Sarah Carratt 4.05.11: Difference between revisions
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=Review of Homework= | =Review of Homework= | ||
*Homework found on Openwetware: [[Sarah Carratt: Week 11]] | *Homework found on Openwetware: [[Sarah Carratt: Week 11]] | ||
*Original data file can be uploaded on [http:// | *Original data file can be uploaded on [http://lionshare.lmu.edu Lionshare] with permission from both [[User:Kam D. Dahlquist | Dr. Kam D. Dahlquist, Ph.D.]] and myself. For more information, [[Special:Emailuser/Sarah Carratt|email me through OpenWetWare]]. | ||
==Timepoints== | ==Timepoints== | ||
*Schade = 0m, 10m, 30m, 120m, 12h, 60h | *Schade = 0m, 10m, 30m, 120m, 12h, 60h | ||
Line 21: | Line 21: | ||
**Comparing fold changes and p.values | **Comparing fold changes and p.values | ||
==Most Significantly Changed Genes== | ==Most Significantly Changed Genes== | ||
*NSR1 | *NSR1 = commonly accepted | ||
* | *NOP8 = gene from homework | ||
=Moving Forward= | |||
==Hierachical Clustering== | |||
*Each row is gene | |||
*Each column is chip | |||
*If a group of genes is all on or off, maybe regulated by same transciption factor...why? Logic of the cell says cell needs all turned on at once because they are all part of same process. | |||
==Gene Ontology (GO)== | |||
*Description of genes, think of this as a process of categorizing genes | |||
*Yeast, flies, mouse, ect. databases combined to organize biological vocabulary so they are consistant in papers, get rid of excess synonyms. | |||
*Written definitions of terms in 3 categories. | |||
**Biological process | |||
**Molecular function | |||
**Cellular component | |||
*Genes are asssigned to terms by model organism databases | |||
=Navigation Guide= | |||
==Individual Assignments== | |||
{| style="width: 50em" | |||
| [[Sarah Carratt: Week 2]] | |||
| [[Sarah Carratt: Week 6]] | |||
| [[Sarah Carratt: Week 11]] | |||
|- | |||
| [[Sarah Carratt: Week 3]] | |||
| [[Sarah Carratt: Week 7]] | |||
| [[Sarah Carratt: Week 12]] | |||
|- | |||
| [[Sarah Carratt: Week 4]] | |||
| [[Sarah Carratt: Week 8]] | |||
| [[Sarah Carratt: Week 13]] | |||
|- | |||
| [[Sarah Carratt: Week 5]] | |||
| [[Sarah Carratt: Week 9]] | |||
| [[Sarah Carratt: Week 14]] | |||
|} | |||
==Class Assignments== | |||
{| style="width: 50em" | |||
| [[BIOL398-01/S11:Class Journal Week 1|Shared Journal: Week 1]] | |||
| [[BIOL398-01/S11:Class Journal Week 6|Shared Journal: Week 6]] | |||
| [[BIOL398-01/S11:Class Journal Week 11|Shared Journal: Week 11]] | |||
|- | |||
| [[BIOL398-01/S11:Class Journal Week 2|Shared Journal: Week 2]] | |||
| [[BIOL398-01/S11:Class Journal Week 7|Shared Journal: Week 7]] | |||
| [[BIOL398-01/S11:Class Journal Week 12|Shared Journal: Week 12]] | |||
|- | |||
| [[BIOL398-01/S11:Class Journal Week 3|Shared Journal: Week 3]] | |||
| [[BIOL398-01/S11:Class Journal Week 8|Shared Journal: Week 8]] | |||
| [[BIOL398-01/S11:Class Journal Week 13|Shared Journal: Week 13]] | |||
|- | |||
| [[BIOL398-01/S11:Class Journal Week 4|Shared Journal: Week 4]] | |||
| [[BIOL398-01/S11:Class Journal Week 9|Shared Journal: Week 9]] | |||
| [[BIOL398-01/S11:Class Journal Week 14|Shared Journal: Week 14]] | |||
|- | |||
