Marmas Week 12/13

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Purpose

The purpose of the project is to analyze the mircroarray data of a previously performed experiment titled "Effects of the Pesticide Thiuram:  Genome-wide Screening of Indicator Genes by Yeast DNA Microarray" (Kitagawa et al., 2002). The group will begin data analysis and organization of deliverables. Milestones are established to keep up with the workload due by the end of the semester. Milestones are can be found on the Fungals Team Page. For the week of November 18th, the Coder/Designer guild will establish a meta data sheet and universalize column header nomenclature.

Account of Activity

Week 11

• A Metadata sheet was made with assistance from Mihir Samdarshi and DeLisa Madere. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
  • Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
  • The Metadata sheet can be found in the Data and Files section of this page.
• To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
  • For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.

Week 12/13

• Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
• A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
• The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
• Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts Kaitlyn and Emma who were more ahead than expected. This has put the project ahead of schedule
  • Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
• Additionally, thanks to Mihir Samdarshi, a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
• Tomorrow (11/26) a database will be started in class to further progress the project

Week12/13 (cont.)

• Database started on MS Access.
• Metadata sheet was separated into references and samples to data.
  • New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
• From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
  • The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
• Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.

Data and Files

Metadata Sheet

• Note: This data sheet is current as of 11:00pm on Nov 25, 2019. Other groups will add information at another time.

Conclusion

The metadata sheet was made alongside Mihir Samdarshi and DeLisa Madere. In conjunction with these two members of the Code/Designer guild to decide on the column headers that would be used for the expression data sheets. Two metadata sheets were made, one consisting of the metadata for each of the examined articles, and one consisting of the sample information. Finally, the database was started in MS Access, but many problems arose, so this will be performed next week.

Acknowledgments

• I would like to acknowledge Dr. Dahlquist for her continous help with this project.
• I would like to acknowledge my group, the FunGals, who are helping with reaching deadlines and understanding the material.
• I would like to acknowledge Mihir Samdarshi for explaining Metadata to me and how to create one.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Marmas (talk) 21:37, 20 November 2019 (PST)

References

• Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. doi: 10.1021/es015705v.