HDelgadi Week 8

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Digital Lab Notebook

Continuation of classwork on Thursday, October 10th [Microarray Analysis Vibrio cholerae]:

  1. Columns B through Q were selected by highlighting the very first row of these 16 columns. Then scroll down to the last row of these columns. Hold down the 'Shift' button and highlight the entire columns. Click on the format button which is directly below the 'Delete' button under the 'Home' tab.
  2. Click on 'Format Cells' and 'Number' under the 'Number' sub-category.
  3. Select two decimal places and click 'OK'.
  4. Follow steps 1 through 3 with columns R and S and select 4 decimal places rather than 2.
  5. Select columns N through S from the very first cells, not just the values, and right click to press the 'Cut' button.
  6. Select column B by right clicking on B and select "Insert Cut Cell" (the cells should shift 6 columns to the right).
  7. Right click on the B header and click on 'Insert'.
  8. The previous B column should shift one column to the right.
  9. Under the new B header, type 'System Code' into the top cell of this column.
  10. Below 'System Code' write the letter 'N'.
  11. Left click on the letter 'N' and press Ctrl C to copy the letter and proceed to the last cell on the column and hold down the shift button along with left clicking this last cell (the entire column should be highlighted).
  12. Press Ctrl V to paste the letter 'N' to all of the cells of the column.
  13. Select File then Save As and under 'Save as type' select 'Text(Tab-delimited)(*.txt)'. Proceed to clicking OK when the signs of warnings begin to pop-up. The *.txt file is necessary to proceed.
  14. Rename the last tab next to statistics, 'forGenMAPP', since it should have changed to the name of the file when saved as the text file.
  15. Click on the arrow pointing down next to the A header (all columns should be highlighted at this point).
  16. Select the 'Data' tab and click on 'Filter' (drop-down arrows should appear for each column).
  17. Click on the drop-down arrow next to 'Pvalue'.
  18. Click on 'Number Filters'.
  19. Click on 'Custom Filter...' and make sure to select 'less than' on the first drop-down menu and type in 0.05 on the drop-down menu right next to it. Make sure to follow steps 17-19 for the additional respective p-values.
    • Genes that have a p-value <0.05:
      1. 948 out of 5222 values
    • Genes that have a p-value <.01:
      1. 235 out of 5222 values
    • Genes that have a p-value <.001:
      1. 24 out of 5222 values
    • Genes that have a p-value <.0001:
      1. 2 out of 5222 values
  20. (The significance of the p-value <0.05 is that there's a significant difference in the values which demonstrates the change of gene expression)
  21. Change the p-value to less than 0.05.
  22. Click on the drop-down arrow next to "Avg_LogFC_all".
  23. Click on 'Number Filters'.
  24. Click on 'Custom Filter...'.
  25. On the first drop-down menu make sure to select 'greater than' and type in 0 on the drop-down menu next to this one.
  26. Follow steps 22-25 for the respective average log fold changes.
    • Average log fold change greater than zero:
      1. 352
    • Average log fold change less than zero:
      1. 596
    • Average log fold change greater than 0.25:
      1. 339
    • Average log fold change less than -0.25:
      1. 579
The Statistical Analysis for Microarrays (SAM) program was used to determine the statistically significant differences in gene expression. Merrell et al.(2002) used at least a twofold change to determine these genes with statistical significant differences whereas we are using a 20% fold change, so we are using a slightly less fold change.

Class Journal Week 1

Week 1

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Week 2

HDelgadi Week 2

Class Journal Week 3

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Week 4

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HDelgadi Week 4

Week 5

HDelgadi Week 5

Class Journal Week 5

Week 6

HDelgadi Week 6

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Week 7

HDelgadi Week 7

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Week 8

HDelgadi Week 8

Class Journal Week 8

Week 9

HDelgadi Week 9

Class Journal Week 9

Week 10

HDelgadi Week 10

Week 11

Team H(oo)KD

HDelgadi Week 11

HDelgadi Project Notebook

Week 12 Status Report

Week 13 Status Report

Week 15 Status Report

Hilda Delgadillo

HDelgadi (talk) 18:48, 13 October 2013 (PDT)

Digital Lab Notebook 2

Continuation of classwork on Tuesday, October 14th [| BIOL367/F10:GenMAPP and MAPPFinder Protocols]:

