Data Analysis

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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.

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:
    1. Review the ANOVA results from Week 8 for accuracy, making corrections if necessary.
    2. If corrections were made to the ANOVA results, re-running stem (Week 10).
    3. Using the YEASTRACT Database to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of Week 10 that we postponed.
    4. Using the YEASTRACT Database to develop a candidate gene regulatory network (part of Week 10 that we postponed).
    5. Using the GRNmap software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
    6. 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