Difference between revisions of "Gene Regulatory Circuits Project"
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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). | 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 [[BIO_systems_project|'''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 | + | In a [[BIO_systems_project|'''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. |
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| − | + | You will work with the following two student annotated systems: | |
| + | |||
| + | * [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Sabrina.ge/BCH411-project CNTF mediated Astrocyte activation] (10 genes) | ||
| + | * [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Bagherig/Project HDL particle clearance] (17 genes) | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | {{task|1 = | ||
| + | |||
| + | * 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: | ||
| + | ** [http://www.regnetworkweb.org/ '''RegNetwork'''] | ||
| + | ** [http://www.grnpedia.org/trrust/ '''TRRUST'''] | ||
| + | ** [https://genome.ucsc.edu '''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 provide useful information.) | ||
| + | |||
| + | |||
| + | * For each of the three resources define: | ||
| + | ** which transcription factors are annotated to each gene (note: write R or python code to process downloaded data) | ||
| + | ** which of those transcription factors are enriched for the system. | ||
| + | |||
| + | }} | ||
| + | |||
| − | |||
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==Deliverables== | ==Deliverables== | ||
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| − | + | ||
| + | ;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. Focus on the workflow. I should be able to take your report and ask a summer student to proceed annotating additional systems using the workflow you have defined. | ||
| + | |||
| + | ;Journal | ||
| + | :Document your activities in your Course Journal. | ||
| + | |||
| + | ;Progress | ||
| + | :Each Tuesday before noon, email me a brief progress update. | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | The last day to submit material is Tuesday, April 3. at midnight. '''No extension will be possible.''' | ||
| + | |||
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==Evaluation== | ==Evaluation== | ||
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| − | + | ||
| + | The entire project will be worth 80 marks. | ||
| + | |||
| + | * Your Annotations will be worth '''40 marks''', they will be evaluated according to my [[ABC-Rubrics#General|'''General''' marking rubrics.]] | ||
| + | |||
| + | * Your Scripts (R or python) will be worth '''10 marks''', they will be evaluated according to my [[ABC-Rubrics#Code|'''Code''' marking rubrics.]] | ||
| + | |||
| + | * Your Final Report will be worth '''20 marks''', it will be evaluated according to my [[ABC-Rubrics#Documentation|'''Documentation''' marking rubrics.]] | ||
| + | |||
| + | * Your Course Journal will be evaluated for worth '''10 marks''' according to my [[ABC-Rubrics#Course_Journal|'''Journal''' marking rubrics.]] | ||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | Note: since no extension will be possible for this project, material that is submitted past the due date cannot be considered. Please get started right away, and aim to finish well before the deadline. | ||
| + | |||
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<references /> | <references /> | ||
| + | <div class="alert"> | ||
| + | Caution: be meticulous in carefully defining and citing all of your sources. Omission of source information will be considered plagiarism. Reference absolutely everything! | ||
| + | </div> | ||
{{Vspace}} | {{Vspace}} | ||
Latest revision as of 03:28, 6 March 2018
Gene Regulatory Circuits
A BCB420 Special Project
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 provide useful information.)
- For each of the three resources define:
- which transcription factors are annotated to each gene (note: write R or python code 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. Focus on the workflow. I should be able to take your report and ask a summer student to proceed annotating additional systems using the workflow you have defined.
- Journal
- Document your activities in your Course Journal.
- Progress
- Each Tuesday before noon, email me a brief progress update.
The last day to submit material is Tuesday, April 3. at midnight. No extension will be possible.
Evaluation
The entire project will be worth 80 marks.
- Your Annotations will be worth 40 marks, they will be evaluated according to my General marking rubrics.
- Your Scripts (R or python) will be worth 10 marks, they will be evaluated according to my Code marking rubrics.
- Your Final Report will be worth 20 marks, it will be evaluated according to my Documentation marking rubrics.
- Your Course Journal will be evaluated for worth 10 marks according to my Journal marking rubrics.
Note: since no extension will be possible for this project, material that is submitted past the due date cannot be considered. Please get started right away, and aim to finish well before the deadline.
Notes
Caution: be meticulous in carefully defining and citing all of your sources. Omission of source information will be considered plagiarism. Reference absolutely everything!
