# Nika Vafadari Week 11

## Electronic Lab Notebook Week 11

### Purpose

To understand the analyzation process of raw microarray data, which can identify the role of specific transcription factors/ genes in controlling the response to various environmental stresses, such as cold shock, by looking at the changes in gene expression.

### Methods

- Strain: dGLN3
- File Name: BIOL398-05_Spring2017_master_microarray_dGLN3
- Time Points: 15, 30, 60, 90, 120
- Replicates per time point: 4

#### Background

This is a list of steps required to analyze DNA microarray data.

- Quantitate the fluorescence signal in each spot
- Calculate the ratio of red/green fluorescence
- Log
_{2}transform the ratios- Steps 1-3 have been performed for you by the GenePix Pro software (which runs the microarray scanner).

- Normalize the ratios on each microarray slide
- Normalize the ratios for a set of slides in an experiment
- Steps 4-5 was performed for you using a script in R, a statistics package (see: Microarray Data Analysis Workflow)
- You will perform the following steps:

- Perform statistical analysis on the ratios
- Compare individual genes with known data
- Steps 6-7 are performed in Microsoft Excel

- Pattern finding algorithms (clustering)
- Map onto biological pathways
- We will use software called STEM for the clustering and mapping

- Identifying regulatory transcription factors responsible for observed changes in gene expression
- Dynamical systems modeling of the gene regulatory network
- The modeling will be performed in MATLAB

#### Statistical Analysis Part 1: ANOVA

The purpose of the witin-stain ANOVA test is to determine if any genes had a gene expression change that was significantly different than zero at * any* timepoint.

- Create a new worksheet, naming it dGLN3_ANOVA
- Copy the first three columns containing the "MasterIndex", "ID", and "Standard Name" from the "Master_Sheet" worksheet for your strain and paste it into your new worksheet. Copy the columns containing the data for your strain and paste it into your new worksheet.
- At the top of the first column to the right of your data, create five column headers of the form dGLN3_AvgLogFC_(TIME) where (TIME) is 15, 30, 60, 90, 120
- In the cell below the dGLN3_AvgLogFC_t15 header, type
`=AVERAGE(`

- Then highlight all the data in row 2 associated with (STRAIN) and t15, press the closing paren key (shift 0),and press the "enter" key.
- This cell now contains the average of the log fold change data from the first gene at t=15 minutes.
- Click on this cell and position your cursor at the bottom right corner. You should see your cursor change to a thin black plus sign (not a chubby white one). When it does, double click, and the formula will magically be copied to the entire column of 6188 other genes.
- Repeat steps (4) through (8) with the t30, t60, t90, and the t120 data.
- Now in the first empty column to the right of the dGLN3_AvgLogFC_t120 calculation, create the column header (dGLN3_ss_HO.
- In the first cell below this header, type
`=SUMSQ(`

- Highlight all the LogFC data in row 2 for your (STRAIN) (but not the AvgLogFC), press the closing paren key (shift 0),and press the "enter" key.
- In the next empty column to the right of dGLN3_ss_HO, create the column headers dGLN3_ss_(TIME) as in (3).
- Make a note of how many data points you have at each time point for your strain. For most of the strains, it will be 4, but for dHAP4 t90 or t120, it will be "3", and for the wild type it will be "4" or "5". Count carefully. Also, make a note of the total number of data points. Again, for most strains, this will be 20, but for example, dHAP4, this number will be 18, and for wt it should be 23 (double-check).
- In the first cell below the header dGLN3_ss_t15, type
`=SUMSQ(<range of cells for logFC_t15>)-<number of data points>*<AvgLogFC_t15>^2`

and hit enter.- The phrase <range of cells for logFC_t15> should be replaced by the data range associated with t15.
- The phrase <number of data points> should be replaced by the number of data points for that timepoint (either 3, 4, or 5).
- The phrase <AvgLogFC_t15> should be replaced by the cell number in which you computed the AvgLogFC for t15, and the "^2" squares that value.
- Upon completion of this single computation, use the Step (7) trick to copy the formula throughout the column.

