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Overview of Systems Biology and Omics Technologies

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Current Medicinal Chemistry, 2016, 23, 1-10 1

REVIEW ARTICLE

Overview of Systems Biology and Omics Technologies

Bensu Karahalil*

Gazi University, Faculty of Pharmacy, Toxicology Department, 06330, Ankara, Turkey

Abstract: Traditional technologies using reductionist approach are relatively insufficient to

ARTICLE HISTORY
Received: June 03, 2016
Revised: August 31, 2016
Accepted: September 23, 2016
DOI: 10.2174/0929867323666160926
150617
Keywords: Systems biology, omics technologies, genomics, transcriptomics, proteomics, metabolomics.
solve problems in a biological system. Rather than a reductionist approach, systems biology
uses a holistic and integrative approach to better figure out the whole process. Both qualita-
tively and quantitatively of biological system provide information about diseases, toxicities,
therapies etc. Omics technologies, which systems biology brings, are valuable tools for
comprehensive analyses. Automated DNA sequencers enabled the sequencing of genomes;
microarray and mass spectrometry analysis permit global transcriptional profiling and lead
to large-scale proteomic and metabolomics analysis. These high-throughput data need to be
interpreted by bioinformatics. So far there has been no concrete published paper that com-
piles omics technologies according to PubMed database. In the present review, it was aimed
to give brief description of systems biology and information on the advantages and disad-
vantages of omics technologies.

1. INTRODUCTION molecular levels such as DNA. These data is integrated

by computational tools and used for systems biology.
Systems biology is an interdisciplinary study field
There are numerous experimental methodologies to be
including biology, computer science, engineering, bio-
combined with systems biology as quantitative analysis
informatics, physics and others that focuses on the sci-
and time-course measurement which makes systems
entific studying of multi interactions in biological sys-
biology different from classic biology. Mostly informa-
tems. It uses a new holism instead of reduction per-
tion is obtained from cell cultures and animal experi-
spective. It provides us to see whole picture within bio-
ments. Mechanistic mathematical models of biochemi-
logical systems instead of the sum of parts. In this con-
cal networks (e.g. signal transduction, genetic and
text, systems biology has caused the fundamental
metabolic networks) has been developed owing to pro-
change in traditional approaches. It is a discovery-
gression in experimental procedures/techniques. Dy-
driven approach when compared to traditional ap-
namic models ensure the development of predictive
proaches, thus it is different from traditional hypothe-
models for organism and appear as a major step for
sis-driven research. It enables to clarify the molecular
systems biology. Scientific data on behavior of organ-
constituents and to sense the underlying cellular proc-
ism from dynamic models help to identify some strate-
ess, predicts how these systems change over time and
gies for different conditions such as treatment strategy
under varying conditions, and develops solutions for
for diseases. Dynamic models collect and organize in-
health and environmental problems. Opinion of serving
dividual information and bring them together for a
to unify separate things is not new; it is based on the
global evaluation. These models ensure the prediction
1950s, such as feedback inhibition in amino acid bio-
and optimization of experiments with simulation stud-
synthetic pathway which was explored in 1957. [1].
ies, the approval of positive or negative hypothesis,
Owing to advances in high-throughput technologies
Furthermore they emphasize the importance and neces-
and related huge data can be generated on the macro-
sity of the components and interactions for the system
*Address correspondence to this author at the Gazi University,
and help to clarify the system's features. [2]. Systems
Faculty of Pharmacy, Toxicology Department, 06330, Ankara, biology studies ensure understanding of biology at the
Turkey; Tel: +90312 202 30 85; Fax: +90312 222 2326; system level. All molecules and their interactions are
E- mails: bensuka@gmail.com or bensu@gazi.edu.tr

