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Project Page: GRNsight Gene Page Project

GRNsight

Project Schedule Checklist

[x]Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
[ ]Group Report (.doc, .docx or .pdf file)
[ ]Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
[ ]Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
[ ]Code (GitHub pull request)
[ ]Each team should coordinate in performing a final integration and integration testing iteration (see Coder milestone for details) which the Interaction and Integration team then submits to the original
[ ]GRNsight GitHub repository as a single, unified pull request from the class project’s fork
[ ]Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
[ ]Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
[ ]PowerPoint of screenshots of stem results (.pptx)
[ ]Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
[ ]YEASTRACT "rank by TF" results (.xlsx)
[ ]GRNmap input workbook (with network adjacency matrix, .xlsx)
[ ]GRNmap output workbook (.xlsx)
[ ]Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

Data Analyst

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.