- Repeat this computation for the t30 through t120 data points. Again, be sure to get the data for each time point, type the right number of data points, and get the average from the appropriate cell for each time point, and copy the formula to the whole column for each computation.
- In the first column to the right of (STRAIN)_ss_t120, create the column header (STRAIN)_SS_full.
- In the first row below this header, type
`=sum(<range of cells containing "ss" for each timepoint>)`

and hit enter. - In the next two columns to the right, create the headers (STRAIN)_Fstat and (STRAIN)_p-value.
- Recall the number of data points from (13): call that total n.
- In the first cell of the (STRAIN)_Fstat column, type
`=((n-5)/5)*(<(STRAIN)_ss_HO>-<(STRAIN)_SS_full>)/<(STRAIN)_SS_full>`

and hit enter.- Don't actually type the n but instead use the number from (13). Also note that "5" is the number of timepoints and the dSWI4 strain has 4 timepoints (it is missing t15).
- Replace the phrase (STRAIN)_ss_HO with the cell designation.
- Replace the phrase <(STRAIN)_SS_full> with the cell designation.
- Copy to the whole column.

- In the first cell below the (STRAIN)_p-value header, type
`=FDIST(<(STRAIN)_Fstat>,5,n-5)`

replacing the phrase <(STRAIN)_Fstat> with the cell designation and the "n" as in (13) with the number of data points total. (Again, note that the number of timepoints is actually "4" for the dSWI4 strain). Copy to the whole column. - Before we move on to the next step, we will perform a quick sanity check to see if we did all of these computations correctly.
- Click on cell A1 and click on the Data tab. Select the Filter icon (looks like a funnel). Little drop-down arrows should appear at the top of each column. This will enable us to filter the data according to criteria we set.
- Click on the drop-down arrow on your (STRAIN)_p-value column. Select "Number Filters". In the window that appears, set a criterion that will filter your data so that the p value has to be less than 0.05.
- Excel will now only display the rows that correspond to data meeting that filtering criterion. A number will appear in the lower left hand corner of the window giving you the number of rows that meet that criterion. We will check our results with each other to make sure that the computations were performed correctly.

***Note:** Stopped at number 14 due to issues with SS calculations. Got negative SS values due to missing data points. Therefore need to fix issue of missing data points and then redo step 14 on.

**SOLUTION= to fix issue replaced number of data points= n with COUNTA(range of cells for logFC_t15) in every calculation with n in order to take into account missing data points.**

#### Calculate the Bonferroni and p value Correction

- Now we will perform adjustments to the p value to correct for the multiple testing problem. Label the next two columns to the right with the same label, (STRAIN)_Bonferroni_p-value.
- Type the equation
`=<(STRAIN)_p-value>*6189`

, Upon completion of this single computation, use the Step (10) trick to copy the formula throughout the column. - Replace any corrected p value that is greater than 1 by the number 1 by typing the following formula into the first cell below the second (STRAIN)_Bonferroni_p-value header:
`=IF(STRAIN_Bonferroni_p-value>1,1,STRAIN_Bonferroni_p-value)`

, where "STRAIN_Bonferroni_p-value" refers to the cell in which the first Bonferroni p value computation was made. Use the Step (10) trick to copy the formula throughout the column.

