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Health Biotech Assignment

The document discusses using microarray analysis and gene ontology to identify disease genes. It proposes a new method that combines Fisher scoring and SVM to select genes, addresses weaknesses of prior methods, and utilizes gene ontology information. The method was tested on cancer datasets and improved classification performance and identified genes involved in cancer growth. It also discusses DNA microarrays, their principles, types including cDNA and oligo DNA microarrays, and applications like studying gene expression and detecting DNA mutations. Protein microarrays are also reviewed for applications like identifying protein interactions and biomarkers for clinical diagnostics.

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Hamza
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53 views

Health Biotech Assignment

The document discusses using microarray analysis and gene ontology to identify disease genes. It proposes a new method that combines Fisher scoring and SVM to select genes, addresses weaknesses of prior methods, and utilizes gene ontology information. The method was tested on cancer datasets and improved classification performance and identified genes involved in cancer growth. It also discusses DNA microarrays, their principles, types including cDNA and oligo DNA microarrays, and applications like studying gene expression and detecting DNA mutations. Protein microarrays are also reviewed for applications like identifying protein interactions and biomarkers for clinical diagnostics.

Uploaded by

Hamza
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Name: Hamza Farooq

Roll number: BSBt02191025

Assignment: Health Biotechnology

Identifying sets of disease gene by micro array analysis


Microarray technology offers one of the most accurate methods for identifying disease-causing
genes. In microarray data, only a few samples are available for a given number of genes, which
is one of their limitations. As a result, gene selection is crucial to improving predictive accuracy
and identifying potential marker genes for diseases. In recent years, machine-based recursive
feature elimination (SVMRFE) has emerged as one of the most popular methods, but its
performance has been reduced because of the small sample size, noisy data, and the fact that
redundant genes aren't removed.

Methods

We propose a novel framework for gene selection which uses the advantageous features of
conventional methods and addresses their weaknesses. In fact, we have combined the Fisher
method and SVMRFE to utilise the advantages of a filtering method as well as an embedded
method. Furthermore, we have added a redundancy reduction stage to address the weakness of
the Fisher method and SVMRFE. In addition to gene expression values, the proposed method
uses Gene Ontology which is a reliable source of information on genes. The use of Gene
Ontology can compensate, in part, for the limitations of microarrays, such as having a small
number of samples and erroneous measurement results.

Results

The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL)
and prostate cancer datasets. The empirical results show that our method has improved
classification performance in terms of accuracy, sensitivity and specificity. In addition, the
study of the molecular function of selected genes strengthened the hypothesis that these genes
are involved in the process of cancer growth.

DNA analysis
The microarray is a recently developed technology used in cancer research and in the
pharmacological treatment of other diseases such as oral lesions. In this technology, a
microscope slide (normally a 2D array made of glass, silicon chips, or nylon membrane) printed
with thousands of minute spots in definite positions is used.
DNA microarray (gene chip, DNA chip, or biochip) is one such technology that either measures
DNA or uses DNA as a part of its detection system. In each of the spots in this array, a known
DNA sequence or gene is orderly arranged.
Principle and Technique

The basic principle behind the DNA microarray is “nucleic acid hybridisation”. In this process,
two complementary strands of a DNA are joined together by hydrogen bonds to form a double-
stranded molecule. This helps researchers to compare and analyse the DNA or RNA molecules
of identical sequences.

The technique consists of three major sections:

1. Preparation of a DNA chip


2. The experiment
3. Collection and analysis of results

Types of DNA microarrays


DNA microarrays are of four types:

1. cDNA microarrays: uses complementary DNA strands formed by transcription of mRNA


2. Oligo DNA microarrays: uses chemically synthesised oligo DNA as probes
3. BAC microarrays: uses template amplified by polymerase chain reaction as the probe
4. SNP microarrays: used to detect polymorphisms within a population

Applications

 To study transcriptomes and proteomes


 To diagnose pathogenic as well as genetic diseases in man
 To identify microbes in the environment with the help of species-specific probes
 To genotype genomes through single nucleotide polymorphism (SNP) analysis
 To detect gene expression of mRNAs of a particular cell at different times
 To measure changes in the level of gene expression
 To observe DNA mutations
 To study genomic gains and losses
Protein microarray analysis

Protein chips have emerged as a promising approach for a wide variety of applications
including the identification of protein–protein interactions, protein–phospholipid interactions,
small molecule targets, and substrates of proteins kinases. They can also be used for clinical
diagnostics and monitoring disease states. This article reviews current methods in the
generation and applications of protein microarrays.
Understanding complex cellular systems will require the identification and analysis of each of
its components and determining how they function together and are regulated. A critical step
in this process is to determine the biochemical activities of the proteins and how these activities
themselves are controlled and modified by other proteins. Traditionally, the biochemical
activities of proteins have been elucidated by studying single molecules, one experiment at a
time. This process is not optimal, as it is slow and labor intensive.

FIGURE 1. (A) Protein microarray technology. Schematic representation of protein


microarrays used for autoantibody detection. Antigens are printed onto a specially coated
microscope slide surface, and serum antibodies (green) are detected by a fluorescently
conjugated secondary antibody (purple). Microarrays are then scanned, and images are
analysed using microarray software. Values are calculated for each antigen based on
mean fluorescent intensity and a statistical analysis is performed. Data can be visualised
in a heat map representation.
(B) Simplified schematic representation of proposed map of primary immunodeficiencies
.

References:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037837
https://en.m.wikipedia.org/wiki/DNA_microarray
https://www.frontiersin.org/articles/10.3389/fimmu.2015.00138/full

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