Gene Regulatory Circuits Project
Gene Regulatory Circuits
This project concerns the application of various information sources to define gene-regulatory circuits in molecular systems.
Context
The definition of molecular systems needs to take their functional components into account, as well as the components that create, assemble and disassemble these functional components. Among the latter, gene regulatory circuits play a particularly important role since they control when a particular system is constituted and becomes active. We can distinguish constitutive circuits (almost always on), developmental circuits (on only in certain cell-types), and regulated circuits (on in response to specific environmental signals or in ordered sequence of events such as the cell cycle).
In a previous set of BCH441 projects, students have curated biological systems, essentially based on Gene Ontology Annotations. In this special project the task is to define the gene regulatory circuits that operate on a select set of those systems, using three different information resources.
Task
You will work with the following two student annotated systems:
- CNTF mediated Astrocyte activation (10 genes)
- HDL particle clearance (17 genes)
Task:
- Access the two project pages and familiarize yourself with the contents.
- Add a section "Gene regulation" to both pages
- Evaluate the following three resources to identify transcription factors which target the genes that were annotated to this system and write your results into the respective two project pages:
- RegNetwork
- TRRUST
- The UCSC Genome Browser (Use the CRCh37/hg19 human genome reference; Encode TF binding, Encode Regulation, and ORegAnno are three tracks that are likely to have useful data.)
- For each of the three resources define:
- which transcription factors are annotated to each gene (note: write a script to process downloaded data)
- which of those transcription factors are enriched for the system
Deliverables
- Annotations
- Submit your annotations on the respective two project pages on the Student Wiki.
- Scripts
- Submit all scripts on a subpage of your User page on the Student Wiki;
- Report
- Write a brief final report about your experiences, your progress, and your results.
- Journal
- Document your activities in your Course Journal.
- Progress
- Each Tuesday before noon, email me a brief progress update.
Evaluation
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Notes
