Lecture 3 - Databases in Bioinformatics (PART 2) | Bioinformatics - Botany PDF Download

 Page 1


Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
18 
Organism-specific databases 
 
In this exercise, we will learn to retrieve information related to a 
particular gene from a model organism-based database.  
Question: What are the gene models known for the Arabidopsis gene, 
GLABRA2? 
1. Access the home page of The Arabidopsis Information Resource (TAIR) 
(http://www.arabidopsis.org/). 
 
2. Type the name of the gene (GLABRA2) in the search box highlighted in the 
above image and click on the “Search” button. 
 
Page 2


Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
18 
Organism-specific databases 
 
In this exercise, we will learn to retrieve information related to a 
particular gene from a model organism-based database.  
Question: What are the gene models known for the Arabidopsis gene, 
GLABRA2? 
1. Access the home page of The Arabidopsis Information Resource (TAIR) 
(http://www.arabidopsis.org/). 
 
2. Type the name of the gene (GLABRA2) in the search box highlighted in the 
above image and click on the “Search” button. 
 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
19 
 
 
3. The search results display multiple loci corresponding to the GLABRA2 
gene indicating that this gene is present in multiple copies in the plant. Of 
the three paralogs present, two have a single gene model while the third 
paralog (At4g00730) has two gene models. 
 
 
5. Click the locus ID of the above gene to see the two gene models. The 
gene models depict the exonic and intronic regions, the 5’ and 3’ UTRs 
(untranslated regions). Variations between the two gene models can 
be clearly seen. 
Page 3


Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
18 
Organism-specific databases 
 
In this exercise, we will learn to retrieve information related to a 
particular gene from a model organism-based database.  
Question: What are the gene models known for the Arabidopsis gene, 
GLABRA2? 
1. Access the home page of The Arabidopsis Information Resource (TAIR) 
(http://www.arabidopsis.org/). 
 
2. Type the name of the gene (GLABRA2) in the search box highlighted in the 
above image and click on the “Search” button. 
 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
19 
 
 
3. The search results display multiple loci corresponding to the GLABRA2 
gene indicating that this gene is present in multiple copies in the plant. Of 
the three paralogs present, two have a single gene model while the third 
paralog (At4g00730) has two gene models. 
 
 
5. Click the locus ID of the above gene to see the two gene models. The 
gene models depict the exonic and intronic regions, the 5’ and 3’ UTRs 
(untranslated regions). Variations between the two gene models can 
be clearly seen. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
20 
As you scroll down the page, you will find several details regarding the gene viz., 
nucleotide sequences (full length genomic and cDNA sequences, full length coding 
sequence, etc.) RNA expression profiles, polymorphisms, mutants and their 
phenotypes, annotation and related references.  
 
Scrolling further down, you will see a section on “External links” which would be 
used to solve the next Practice Exercise. 
Page 4


Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
18 
Organism-specific databases 
 
In this exercise, we will learn to retrieve information related to a 
particular gene from a model organism-based database.  
Question: What are the gene models known for the Arabidopsis gene, 
GLABRA2? 
1. Access the home page of The Arabidopsis Information Resource (TAIR) 
(http://www.arabidopsis.org/). 
 
2. Type the name of the gene (GLABRA2) in the search box highlighted in the 
above image and click on the “Search” button. 
 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
19 
 
 
3. The search results display multiple loci corresponding to the GLABRA2 
gene indicating that this gene is present in multiple copies in the plant. Of 
the three paralogs present, two have a single gene model while the third 
paralog (At4g00730) has two gene models. 
 
 
5. Click the locus ID of the above gene to see the two gene models. The 
gene models depict the exonic and intronic regions, the 5’ and 3’ UTRs 
(untranslated regions). Variations between the two gene models can 
be clearly seen. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
20 
As you scroll down the page, you will find several details regarding the gene viz., 
nucleotide sequences (full length genomic and cDNA sequences, full length coding 
sequence, etc.) RNA expression profiles, polymorphisms, mutants and their 
phenotypes, annotation and related references.  
 
Scrolling further down, you will see a section on “External links” which would be 
used to solve the next Practice Exercise. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
21 
 
Gene expression databases 
 
In this exercise, we will learn to retrieve information related to 
expression profiling of any gene in a model system. 
Question: Retrieve the expression profile of the GLABRA2 gene over 
various developmental stages of Arabidopsis. 
 
1. We begin this exercise from the window on “External links” which was 
displayed in the previous exercise. 
Page 5


Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
18 
Organism-specific databases 
 
In this exercise, we will learn to retrieve information related to a 
particular gene from a model organism-based database.  
Question: What are the gene models known for the Arabidopsis gene, 
GLABRA2? 
1. Access the home page of The Arabidopsis Information Resource (TAIR) 
(http://www.arabidopsis.org/). 
 
2. Type the name of the gene (GLABRA2) in the search box highlighted in the 
above image and click on the “Search” button. 
 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
19 
 
 
3. The search results display multiple loci corresponding to the GLABRA2 
gene indicating that this gene is present in multiple copies in the plant. Of 
the three paralogs present, two have a single gene model while the third 
paralog (At4g00730) has two gene models. 
 
 
5. Click the locus ID of the above gene to see the two gene models. The 
gene models depict the exonic and intronic regions, the 5’ and 3’ UTRs 
(untranslated regions). Variations between the two gene models can 
be clearly seen. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
20 
As you scroll down the page, you will find several details regarding the gene viz., 
nucleotide sequences (full length genomic and cDNA sequences, full length coding 
sequence, etc.) RNA expression profiles, polymorphisms, mutants and their 
phenotypes, annotation and related references.  
 
Scrolling further down, you will see a section on “External links” which would be 
used to solve the next Practice Exercise. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
21 
 
Gene expression databases 
 
In this exercise, we will learn to retrieve information related to 
expression profiling of any gene in a model system. 
Question: Retrieve the expression profile of the GLABRA2 gene over 
various developmental stages of Arabidopsis. 
 
1. We begin this exercise from the window on “External links” which was 
displayed in the previous exercise. 
Databases in Bioinformatics 
 
Institute of Lifelong Learning, University of Delhi 
 
22 
 
 
 
2. Click on the eFP Browser link. A new window will be displayed in which you 
would be able to see the expression pattern of the gene query on scrolling 
down the page. The expression profile, by default, is highlighted over various 
developmental stages (vegetative as well as reproductive) of the plant. Color 
coding of the expression levels allows the user to analyze quantitative 
variation in gene expression in different tissues at different stages. Clicking 
the drop down menu (highlighted below by a red box) would allow you to 
select other experimental/natural conditions viz., biotic and abiotic stresses, 
natural variation in germplasm, etc. under which the expression profile of this 
gene has been studied.