| [[BIOL398-01/S11:Class Journal Week 5|Shared Journal: Week 5]] | |||
| [[BIOL398-01/S11:Class Journal Week 10|Shared Journal: Week 10]] | |||
|} | |||
==Class Notes== | |||
{| style="width: 50em" | |||
| [[Media:Biomath Notes 1.1.doc|Sarah Carratt_1.18.11]] | |||
| [[Media:Biomath Notes 6.doc|Sarah Carratt_2.3.11]] | |||
| [[Media:Biomath Notes 11.doc|Sarah Carratt_2.22.11]] | |||
|- | |||
| [[Media:Biomath Notes 2.doc|Sarah Carratt_1.20.11]] | |||
| [[Media:Biomath Notes 7.doc|Sarah Carratt_2.8.11]] | |||
| [[Media:Biomath Notes 12.doc|Sarah Carratt_2.24.11]] | |||
|- | |||
| [[Media:Biomath Notes 3.doc|Sarah Carratt_1.25.11]] | |||
| [[Media:Biomath Notes 8.doc|Sarah Carratt_2.10.11]] | |||
| [[Media:Biomath Notes 13.doc|Sarah Carratt_3.1.11]] | |||
|- | |||
| [[Media:Biomath Notes 4.doc|Sarah Carratt_1.27.11]] | |||
| [[Media:Biomath Notes 9.doc|Sarah Carratt_2.15.11]] | |||
| [[Media:Biomath Notes 14.doc|Sarah Carratt_3.3.11]] | |||
|- | |||
| [[Media:Biomath Notes 5.doc|Sarah Carratt_2.1.11]] | |||
| [[Media:Biomath Notes 10.doc|Sarah Carratt_2.17.11]] | |||
| [[Media:Biomath Notes 15.doc|Sarah Carratt_3.8.11]] | |||
|} | |||
==Internal Links== | |||
{| style="width: 50em" | |||
| [[BIOL398-01/S11|BIOL398-01/S11:Assignments]] | |||
| [[BIOL398-01/S11:People]] | |||
| [[User:Sarah Carratt|BIOL398-01/S11:Sarah Carratt]] | |||
|} | |||
[[Category:BIOL398-01/S11]] | |||
[[Category: Biomathematical Modeling]] |
Latest revision as of 10:11, 5 April 2011
Review of Homework
- Homework found on Openwetware: Sarah Carratt: Week 11
- Original data file can be uploaded on Lionshare with permission from both Dr. Kam D. Dahlquist, Ph.D. and myself. For more information, email me through OpenWetWare.
Timepoints
- Schade = 0m, 10m, 30m, 120m, 12h, 60h
- wt and Dgln3 = 15, 30, 60, 90, 120
Resaon for Statistics
- Is this computed ratio a true difference or a fluxuation due to noise?
- T statistic to P value
- Things that are part of the equation...
- size of effect, aka, is it a big difference?
- amount of variation
- number of replicates
- Schade (confusing)
- wt (4,5,4,5,5)
- Dgln3 (4,4,4,4,4)
P Values
- more than 300 p values significant by chance = part of problem, use as guide only
- multiple testing problem corrected by:
- Bonferroni corrections
- Comparing fold changes and p.values
Most Significantly Changed Genes
- NSR1 = commonly accepted
- NOP8 = gene from homework
Moving Forward
Hierachical Clustering
- Each row is gene
- Each column is chip
- If a group of genes is all on or off, maybe regulated by same transciption factor...why? Logic of the cell says cell needs all turned on at once because they are all part of same process.
Gene Ontology (GO)
- Description of genes, think of this as a process of categorizing genes
- Yeast, flies, mouse, ect. databases combined to organize biological vocabulary so they are consistant in papers, get rid of excess synonyms.
- Written definitions of terms in 3 categories.
- Biological process
- Molecular function
- Cellular component
- Genes are asssigned to terms by model organism databases
Individual Assignments
Class Assignments
Class Notes
Internal Links
BIOL398-01/S11:Assignments | BIOL398-01/S11:People | BIOL398-01/S11:Sarah Carratt |