Hands on Bioinformatics

Tanvir Alam
College of Science and Engineering
Hamad Bin Khalifa University

@TanvirAlam 1
Tools Installation

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Anaconda: Windows/Mac/Linux
INSTALLATION of Anaconda: 1
Python will be automatically installed if you Creating a new working
use latest version of anaconda environment (Optional)
• Follow the guideline mentioned here:
https://docs.anaconda.com/anaconda/ins
tall/ • conda create --name ngs python=3.7.3
anaconda
• Download link: • conda activate ngs
https://www.anaconda.com/products/indi
vidual • conda install -c channelName
packageName
• Please look at the terminal. Whenever it • conda install packageName
ask for a decision “Yes/NO”, type “Yes”.
• conda deactivate
• Don’t just press Enter.

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BioPython: Windows/Mac/Linux
INSTALLATION of BioPython under 2
Anaconda: Creating a new working
Python will be automatically installed if environment (Optional)
you use latest version of anaconda
• Follow the guideline mentioned here: • conda create --name ngs
python=3.7.3 anaconda
https://github.com/biopython/biopyth
• conda activate ngs
on/blob/master/README.rst
• conda install biopython
• After installing conda, you can also use
• conda deactivate
pip install biopython

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 3
RStudio Download R and Rstudio
https://posit.co/download/rstudio-
desktop/

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Examples

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Example : Gene

• Name : ANGPTL7 (angiopoietin like 7)

• chr1: 11,189,289-11,195,981
• UCSC Genome Browser (Paste any of the following)
• ANGPTL7
• chr1:11189289-11195981
• Ensembl:
https://asia.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG000001
71819;r=1:11189355-11195981
• Coding DNA Sequence (CDS):
• https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS
128.1

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Example : Protein Paxillin

• UniProt (Protein):
• https://www.uniprot.org/uniprot/P49023
• Transcript:
https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=
ENSG00000089159;r=12:120210447-120265771;t=ENST00000228307
• Coding DNA Sequence (CDS):
https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DA
TA=CCDS44997

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Genome Browser 1

1. Go to UCSC Genome Browser: https://genome.ucsc.edu/

2. Select “Genomes >> Human GrCh38/hg38”

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Genome Browser
1. Type “chr7:55019017 - 55211628” in the search box
2. Then click “GO”

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Genome Browser

• Scroll down and under “Phenotype and Literature” , select “full” under
“ClinVar Variants”

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Uniprot 2

1. Go To : https://www.uniprot.org/
2. TYPE “egfr” in the search box

3. Select “EGFR_HUMAN”

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Uniprot
1. Select the tab “Variant Viewer”

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Uniprot
• Click “Feature viewer” • Under “PDBe Coverage you will find
protein stuructu”
• If you click “2ITY” it will open the 3D
structure of protein and lignad

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Transcriptomics

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Transcriptome

• A transcriptome is the full range of RNA molecules expressed by an

organism.
• It can can also be used to describe the array of RNA transcripts produced in a
particular cell or tissue type.
• In contrast with the genome, which is characterized by its stability, the
transcriptome actively changes.
• In fact, an organism's transcriptome varies depending on many factors, including
• stage of development
• environmental conditions
• response to a particular condition or treatment
• Different cells or tissues
• Binding of different transcription factors (TF)

https://www.nature.com/scitable/definition/transcriptome-296/ ©Tanvir Alam 16

Gene Expression
• The most intuitive way to investigate a certain phenotype is to measure
the expression levels of genes(RNA or proteins) present at a given time in
the cell.
• Measuring the concentration of proteins can be difficult, due to their varying
locations, modifications, and contexts in which they are found, as well as due to
the incompleteness of the proteome.
• mRNA expression levels, however, are easier to measure, and are often a
good approximation
• By measuring the mRNA, we analyze regulation at the transcription level, without
the added complications of translational regulation and active protein degradation,
which simplifies the analysis at the cost of losing information.

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Computational Biology: Genomes, Networks, Evolution. MIT Press, Manolis Kellis
MicroArray – A technique for Gene Expression
• Microarrays allow the analysis of the expression levels of thousands of
preselected genes in one experiment.
• A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously
detect the expression of thousands of genes from a sample (e.g., from a tissue).
• It is a two-dimensional array on a solid substrate—usually a glass slide or silicon
thin-film cell—that assays (tests)
• The "gene chip" industry started to grow significantly after the 1995 Science
Magazine article by the Ron Davis and Pat Brown labs at Stanford University
• Microarrays are microscope slides that are printed with thousands of tiny spots
in defined positions, with each spot containing a known DNA sequence or gene.
Often, these slides are referred to as gene chips or DNA chips.

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Computational Biology: Genomes, Networks, Evolution. MIT Press, Manolis Kellis
MicroArray Chip

Original image of a Chip

and scanning electron
microscope (SEM)
image
Illumina Microarray Chip
doi:10.1371/journal.pone.0013179

• Chip design:
• Each spot will represent different gene
• At each spot, cDNA of a gene will be planted on Chip.
• DNA Microarray Chip: (start at 1:50)
https://www.youtube.com/watch?v=0ATUjAxNf6U
https://www.youtube.com/watch?v=NgRfc6atXQ8
https://www.mdpi.com/2076-3905/3/4/245/htm

https://www.biolabtech.com.ua/en/products/nabori-mikromatric-dlya-genotipuvannya-ta-epigenetichnih-doslidzhen.html#
©Tanvir Alam 19
MicroArray Analysis: Steps
1. To perform a microarray analysis, mRNA
molecules are typically collected from both
an experimental sample and a reference
sample.
• For example, the reference sample could be
collected from a healthy individual, and the
experimental sample could be collected from an
individual with a disease like cancer.
2. The two mRNA samples are then converted
into complementary DNA (cDNA), and each
sample is labeled with a fluorescent probe
of a different color.
• For instance, the experimental cDNA sample
may be labeled with a red fluorescent dye,
whereas the reference cDNA may be labeled
with a green fluorescent dye.
• The two samples are then mixed together and
allowed to bind to the microarray slide.
3. The process in which the cDNA molecules
bind to the DNA probes on the slide is
called hybridization.

https://www.nature.com/scitable/definition/microarray-202/ ©Tanvir Alam 20

Image source : https://en.wikipedia.org/wiki/DNA_microarray
MicroArray Analysis: Steps
4. Following hybridization, microarray is
scanned to measure the expression of each
gene printed on the slide. Laster excites the
fluorescent dye and emissions are detected
• If the expression of a particular gene is higher in
the experimental sample than in the reference
sample, then the corresponding spot on the
microarray appears red.
• If the expression in the experimental sample is
lower than in the reference sample, then the spot
appears green.
• if there is equal expression in the two samples,
then the spot appears yellow.
• If there is no expression, then it becomes dark.

5. The data gathered through microarrays can

be used to create gene expression profiles,
of many genes in response to different
condition or treatment.
Img source: https://microbenotes.com/dna-microarray/

https://www.nature.com/scitable/definition/microarray-202/ ©Tanvir Alam 21

Thank You

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