Difference between revisions of "Data Analysis"
From LMU BioDB 2017
(Initial stub-out of data analysis guild page.) |
Kdahlquist (talk | contribs) (laid out milestones) |
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{{GRNsight Gene Page Project Links}} | {{GRNsight Gene Page Project Links}} | ||
| − | + | GRNsight is a web application and service for visualizing models of gene regulatory networks. The role of the Data Analyst will be to complete the analysis of the Dahlquist Lab microarray dataset that was begun in the [[Week 8]] and [[Week 10]] assignments so that new insights can be gleaned by visualizing the data with GRNsight. The Data Analysts are the end-users of the software, ultimately determining if the new features are useful to them in their biological interpretation of the cold shock experiments. | |
== Guild Members == | == Guild Members == | ||
| − | * Page Design: | + | * Page Design: Mary (dCIN5 dataset) |
| − | * Gene Database APIs: | + | * Gene Database APIs: Dina (dGLN3 dataset) |
| − | * JASPAR API: | + | * JASPAR API: Antonio (dZAP1 dataset) |
| − | * Interaction and Integration: | + | * Interaction and Integration: Emma (wild type dataset) |
== Milestones == | == Milestones == | ||
| Line 14: | Line 14: | ||
The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together. | The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together. | ||
| − | + | === Milestone 1: Annotated Bibliography === | |
| + | |||
| + | * For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast. | ||
| + | |||
| + | === Milestone 2: Journal Club Presentation === | ||
| + | |||
| + | * For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21. | ||
| + | |||
| + | === Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight === | ||
| + | |||
| + | * For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically: | ||
| + | *# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary. | ||
| + | *# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]). | ||
| + | *# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem. | ||
| + | *# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network. | ||
| + | *# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network. | ||
| + | *# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight]. | ||
| + | * As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features. | ||
{{GRNsight Gene Page Project Links}} | {{GRNsight Gene Page Project Links}} | ||
[[Category:Group Projects]] | [[Category:Group Projects]] | ||
Revision as of 22:03, 7 November 2017
| GRNsight Gene Page Project Links | |||||||
|---|---|---|---|---|---|---|---|
| Overview | Deliverables | Reference Format | Guilds | Project Manager | Quality Assurance | Data Analysis | Coder |
| Teams | Page Desiigner | Lights, Camera, InterACTION! | Gene hAPI | JASPAR the Friendly Ghost | |||
GRNsight is a web application and service for visualizing models of gene regulatory networks. The role of the Data Analyst will be to complete the analysis of the Dahlquist Lab microarray dataset that was begun in the Week 8 and Week 10 assignments so that new insights can be gleaned by visualizing the data with GRNsight. The Data Analysts are the end-users of the software, ultimately determining if the new features are useful to them in their biological interpretation of the cold shock experiments.
Contents
Guild Members
- Page Design: Mary (dCIN5 dataset)
- Gene Database APIs: Dina (dGLN3 dataset)
- JASPAR API: Antonio (dZAP1 dataset)
- Interaction and Integration: Emma (wild type dataset)
Milestones
The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together.
Milestone 1: Annotated Bibliography
- For the Week 11 assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.
Milestone 2: Journal Club Presentation
- For the Week 12 assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.
Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight
- For Week 14 and Week 15, the Data Analysts will review and complete the microarray data analysis begun with the Week 8 and Week 10 assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
- Review the ANOVA results from Week 8 for accuracy, making corrections if necessary.
- If corrections were made to the ANOVA results, re-running stem (Week 10).
- Using the YEASTRACT Database to determine which transcription factors are candidates for regulating the genes in a cluster from stem.
- Using the YEASTRACT Database to develop a candidate gene regulatory network.
- Using the GRNmap software to model the gene regulatory network.
- Visualizing the results with GRNsight.
- As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.
| GRNsight Gene Page Project Links | |||||||
|---|---|---|---|---|---|---|---|
| Overview | Deliverables | Reference Format | Guilds | Project Manager | Quality Assurance | Data Analysis | Coder |
| Teams | Page Desiigner | Lights, Camera, InterACTION! | Gene hAPI | JASPAR the Friendly Ghost | |||