0929-8673/16 $58.00+.00 © 2016 Bentham Science Publishers

2 Current Medicinal Chemistry, 2016, Vol. 23, No. 36
classified instead of identifying each component of a
cell/organism.. Network modeling is an essential mod-
elling. There are two major methodologies in the net-
work. i. Static large scale biological network modelling
integrates, visualizes and topologically makes model-
ing all omics data sets obtained from high throughput
techniques. ii. Dynamic quantitative modeling investi-
gates dynamics of biological systems via computational
simulation and mathematical modeling [3].
‘-Omics’ is a relatively new concept and means to a
domain in biology ending in -omics, such as genomics,
proteomics or metabolomics. The suffix –ome is
used for the objects, such as the genome, proteome or
metabolome [4]. In the 1920s, Hans Winkler who was
a botanist, merged the words ‘GENe’ and ‘chromo-
sOME’” to describe a body of genes called genome It is
known that omics involves a mass or large number of
measurements per endpoint. Now, there are more than
1000 omics fields [5]. Omics technologies are aimed at
primarily four omics research fields namely, genomics,
transcriptomics, proteomics or metabolomics. Over
time, omics is constantly being added, such as, lipi-
domics which is the study of the structure and function
of the complete set of lipids, nutrigenomics which is
the study of how foods affect our genes. Previous re-
search fields, before using omics concept, were termed
genetics, pharmacogenetics, toxicogenetics which pro-
vide the static sequences of genes, proteins. ‘Omics’
term is evolved and accepted for different systems in
biologic applications.
-Omics have brought new technologies and have
been used in the definition of new generation technolo-
gies as a suffix. New generation/novel technologies are
called genomics and transcriptomics which are gene
expression profiling, proteomics which facilitates
global analysis of proteins, metabolomics which repre-
sents the collection of all metabolites and pharmacoge-
nomics and toxicogenomics which reveal the dynamic
function and their interactions. “Traditional” or ‘pre-
omics’ words are used for old or previous methodolo-
gies/technologies throughout this review. The omics
technologies provide simultaneously measurement of
the number of proteins/genes/ metabolites and enables
to get large scale data in a little while. Understanding
the whole picture of biological system better can be
provided by the collective analysis of all omics. [6].
Systems biology is to understand the regulation of
cell behavior in the cell, such as mRNA, proteins, me-
tabolites etc. [7]. With traditional methods, only a few
gene variations are analyzed and identified by Polym-
erase Chain Reaction (PCR) technique or proteins are
Bensu Karahalil
detected by chemical methods such as Coomassie
(Bradford) and Modified Lowry, which are based on
the direct measurements of absorbance. The targeted
identification of proteins or the targeted analysis of
genes is performed by these traditional methods. In our
previous study, it is a perfect example to demonstrate
that traditional methods are target oriented method;
oxidative damage to DNA was investigated in both
Compartments (mitochondria and nucleus) in differ-
ent lung cancer cell lines [8].
Different oxidized DNA bases were seen in cancer
cell samples but not from surrounding tissue within the
same patient. The activities of four Base Excision Re-
pair (BER) enzymes 8-oxoguanine glycosylase
(OGG1), oxidized pyrimidine (NTH1), Uracil-DNA
glycosylase (UDG) and AP- endonuclease (APE1)
were measured by oligonucleotide incision assay and to
test we studied on only mitochondrial extracts but also
mitochondrial extracts without any nuclear extract con-
tamination,Western Blotting Assay was performed us-
ing Lamin B2 which is a nuclear protein. Individual
susceptibility was showed by Restriction Fragment
Length Polymorphism (RFLP -PCR). Our aim
was to show the impacts and activities of oxidative
DNA damage and repair in both mitochondrial and nu-
clear extracts and to make comparisons between them.
The key point of the study was firstly to check whether
mitochondrial extracts had nuclear contaminations. It
was decided to analyze the OGG1 Ser326Cys gene
polymorphism in tumor and surrounding tissue samples
because changes in 8-oxoguanine (8-oxoG) incision
were observed in both extracts. Thus, matrix protein for
checking nuclear contamination and OGG1 gene for
OGG1 enzyme activity were selected. These were se-
lected target oriented end points [8].
A limited number of gene polymorphisms have
been analyzed in pre-genomic period. One or generally
up to 10 targeted oriented gene polymorphisms or can-
didate genes were studied in population- or hospital
based gene-disease or drug-adverse effect association
studies. A couple of proteins or metabolites, which
have a functional structure, were selected and identified
in studies of pre-omics period. After entering genomic
era, the most obvious advantage of omics technologies
is to analyze thousands of proteins/genes/metabolites
instead of only a few proteins/genes/metabolites. The
fundamental target of omics methods is the non-
targeted recognition of all gene products such as tran-
scripts. In recent years, omics technologies are used for
biomarker discovery such as new disease biomarkers,