  1. Select the top row, click 'Data' and under data click 'Filter'. Upon clicking 'Filter' drop-down arrows will appear for the entire row that was selected.
  2. Click on the drop-down arrow for 'Errors' and make sure to click on the 'Blank' box, so that it is not filled in. Press 'Okay'.
      1. Record the number of errors. For your journal assignment, open the .EX.txt file and use the Data > Filter > Autofilter function to determine what the errors were for the rows that were not converted. Record this information in your individual journal page.
    • 122 Errors found on the.EX.txt file
    • This is what appears in the 'Error' column: 'Gene not found in OrderedLocusNames or any related system'. The last row however, also contains 'No Gene ID' in addition to the previous comment.
      1. It is likely that you will have a different number of errors than your buddy who is using a different version of the Vibrio cholerae Gene Database. Which of you has more errors? Why do you think that is? Record your answers in your journal page.
    • My buddy has more errors,722, since his Gene Database is from the year 2009 whereas mine is from 2010, so there were continuous updates performed on the newer database which corrected the previous errors.
      1. Upload your exceptions file: EX.txt to your wiki page.
    • .EX.txt HD_20131014
      1. Upload your .gex file to your journal entry page for later retrieval.
    • .gex HD_20131014
      1. List the top 10 Gene Ontology terms in your individual journal entry. (DECREASED Criteria for MAPPFinder Procedure)
    • Glucose Catabolic Process
    • Hexose Catabolic Process
    • Glycolysis
    • Monosaccharide Catabolic Process
    • Cytoplasm
    • Alcohol CCtabolic Process
    • Cellular Carbohydrate Catabolic Process
    • Glucose Metabolic Process
    • Protein Folding
    • Hexose Metabolic Process
      1. Compare your list with your buddy who used a different version of the Gene Database. Are your terms the same or different? Why do you think that is? Record your answer in your individual journal entry.
    • My buddy used the Increased Criteria... (FINISH THIS PART)
  3. On the MAPPFinder Browser, type in or copy and paste the name of one of the given genes mentioned by Merrell et al. (2002). I have personally chosen VC0028. Look to the right and you will find the drop-down menu, click on it, and select OrderedLocusNames.
  4. Click on Gene ID Search.
  5. The GO terms associated with this gene is highlighted in blue.
      1. List the GO terms associated with each of those genes in your individual journal. (Note: they might not all be found.) Are they the same as your buddy who is using a different Gene Database? Why or why not?
    • VC0028:
      1. Branched chain family amino acid biosynthetic process
      2. Cellular Amino Acid Biosynthetic process
      3. Metabolic Process
      4. Metal Ion Binding
      5. Iron-Sulfur Cluster Binding
      6. 4 Iron, 4 Sulfur Cluster Binding
      7. Catalytic Activity
      8. Lyase Activity
      9. Dihydroxy-acid Dehydratase Activity
    • VC0941:
      1. Glycine Metabolic Process
      2. L-serine Metabolic Process
      3. One-Carbon Metabolic Process
      4. Cytoplasm
      5. Pyridoxal Phosphate Binding
      6. Catalytic Activity
      7. Transferase Activity
      8. Glycine Hydroxymethyltransferase Activity
    • VC0869
      1. Glutamine Metabolic Process
      2. Purine Nucleotide Biosynthetic Process
      3. 'de novo' IMP Biosynthetic Process
      4. Cytoplasm
      5. Nucleotide Binding
      6. ATP binding
      7. Catalytic Activity
      8. Ligase Activity
      9. Phosphoribosylformyglycinamidine Synthase Activity
    • VC0051:
      1. Purine Nucleotide Biosynthetic Process
      2. 'de novo' IMP Bisynthetic Process
      3. Nucleotide Binding
      4. ATP Binding
      5. Catalytic Activity
      6. Lyase Activity
      7. Carboxy-lyase Activity
      8. Phosphoribosylaminoimidazole
    • VC0647:
      1. mRNA Catabolic Process
      2. RNA Processing
      3. Cytoplasm
      4. Mitochondrion
      5. RNA Binding
      6. 3'-5'-exoribonuclease Activity
      7. Transferase Activity
      8. Nucleotidyltransferase Activity
      9. Polyribonucleotide Nucleotidyltransferase Activity
    • VC0468:
      1. Glutathione Biosynthetic Process
      2. Metal Ion Binding
      3. Nucleotide Binding
      4. ATP Binding
      5. Catalytic Activity
      6. Ligase Activity
      7. Glutathione Synthase Activity
    • VC2350:
      1. Deoxyribonucleotide Catabolic Process
      2. Metabolic Process
      3. Cytoplasm
      4. Catalytic Activity
      5. Lyase Activity
      6. Deoxyribose-phosphate aldolase Activity
    • VCA0583:
      1. Transport
      2. Outer Membrane-Bounded Periplasmic Space
      3. Transporter Activity
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