# James P. McDonald Week 9

### From OpenWetWare

(Difference between revisions)

(Bonferroni correction question) |
Current revision (20:47, 2 April 2013) (view source)m (→ZAP1: fixed grammar) |
||

(4 intermediate revisions not shown.) | |||

Line 3: | Line 3: | ||

*Each time point had 4 replicates. | *Each time point had 4 replicates. | ||

*The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula. | *The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula. | ||

- | *Genes with p value <0.05 | + | *Genes with p value < 0.05 |

**t15: 771 | **t15: 771 | ||

**t30: 1150 | **t30: 1150 | ||

Line 9: | Line 9: | ||

**t90: 364 | **t90: 364 | ||

**t120: 375 | **t120: 375 | ||

- | *Genes with p value <0.01 | + | *Genes with p value < 0.01 |

**t15: 189 | **t15: 189 | ||

**t30: 340 | **t30: 340 | ||

Line 15: | Line 15: | ||

**t90: 73 | **t90: 73 | ||

**t120: 75 | **t120: 75 | ||

- | *Genes with p value <0.001 | + | *Genes with p value < 0.001 |

**t15: 20 | **t15: 20 | ||

**t30: 35 | **t30: 35 | ||

Line 21: | Line 21: | ||

**t90: 7 | **t90: 7 | ||

**t120: 3 | **t120: 3 | ||

- | *Genes with p value <0.0001 | + | *Genes with p value < 0.0001 |

**t15: 4 | **t15: 4 | ||

**t30: 6 | **t30: 6 | ||

Line 27: | Line 27: | ||

**t90: 0 | **t90: 0 | ||

**t120: 0 | **t120: 0 | ||

- | *Genes still significantly changed at p <0.05 after Bonferroni correction | + | *Genes still significantly changed at p < 0.05 after Bonferroni correction |

**t15: 1 | **t15: 1 | ||

**t30: 2 | **t30: 2 | ||

Line 33: | Line 33: | ||

**t90: 0 | **t90: 0 | ||

**t120: 0 | **t120: 0 | ||

- | * | + | *Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? (time = t60) |

+ | **786 | ||

+ | *Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? (time = t60) | ||

+ | **824 | ||

+ | *Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? (time = t60) | ||

+ | **755 | ||

+ | *How many have an average log fold change of < -0.25 and p < 0.05? (time = t60) | ||

+ | **763 | ||

+ | *NSR1 Average Fold Change | ||

+ | **t15: 1.45 | ||

+ | **t30: 1.57 | ||

+ | **t60: 1.82 | ||

+ | **t90: -0.81 | ||

+ | **t120: -0.03 | ||

+ | *NSR1 P value | ||

+ | **t15: 0.0481 | ||

+ | **t30: 0.0023 | ||

+ | **t60: 0.0020 | ||

+ | **t90: 0.0680 | ||

+ | **t120: 0.8963 | ||

+ | *NSR1 expression is significantly changed at p < 0.05 at t15, t30, and t60. It is more significant at p < 0.01 at t30 and t60. | ||

+ | *The gene with the lowest p value at t120 is PNS1 (YOR161C). | ||

+ | **Function: Its function is unknown but it has similarity to Torpedo californica (tCTL1p) which is postulated to be a choline transporter. | ||

+ | **Since the function of the gene is unknown, it is difficult to say why the cell is changing this gene's expression under cold shock. It does say that the gene is similar to a choline transporter so maybe under cold shock the cell does not need to transport choline but focus on surviving, and therefore shuts down the activity of this gene. | ||

{{James P. McDonald}} | {{James P. McDonald}} | ||

[[Category:BIOL398-03/S13]] | [[Category:BIOL398-03/S13]] |

## Current revision

## Contents |

## Microarray Data Analysis

### ZAP1

- Each time point had 4 replicates.
- The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula.
- Genes with p value < 0.05
- t15: 771
- t30: 1150
- t60: 1610
- t90: 364
- t120: 375

- Genes with p value < 0.01
- t15: 189
- t30: 340
- t60: 592
- t90: 73
- t120: 75

- Genes with p value < 0.001
- t15: 20
- t30: 35
- t60: 80
- t90: 7
- t120: 3

- Genes with p value < 0.0001
- t15: 4
- t30: 6
- t60: 8
- t90: 0
- t120: 0

- Genes still significantly changed at p < 0.05 after Bonferroni correction
- t15: 1
- t30: 2
- t60: 0
- t90: 0
- t120: 0

- Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? (time = t60)
- 786

- Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? (time = t60)
- 824

- Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? (time = t60)
- 755

- How many have an average log fold change of < -0.25 and p < 0.05? (time = t60)
- 763

- NSR1 Average Fold Change
- t15: 1.45
- t30: 1.57
- t60: 1.82
- t90: -0.81
- t120: -0.03

- NSR1 P value
- t15: 0.0481
- t30: 0.0023
- t60: 0.0020
- t90: 0.0680
- t120: 0.8963

- NSR1 expression is significantly changed at p < 0.05 at t15, t30, and t60. It is more significant at p < 0.01 at t30 and t60.
- The gene with the lowest p value at t120 is PNS1 (YOR161C).
- Function: Its function is unknown but it has similarity to Torpedo californica (tCTL1p) which is postulated to be a choline transporter.
- Since the function of the gene is unknown, it is difficult to say why the cell is changing this gene's expression under cold shock. It does say that the gene is similar to a choline transporter so maybe under cold shock the cell does not need to transport choline but focus on surviving, and therefore shuts down the activity of this gene.

## Class Links

- James P. McDonald
- BIOL 398 Home Page
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 11 Assignment
- Week 12 Assignment
- Week 13 Assignment
- Week 14 Assignment

## Journal Entries and Assignments

- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 8
- Class Journal Week 9
- Class Journal Week 11
- Class Journal Week 12
- Class Journal Week 13
- Class Journal Week 14
- James P. McDonald Week 2
- James P. McDonald Week 3
- James P. McDonald Week 4
- James P. McDonald Week 5
- James P. McDonald Week 6
- James P. McDonald Week 8
**James P. McDonald Week 9**- James P. McDonald Week 11
- James P. McDonald Week 12
- James P. McDonald Week 13
- James P. McDonald Week 14