#### Calculate the Benjamini & Hochberg p value Correction

- Insert a new worksheet named "(STRAIN)_ANOVA_B-H".
- Copy and paste the "MasterIndex", "ID", and "Standard Name" columns from your previous worksheet into the first two columns of the new worksheet.
- For the following, use Paste special > Paste values. Copy your unadjusted p values from your ANOVA worksheet and paste it into Column D.
- Select all of columns A, B, C, and D. Sort by ascending values on Column D. Click the sort button from A to Z on the toolbar, in the window that appears, sort by column D, smallest to largest.
- Type the header "Rank" in cell E1. We will create a series of numbers in ascending order from 1 to 6189 in this column. This is the p value rank, smallest to largest. Type "1" into cell E2 and "2" into cell E3. Select both cells E2 and E3. Double-click on the plus sign on the lower right-hand corner of your selection to fill the column with a series of numbers from 1 to 6189.
- Now you can calculate the Benjamini and Hochberg p value correction. Type (STRAIN)_B-H_p-value in cell F1. Type the following formula in cell F2:
`=(D2*6189)/E2`

and press enter. Copy that equation to the entire column. - Type "STRAIN_B-H_p-value" into cell G1.
- Type the following formula into cell G2:
`=IF(F2>1,1,F2)`

and press enter. Copy that equation to the entire column. - Select columns A through G. Now sort them by your MasterIndex in Column A in ascending order.
- Copy column G and use Paste special > Paste values to paste it into the next column on the right of your ANOVA sheet.

**Note: Excel file titled NV FIXED 2 BIOL398-05_Spring2017_master_microarray_dGLN3 posted on box in Nika Week 11 folder**

#### Sanity Check: Number of genes significantly changed

Before we move on to further analysis of the data, we want to perform a more extensive sanity check to make sure that we performed our data analysis correctly. We are going to find out the number of genes that are significantly changed at various p value cut-offs.

- Go to your (STRAIN)_ANOVA worksheet.
- Select row 1 (the row with your column headers) and select the menu item Data > Filter > Autofilter (The funnel icon on the Data tab). Little drop-down arrows should appear at the top of each column. This will enable us to filter the data according to criteria we set.
- Click on the drop-down arrow for the unadjusted p value. Set a criterion that will filter your data so that the p value has to be less than 0.05.
**How many genes have p < 0.05? and what is the percentage (out of 6189)?**- 2088 genes with p-value <0.05, 33.74%
**How many genes have p < 0.01? and what is the percentage (out of 6189)?**- 1232 genes with p-value <0.01, 19.91%
**How many genes have p < 0.001? and what is the percentage (out of 6189)?**- 594 genes with p-value <0.001, 9.60%
**How many genes have p < 0.0001? and what is the percentage (out of 6189)?**- 236 genes with p-value <0.0001, 3.81%
- When we use a p value cut-off of p < 0.05, what we are saying is that you would have seen a gene expression change that deviates this far from zero by chance less than 5% of the time.
- We have just performed 6189 hypothesis tests. Another way to state what we are seeing with p < 0.05 is that we would expect to see this a gene expression change for at least one of the timepoints by chance in about 5% of our tests, or 309 times. Since we have more than 309 genes that pass this cut off, we know that some genes are significantly changed. However, we don't know
*which*ones. To apply a more stringent criterion to our p values, we performed the Bonferroni and Benjamini and Hochberg corrections to these unadjusted p values. The Bonferroni correction is very stringent. The Benjamini-Hochberg correction is less stringent. To see this relationship, filter your data to determine the following: **How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?**- 72 genes with p-value <0.05, 1.16%
**How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?**- 1231 genes with p-value <0.05, 19.89%
- In summary, the p value cut-off should not be thought of as some magical number at which data becomes "significant". Instead, it is a moveable confidence level. If we want to be very confident of our data, use a small p value cut-off. If we are OK with being less confident about a gene expression change and want to include more genes in our analysis, we can use a larger p value cut-off.
- Comparing results with known data: the expression of the gene
*NSR1*(ID: YGR159C)is known to be induced by cold shock.Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis.*Find*NSR1*in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?* - The unadjusted p-value is 1.72E-4, Bonferonni-corrected is 1.064, and B-H-corrected is 3.56E-3. The average Log fold change at t=15 is 3.5062, at t=30 is 4.5319, at t=60 is 2.7592, at t=90 is -1.850, and at t=120 is -1.8674.
- We will compare the numbers we get between the wild type strain and the other strains studied, organized as a table. Use this sample PowerPoint slide to see how your table should be formatted.

