Alyssa N Gomes Week 12 Journal

This week we are working with YEASTRACT. Our experiment is analyzing the 6000 genes in yeast (targets) and looking more directly at the 250 that code for transcription (regulators). We'll be looking at the binding studies (Lee et al 2002), expression studies, location of DNA binding sites of transcription factors. All three factors have potential for false positives, but binding studies also has a chance for false negative. What we need is a list of transcription factors that help us see the generated gene regulatory network.

Methods

1. Turn on the file extensions
2. By downloading your selected gene profile and downloading it from LionShare, we open it in Excel
3. Going onto the YEASTRACT website, click rank by RF on the left-hand side
4. Paste your list of Gene Symbols from your selected gene profile into the Target Genes window
5. Check the box "Check for all TFs" and make sure all are set on the default (DNA binding plus expression evidence, TF acting as activator or inhibitor) and click Search
6. The p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant"
   • How many transcription factors are green or "significant"? 23

List the "significant" transcription factors on your wiki page, along with the corresponding "% in user set", "% in YEASTRACT", and "p value". Are CIN5, GLN3, HMO1, and ZAP1 on the list? The significant factors are:

• There are 24 transcription factors that are green or "significant"

1. "Significant" transcription factors:
   •  Sfp1p
     • % in user set: 79.53%
     • % in Yeastract: 9.41%
     • p-value: 0
   •  Fkh2p
     • % in user set: 21.44%%
     • % in Yeastract: 15.76%%
     • p-value: 0
   •  Yhp1p
     • % in user set: 38.60%%
     • % in Yeastract: 15.38%%
     • p-value: 0
   •  Yox1p
     • % in user set: 41.13%%
     • % in Yeastract: 14.78%%
     • p-value: 0
   •  Cyc8p
     • % in user set: 0.39%
     • % in Yeastract: 100.00%
     • p-value: 0
   •  YLR278C
     • % in user set: 14.62%%
     • % in Yeastract: 17.65%%
     • p-value: 2.9E-14
   •  Ace2p
     • % in user set: 81.29%%
     • % in Yeastract: 8.73%%
     • p-value: 6.4E-14
   •  Rif1p
     • % in user set: 12.87%
     • % in Yeastract: 18.44%%
     • p-value: 1.25E-13
   •  Msn2p
     • % in user set: 63.35%%
     • % in Yeastract: 9.53%%
     • p-value: 1.69E-13
   •  Cse2p
     • % in user set: 21.25%%
     • % in Yeastract: 14.05%%
     • p-value: 4.67E-13
   •  Stb5p
     • % in user set: 27.88%%
     • % in Yeastract: 12.31%%
     • p-value: 2.672E-12
   •  Ndt80p
     • % in user set: 15.59%%
     • % in Yeastract: 14.08%%
     • p-value: 7.8902E-10
   •  Asg1p
     • % in user set: 8.77%%
     • % in Yeastract: 17.58%%
     • p-value: 4.5755E-09
   •  Msn4p
     • % in user set: 47.95%%
     • % in Yeastract: 9.59%%
     • p-value: 4.6451E-09
   •  Mig2p
     • % in user set: 9.75%%
     • % in Yeastract: 16.29%%
     • p-value: 1.0326E-08
   •  Snf2p
     • % in user set: 40.35%
     • % in Yeastract: 9.95%
     • p-value: 1.0656E-08
   •  Swi5p
     • % in user set: 38.21%
     • % in Yeastract: 10.08%
     • p-value: 1.1467E-08
   •  Spt20p
     • % in user set: 38.01%
     • % in Yeastract: 10.07%
     • p-value: 1.4665E-08
   •  Snf6p
     • % in user set: 46.98%
     • % in Yeastract: 9.13%
     • p-value: 9.9913E-07
   •  Pdr1p
     • % in user set: 28.46%
     • % in Yeastract: 10.15%
     • p-value: 2.4577E-06
   •  Gcr2p
     • % in user set: 25.73%
     • % in Yeastract: 10.09%
     • p-value: 7.7693E-06
   •  Gat3p
     • % in user set: 10.92%
     • % in Yeastract: 12.56%
     • p-value: 1.1840E-05
   •  Mcm1p
     • % in user set: 31.19%
     • % in Yeastract: 9.58%
     • p-value: 1.4349E-05
   • Pop2p
     • % in user set: 5.46%
     • % in Yeastract: 15.64%
     • p-value: 2.8483E-05

• CIN5, GLN3, HMO1, and ZAP1 are not listed on the significant value list, but are listed under the red/insignificant value genes
• 22 Transcription factors appeared on both lists. They were
  •  Ace2p
  •  Asg1p
  •  Cse2p
  •  Cyc8p
  •  Fkh2p
  •  Gcr2p
  •  Mcm1p
  •  Mig2p
  •  Msn2p
  •  Msn4p
  •  Ndt80p
  •  Pdr1p
  •  Rif1p
  •  Sfp1p
  •  Snf2p
  •  Snf6p
  •  Spt20p
  •  Stb5p
  •  Swi5p
  •  Yhp1p
  •  YLR278C
  •  Yox1p
• Both Tessa and I had 15-30 transcription factors so we did not undergo the procedure of adding more
• The Excel sheet with document binding plus expression had 153 edges.
• The Excel Sheet with DNA binding had 33 edges.
• The DNA Binding PLUS Expression had 10 edges.
• The DNA Binding PLUS Expression had 8 edges.
• PPT: Tessa Morris and Alyssa Gomes PPT