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.
Read More