#### Clustering and GO Term Enrichment with stem

**Prepare your microarray data file for loading into STEM.**- Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
- Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "(STRAIN)_stem" worksheet.
- Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
- Filter the data on the B-H corrected p value to be > 0.05 (that's
**greater than**in this case).- Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.

- Delete all of the data columns
for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).**EXCEPT** - Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
- Save your work. Then use
*Save As*to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.- Note that you should turn on the file extensions if you have not already done so.

**Now download and extract the STEM software.**Click here to go to the STEM web site.- Click on the download link, register, and download the
`stem.zip`

file to your Desktop. - Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item
*7-zip > Extract Here*. - This will create a folder called
`stem`

. Inside the folder, double-click on the`stem.jar`

to launch the STEM program.

- Click on the download link, register, and download the
**Running STEM**- In section 1 (Expression Data Info) of the the main STEM interface window, click on the
*Browse...*button to navigate to and select your file.- Click on the radio button
*No normalization/add 0*. - Check the box next to
*Spot IDs included in the data file*.

- Click on the radio button
- In section 2 (Gene Info) of the main STEM interface window, select
*Saccharomyces cerevisiae (SGD)*, from the drop-down menu for Gene Annotation Source. Select*No cross references*, from the Cross Reference Source drop-down menu. Select*No Gene Locations*from the Gene Location Source drop-down menu. - In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
- In section 4 (Execute) click on the yellow Execute button to run STEM.

- In section 1 (Expression Data Info) of the the main STEM interface window, click on the
**Viewing and Saving STEM Results**- A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
- Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
- Take a screenshot of this window (on a PC, simultaneously press the
`Alt`

and`PrintScreen`

buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.

- Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
- Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
- At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
- Upload these files to OpenWetWare and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).

- For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
- Upload these files to OpenWetWare and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).

- A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
**Analyzing and Interpreting STEM Results**- Select
of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints.**one**Answer the following:**Each member of your group should choose a different profile.**

- Select

**Why did you select this profile? In other words, why was it interesting to you?****Chose profile 45 due to its large size (most number of genes) and clear cold shock/recovery up/down pattern.****How many genes belong to this profile?****440 genes assigned****How many genes were expected to belong to this profile?****30.5 genes expected**Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.**What is the p value for the enrichment of genes in this profile?****p-value=0.00 (significant)**

- Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05.
The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05.**How many GO terms are associated with this profile at p < 0.05?****How many GO terms are associated with this profile with a corrected p value < 0.05?** **262 go terms with p-value <0.05****33 go terms with corrected p-value <0.05**

- Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
- Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
- Note whether the same GO terms are showing up in multiple clusters.

**Look up the definitions for each of the terms at http://geneontology.org. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the Δgln3 and Δswi4 groups)?**- To easily look up the definitions, go to http://geneontology.org.
- Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
- In the results page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
- The definition will be on the next results page, e.g. here.

- Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.

### Results

#### Sanity Check: Number of genes significantly changed=

**How many genes have p < 0.05? and what is the percentage (out of 6189)?**- 2088 genes with p-value <0.05, 33.74%
**How many genes have p < 0.01? and what is the percentage (out of 6189)?**- 1232 genes with p-value <0.01, 19.91%
**How many genes have p < 0.001? and what is the percentage (out of 6189)?**- 594 genes with p-value <0.001, 9.60%
**How many genes have p < 0.0001? and what is the percentage (out of 6189)?**- 236 genes with p-value <0.0001, 3.81%

**How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?**- 72 genes with p-value <0.05, 1.16%
**How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?**- 1231 genes with p-value <0.05, 19.89%

*Find*NSR1*in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?*- The unadjusted p-value is 1.72E-4, Bonferonni-corrected is 1.064, and B-H-corrected is 3.56E-3. The average Log fold change at t=15 is 3.5062, at t=30 is 4.5319, at t=60 is 2.7592, at t=90 is -1.850, and at t=120 is -1.8674.

