Difference between revisions of "BIN-EXPR-GEO"
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== Abstract == | == Abstract == | ||
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Introduction to the contents and utilities of the GEO mRNA expression database. | Introduction to the contents and utilities of the GEO mRNA expression database. | ||
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== This unit ... == | == This unit ... == | ||
=== Prerequisites === | === Prerequisites === | ||
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You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources: | You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources: | ||
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*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control. | *<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control. | ||
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You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
*[[BIN-EXPR-Analysis|BIN-EXPR-Analysis (Expression Analysis)]] | *[[BIN-EXPR-Analysis|BIN-EXPR-Analysis (Expression Analysis)]] | ||
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=== Objectives === | === Objectives === | ||
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This unit will ... | This unit will ... | ||
* ... introduce the contents and utilities of the GEO mRNA expression database. | * ... introduce the contents and utilities of the GEO mRNA expression database. | ||
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=== Outcomes === | === Outcomes === | ||
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After working through this unit you ... | After working through this unit you ... | ||
* ... can access GEO, find expression datasets and analyze them with the provided tools. | * ... can access GEO, find expression datasets and analyze them with the provided tools. | ||
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=== Deliverables === | === Deliverables === | ||
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*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit. | *<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit. | ||
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these. | *<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these. | ||
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]]. | *<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]]. | ||
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== Contents == | == Contents == | ||
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{{Smallvspace}} | {{Smallvspace}} | ||
The transcriptome is the set of a cell's mRNA molecules. The transcriptome originates from the genome, mostly, that is, and it results in the proteome, again: mostly. RNA that is {{WP|Transcription (genetics)|transcribed}} from the genome is not yet fit for translation but must be processed: {{WP|RNA splicing|splicing}} is ubiquitous<ref>Strictly speaking, splicing is an {{WP|Eukaryote|eukaryotic}} achievement, however there are examples of splicing in {{WP|Prokaryote|prokaryotes}} as well.</ref> and in addition {{WP|RNA editing}} has been encountered in many species. Some authors therefore refer to the ''exome''—the set of transcribed {{WP|exons}}— to indicate the actual coding sequence. | The transcriptome is the set of a cell's mRNA molecules. The transcriptome originates from the genome, mostly, that is, and it results in the proteome, again: mostly. RNA that is {{WP|Transcription (genetics)|transcribed}} from the genome is not yet fit for translation but must be processed: {{WP|RNA splicing|splicing}} is ubiquitous<ref>Strictly speaking, splicing is an {{WP|Eukaryote|eukaryotic}} achievement, however there are examples of splicing in {{WP|Prokaryote|prokaryotes}} as well.</ref> and in addition {{WP|RNA editing}} has been encountered in many species. Some authors therefore refer to the ''exome''—the set of transcribed {{WP|exons}}— to indicate the actual coding sequence. | ||
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Revision as of 01:12, 6 January 2018
The NCBI GEO Gene Expression database
Keywords: NCBI GEO: finding and analyzing expression profiles
Contents
Abstract
Introduction to the contents and utilities of the GEO mRNA expression database.
This unit ...
Prerequisites
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
- The Central Dogma: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
You need to complete the following units before beginning this one:
Objectives
This unit will ...
- ... introduce the contents and utilities of the GEO mRNA expression database.
Outcomes
After working through this unit you ...
- ... can access GEO, find expression datasets and analyze them with the provided tools.
Deliverables
- Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
- Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
- Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
Contents
The transcriptome is the set of a cell's mRNA molecules. The transcriptome originates from the genome, mostly, that is, and it results in the proteome, again: mostly. RNA that is transcribed from the genome is not yet fit for translation but must be processed: splicing is ubiquitous[1] and in addition RNA editing has been encountered in many species. Some authors therefore refer to the exome—the set of transcribed exons— to indicate the actual coding sequence.
Microarray technology — the quantitative, sequence-specific hybridization of labelled nucleotides in chip-format — was the first domain of "high-throughput biology". Today, it has largely been replaced by RNA-seq: quantification of transcribed mRNA by high-throughput sequencing and mapping reads to genes. Quantifying gene expression levels in a tissue-, development-, or response-specific way has yielded detailed insight into cellular function at the molecular level, with recent results of single-cell sequencing experiments adding a new level of precision. But not all transcripts are mapped to genes: we increasingly realize that the transcriptome is not merely a passive buffer of expressed information on its way to be translated into proteins, but contains multiple levels of complex, regulation through hybridization of small nuclear RNAs[2].
NCBI's GEO database stores expression data and experiment matadata and makes it publicly available.
Task:
Read the article below for a comprehensive current introduction to the GEO database. But do some active reading in the sense that you actually access the GEO database and follow along on the Web with what is being described in the paper.
| Clough & Barrett (2016) The Gene Expression Omnibus Database. Methods Mol Biol 1418:93-110. (pmid: 27008011) |
|
[ PubMed ] [ DOI ] The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome-protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/. |
Notes
- ↑ Strictly speaking, splicing is an eukaryotic achievement, however there are examples of splicing in prokaryotes as well.
- ↑
(2015) The noncoding explosion. Nat Struct Mol Biol 22:1. (pmid: 25565024) Jarvis & Robertson (2011) The noncoding universe. BMC Biol 9:52. (pmid: 21798102)
Self-evaluation
If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2017-11-10
Version:
- 1.0
Version history:
- 1.0 First live version
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
