Difference between revisions of "BIN-EXPR-GEO"

From "A B C"
Jump to navigation Jump to search
m (Created page with "<div id="BIO"> <div class="b1"> The NCBI GEO Gene Expression database </div> {{Vspace}} <div class="keywords"> <b>Keywords:</b>  NCBI GEO: finding and anlysing ...")
 
m
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
<div id="BIO">
+
<div id="ABC">
−
  <div class="b1">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
The NCBI GEO Gene Expression database
 
The NCBI GEO Gene Expression database
−
  </div>
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
−
 
+
(NCBI GEO: finding and analyzing expression profiles)
−
  {{Vspace}}
+
</div>
−
 
 
−
<div class="keywords">
 
−
<b>Keywords:</b>&nbsp;
 
−
NCBI GEO: finding and anlysing expression profiles
 
 
</div>
 
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
−
 
 
−
 
 
−
__TOC__
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
{{STUB}}
 
−
 
 
−
{{Vspace}}
 
  
  
 +
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
 +
<div style="font-size:118%;">
 +
<b>Abstract:</b><br />
 +
<section begin=abstract />
 +
Introduction to the contents and utilities of the GEO mRNA expression database.
 +
<section end=abstract />
 
</div>
 
</div>
−
<div id="ABC-unit-framework">
+
<!-- ============================  -->
−
== Abstract ==
+
<hr>
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "abstract" -->
+
<table>
−
...
+
<tr>
−
 
+
<td style="padding:10px;">
−
{{Vspace}}
+
<b>Objectives:</b><br />
−
 
+
This unit will ...
−
 
+
* ... introduce the contents and utilities of the GEO mRNA expression database.
−
== This unit ... ==
+
</td>
−
=== Prerequisites ===
+
<td style="padding:10px;">
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "prerequisites" -->
+
<b>Outcomes:</b><br />
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
+
After working through this unit you ...
−
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:
+
* ... can access GEO, find expression datasets and analyze them with the provided tools.
−
<!-- included from "FND-prerequisites.wtxt", section: "central_dogma" -->
+
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================ -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<li><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.</li>
 +
<li><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.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
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:<br />
 
*<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.
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
+
This unit builds on material covered in the following prerequisite units:<br />
−
You need to complete the following units before beginning this one:
+
*[[BIN-EXPR-Analysis|BIN-EXPR-Analysis (Expression Analysis)]]
−
*[[BIN-NCBI]]
+
*[[BIN-Data_integration|BIN-Data_integration (Data Integration)]]
−
*[[FND-EXPR-Measurements]]
+
<section end=prerequisites />
−
-->
+
<!-- ============================  -->
 +
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
=== Objectives ===
 
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "objectives" -->
 
−
...
 
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
=== Outcomes ===
+
__TOC__
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "outcomes" -->
 
−
...
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Deliverables ===
 
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "deliverables" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
−
*<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.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
Line 76: Line 67:
  
 
=== Evaluation ===
 
=== Evaluation ===
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "evaluation" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
−
:This unit is not evaluated for course marks.
+
<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "contents" -->
+
{{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''&mdash;the set of transcribed {{WP|exons}}&mdash; to indicate the actual coding sequence.
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
== Further reading, links and resources ==
 
−
<!-- {{#pmid: 19957275}} -->
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
−
 
 
−
{{Vspace}}
 
  
 +
'''Microarray technology''' &mdash; the quantitative, sequence-specific hybridization of labelled nucleotides in chip-format &mdash; was the first domain of "high-throughput biology". Today, it has largely been replaced by {{WP|RNA-Seq|'''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<ref>{{#pmid: 25565024}} {{#pmid: 21798102}}</ref>.
  
−
== Notes ==
+
NCBI's GEO database stores expression data and experiment matadata and makes it publicly available.
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "notes" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
−
<references />
 
  
−
{{Vspace}}
+
{{Task|1=
 +
* Navigate to [http://www.ncbi.nlm.nih.gov/geo/ '''the GEO database'''];
 +
* Open the article below;
 +
* Read through the article and explore the features it discusses on the GEO Website.
  
 +
{{#pmid: 27008011}}
  
−
</div>
+
}}
−
<div id="ABC-unit-framework">
 
−
== Self-evaluation ==
 
−
<!-- included from "../components/BIN-EXPR-GEO.components.wtxt", section: "self-evaluation" -->
 
−
<!--
 
−
=== Question 1===
 
  
−
Question ...
 
  
−
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
−
Answer ...
 
−
<div class="mw-collapsible-content">
 
−
Answer ...
 
−
 
−
</div>
 
−
  </div>
 
−
 
−
  {{Vspace}}
 
−
 
−
-->
 
  
 
{{Vspace}}
 
{{Vspace}}
Line 134: Line 92:
  
  
−
{{Vspace}}
+
== Notes ==
−
 
+
<references />
−
 
 
−
<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_ask" -->
 
−
 
 
−
----
 
  
 
{{Vspace}}
 
{{Vspace}}
  
−
<b>If in doubt, ask!</b> 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.
 
−
 
−
----
 
−
 
−
{{Vspace}}
 
  
 
<div class="about">
 
<div class="about">
Line 157: Line 106:
 
:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
−
:2017-08-05
+
:2020-09-24
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:0.1
+
:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1 2020 Updates
 +
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
−
[[Category:ABC-units]]
 
−
<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
 +
[[Category:ABC-units]]
 +
{{UNIT}}
 +
{{LIVE}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 05:44, 25 September 2020

The NCBI GEO Gene Expression database

(NCBI GEO: finding and analyzing expression profiles)


 


Abstract:

Introduction to the contents and utilities of the GEO mRNA expression database.

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.

    • 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.

    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    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:

    • Navigate to the GEO database;
    • Open the article below;
    • Read through the article and explore the features it discusses on the GEO Website.
    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

    1. ↑ Strictly speaking, splicing is an eukaryotic achievement, however there are examples of splicing in prokaryotes as well.
    2. ↑
      (2015) The noncoding explosion. Nat Struct Mol Biol 22:1. (pmid: 25565024)

      [ PubMed ] [ DOI ]

      Jarvis & Robertson (2011) The noncoding universe. BMC Biol 9:52. (pmid: 21798102)

      [ PubMed ] [ DOI ]


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-24

    Version:

    1.1

    Version history:

    • 1.1 2020 Updates
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-EXPR-GEO&oldid=11650"