phylogenetic tree and system-wide understanding of
System Biology and Technologies
toxicity or action mechanism of xenobiotics, identifica-
tion of signaling molecules associated with all devel-
opment stage of cell (growth, metabolism, and death)
and early detection of cancer. Omics aids to understand
biological processes in comparison to previous tradi-
tional methods. It ensures more accurately and pre-
cisely diagnosis and treatment of disease through com-
prehensive data analysis. Especially, it would give op-
portunity to diagnose diseases in very early stage and
take protective measurements for toxicities since omics
clarify the mechanisms underlying the xenobiotic tox-
icity and development of diseases. Thousands of data
from different omics need to be efficiently integrated
for interpreting of hypothesis or data. Data integration
is very important for interpretation of data. Efficient
integration of data enables accurate and robust results
but omics data is quite challenging due to the data inte-
gration which is computational or/and combination of
data or simultaneous analysis of multiple variables on
multiple datasets. It is important to improve productiv-
ity for stored data and to search mechanisms in dis-
eases and to get accurate and robust outcomes [9]. Dur-
ing collecting data, there are many problems such as
data heterogeneity, small sample size in comparison to
many parameters, confirmation and interpretation of
data due to many interactions in biological system and
deficient information on those systems. To be able to
solve these challenges, new statistical methods need to
be improved. Meetings on omics data have been made
to review of current technologies on data and the meth-
ods for a whole analysis. Recent meeting was sup-
ported by European Projects (the FP7 STATegra pro-
ject (http: //stategra. eu/) and the COST Action SeqA-
head (http://seqahead.eu/), two EU-funded initiatives)
[10].
As previously mentioned above,omics technologies
are aimed at primarily three fields namely, genomics,
proteomics or metabolomics. After four omics research
fields are briefly defined, omics technologies and their
advantages and disadvantages will be discussed in (Ta-
ble 1).
2. GENOMICS
Genomics is a genome research through analysis of
the nucleotide sequences, genome structure and its
composition. It allows finding out individuals with the
genetic variants; therefore, it provides relationship be-
tween genes / their variants and disease or response to
therapy. Genetic variations enable the elucidation of
genetic basis of diseases using Genome Wide Associa-
tion Study (GWAS), candidate gene case-control asso-
Current Medicinal Chemistry, 2016, Vol. 23, No. 36 3
ciation studies, and genome-wide linkage analyses.
PCR, microarrays or sequencing (Sanger sequencing or
Next Generation Sequencing; NGS) methods are used
for analyses and are used to obtain insight into the ge-
nomic information that contains the basic information
for the production of all cellular proteins via transcrip-
tion and translation. Sanger Sequencing which is a gold
standard by Capillary Electrophoresis sequences long
DNA fragments since the technology was evolved;
NGS was also used to sequence DNA fragments; how-
ever data should be verified with Sanger Sequence
technique. PCR, RFLP-PCR techniques is routinely
used for known SNP and disease association studies
and if verification is needed , Sanger Sequence tech-
nique should be used. Genotyping especially GWAS is
commonly used and focuses on the genome sequence
[11].
There have been many published family-based and
population-/ hospital -based genetic studies
to demonstrate associations of gene polymorphisms
with disease susceptibility. SNPs are variations in a
single nucleotide in the genome and their frequencies
are more than 1%. SNPs have been used in case-control
studies to identify susceptible genes for many diseases
such as cancer and neurological disorders [12]. They
can be used as genetic biomarkers to identify genetic
loci for disease. The most common diseases such as
cancer, obesity, coronary artery disease, hypertension,
are raised by various genetic and environmental factors
and their interactions. Genetic polymorphism-disease
association studies give us information on individual
susceptibility and show relationship between gene po-
lymorphisms and diseases [13-16]. Especially genetic
factors are essential contributors to the pathogenesis of
the diseases. Identification of SNPs provides valuable
information for early diagnosis, prevention and treat-
ment of common diseases. Furthermore, adverse reac-
tion induced by drugs can be observed in some patients
while not in others.. Studies on gene polymorphisms,
especially on metabolizing enzymes, clearly demon-
strate the individual susceptibility to some drugs and
different responses among individuals [17, 18].
Although SNPs are important tools to find out the
risk of acquiring disease, it is very difficult to genotype
hundreds of SNP especially in large scale case control
association studies. In the last decades, sequencing and
genotyping of hundreds or thousands of gene se-
quences can be made easily and doe not need to use
perform time-consuming PCR assays. There are a
number of different genotyping methods including re-
striction fragment length polymorphism (RFLP), allele
4 Current Medicinal Chemistry, 2016, Vol. 23, No. 36 Bensu Karahalil

