office door.