#### Analyzing and Interpreting STEM Results

**Why did you select this profile? In other words, why was it interesting to you?**- Chose profile 45 due to its large size (most number of genes) and clear cold shock/recovery up/down pattern.
**How many genes belong to this profile?**- 440 genes assigned
**How many genes were expected to belong to this profile?**- 30.5 genes expected
**What is the p value for the enrichment of genes in this profile?**- p-value=0.00 (significant)
**How many GO terms are associated with this profile at p < 0.05?**- 262 go terms with p-value <0.05
**How many GO terms are associated with this profile with a corrected p value < 0.05?**- 33 go terms with corrected p-value <0.05

- Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
- RNA 3'-end processing (GO:0031123): Any process involved in forming the mature 3' end of an RNA molecule.
- Source: GOC:mah http://amigo.geneontology.org/amigo/term/GO:0031123

- organic cyclic compound binding (GO:0097159):Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. **Source: GOC:sjw http://amigo.geneontology.org/amigo/term/GO:0097159
- snRNA processing (GO:0016180): Any process involved in the conversion of a primary small nuclear RNA (snRNA) transcript into a mature snRNA molecule.
- Source: GOC:jl http://amigo.geneontology.org/amigo/term/GO:0016180

- exonucleolytic trimming involved in rRNA processing: (GO:0000459): Exonucleolytic digestion of a pre-rRNA molecule in the process to generate a mature rRNA molecule.
- Source: GOC:curators http://amigo.geneontology.org/amigo/term/GO:0000459

- ribosomal large subunit export from nucleus (GO:0000055): The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
- Source: GOC:mah http://amigo.geneontology.org/amigo/term/GO:0000055

- intracellular organelle (GO:0043229): Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
- Source: GOC:go_curators http://amigo.geneontology.org/amigo/term/GO:0043229

### Data and Files

- Excel file titled NV FIXED 2 BIOL398-05_Spring2017_master_microarray_dGLN3 posted on box in Nika Week 11 folder
- GO List Files
- Gene List Files
- Week 11 Figures Powerpoint
- All posted files also in Nika Week 11 folder on box

### Conclusion

In order to fix the negative SS values for each time point the <number of data points> in `=SUMSQ(<range of cells for logFC_t15>)-<number of data points>*<AvgLogFC_t15>^2`

equation need to be adjusted in order to take into account missing data points. For example, each time point has approximately 300 genes with missing data points. For these we would have to take into account the number of data points actually present and enter it into <number of data points>. However, manually doing this for each time point will take a long period of time. Therefore, a solution must be created that somehow takes into account the missing data points to solve this issue because with negative SS values the correct p values cannot be solved for.

- Updated Conclusion: By analyzing the microarray data we were able to determine the number of genes with statistically significant data in terms of changes in mRNA levels, thus indicating their potential involvement in the early response to cold shock within yeast. In addition, we were able to determine that certain genes may play a larger role in controlling this response and that different clusters of genes may work together in a gene regulatory network in order to control the response to cold shock.

### Acknowledgments

- Methods copied and pasted from Week 11 Assignment referenced below and altered accordingly to fit data.
- Data for dGLN3 retrieved from box folder provided by Dr. Dahlquist.
- Spoke to my homework partner Conor Keith in class and over text while completing the assignment in order to determine how to fix missing data points.
- Definitions for GO terms copied and pasted directly from http://geneontology.org. Sources linked next to definitions.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
**Nika Vafadari 13:44, 28 March 2017 (EDT)**:

### References

- Dahlquist, Kam D. (2017) BIOL398-05/S17:Week 11. Retrieved from http://www.openwetware.org/wiki/BIOL398-05/S17:Week_11 on 28 March 2017.

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