Table 1. Advantages and disadvantages of omics technologies.

Omics Technologies Advantages Disadvantages

Genomics
(RFLP, ASO, AFLP PCR,  Identification of SNPs provides valuable infor-  It is difficult to predict the final biological
RAPD, DNA microarrays mation for early diagnosis, prevention and treat- effect of DNA by only genome analysis due to
etc.) ment of common diseases. post-transcriptional and post-translational
changes and epigenetics.
 Studies on gene polymorphisms, especially on
metabolizing enzymes, clearly demonstrate the
individual susceptibility to some drugs and dif-
ferent responses among individuals.
For example; For example;
o Affymetrix SNP GeneChip and IIIumina Gold- o NGS, PCR, RFLP-PCR techniques for se-
enGate BeadChips assays; optimum methods for quencing DNA fragments; however data
high number of SNP and a small sample size in should be verified with Sanger Sequence tech-
genome wide or large-scale study group. nique.
o TaqMan assay; ptimum method for a low num-
ber of SNP and a large sample size
Transcriptomics
(Microarray, hybridiza-  Identification of the major pathways involved in  Inadequate data due to post-translational
tion-based sequence-base, drug response and toxicity. modifications.
Taq-based methods etc.)
 Good reproducibility for inter laboratory studies  Changes in the transcriptome are not be able
to show a variation in the pattern of “end-
products”.
For example;  Cross-contamination - cross-hybridization and
printing consistency.
o It is easy to use commercially available pre-
made chips and relatively affordable for an ar-  Difficulty the interpretation and statistical
rays and scanner setup. evaluation for massive amount of data.
o Plates are suitable for work because they are  Measurement as a relative abundance; not
small. absolute
o Method is very fast and thousands of genes can
be analyzed at once.
o Many comparisons and replicates can be per-
formed since it is cost-effective.
Sequence –based, Taq  Relatively low throughput, not cheap and
base- methods (SAGE; qualitative
CAGE, MPSS etc.)
 High throughput and give precise “digital” gene  Expensive and difficult separation of isoforms
expression level during analysis.
RNA-seq, Whole Tran-  Provide new transcriptomic views
scriptome Shotgun Se-
quencing; WTSS  Accuracy on transcription level
 High throughput
EST  Prediction of absolute mRNA abundance  Expensive, time-consuming
 Useful for gene discovery.
SAGE  More efficient than large-scale EST sequencing  Difficult to map tags to genes.
 Prediction of absolute transcript abundance. o For different states such as tissue, gender, it
must be repeated.
System Biology and Technologies Current Medicinal Chemistry, 2016, Vol. 23, No. 36 5

(Table 1) contd….

Omics Technologies Advantages Disadvantages

Proteomics and
Metabolomics
(MS-based Proteomics,
MS, NMR, LC-MS, GC-
MS, EC, HPLC, TOF etc.)
Gel based proteomics  Enable the analysis of proteins with low abun-
2DGE
 Expensive, fairly insensitive to low copy pro-
teins not use for entire proteome.
 Precipitation at isoelectric point (pI)
 Different results due to post-translational
modification
dance in complex samples

Gel free proteomics Provides the quantitative comparative analysis using  Proteins without lysine cannot be labeled.
a single gel. Cost is increased due to requiring special
2D-DIGE equipment.
Eliminate post-electrophoretic processing steps such
as fixing and destaining
Increase reproducibility by directly comparing sam-
ples under similar electrophoretic conditions

Metabolomics technologies  Metabolomics has more advantages than ge-

nomics and proteomics. Endogenous metabo-
lites are fewer than genes, transcripts and pro-
teins, so less data is available to be interpreted.
 Finding biomarkers of diseases such as cancer.
TOF  High sensitivity, no upper mass limit
MS, NMR spectroscopy  Good sensitivity (femtomolar to attomolar)
MS-based Proteomics
LC-MS,GC-MS, CE High-throughput (detection of hundreds of individual
species within a single sample)
Adding known amounts of internal isotope-labeled
standards provides accuracy for specific molecules.
MS When coupling MS with LC or GC, good sensitivity
and selectivity
 Low mass resolution
 Little/lack of information on protein since the
peptides might not have all come from a sin-
gle protein species.
There is peptide co-elution, scanning and sensitiv-
ity limitations
 The MS signal intensity is affected by sample
preparation method used and its molecular
environment, therefore quantification prob-
lem.
 Use of internal isotope-labeled standards
is not practical for purely discovery-driven
metabolomics research.
Microarrays provide for the abundance measure-
ment of a finite set of target transcripts, but typical
MS analysis does not.

specific oligonucleotide (ASO) probes, amplified
fragment length polymorphism (AFLP), polymerase
chain reaction (PCR), random amplified polymorphic
DNA (RAPD), and DNA microarrays. These methods
are used to analyze genetic variations. SNPs and copy
number variants (CNVs) that have an abnormal or a
normal variation in the number of copies of one or
more sections of the DNA, are the most common
sources of genetic variations [19]. There are different
types of structural genotyping methods and selection of
these methods depends on the number of SNPs and
sample size of population. Affymetrix SNP GeneChip
and IIIumina GoldenGate BeadChips assays are the
optimum methods for high number of SNP and a small
sample size in genome wide or large-scale study group.
If study group involves a low number of SNP and a
large sample size, the TaqMan assay is preferred tech-
nology. Deduction from appropriate and accurate tech-
6 Current Medicinal Chemistry, 2016, Vol. 23, No. 36
nology provides highly accurate, precise results and it
has become time-efficient and cost effective [20].
The advantage of genomics is to provide the identi-
fication of genes and pathways deregulated or regu-
lated in many diseases including cancer and specific
states based on omics data. Omics data and technolo-
gies used in genomics help for early and accurate diag-
nosis and management of disease. Furthermore, they
provide understanding the mechanism of disease and
exploring disease and discovery of novel diagnostic,
prognostic, and therapeutic biomarkers. All these im-
provements ultimately improve patient outcomes [21].
Genomics represents a disadvantage to predict the
biological effect. Although genomics and DNA se-
quence analysis provide a valuable data, it is difficult to
predict the final biological effect of variation/s in
DNAby only genome analysis because of post-
transcriptional and post-translational changes, epige-
netics [22].
3. TRANSCRIPTOMICS
Transcriptomics is related to the proteins and gene
expression. It is used to predict the changes on protein
levels and activities [22]. The transcriptome is the
complete set of transcripts including mRNA in a cell
and the quantity of transcripts.
It is possible to set up a link between a genotype
and an expression phenotype since mRNAs match with
particular genes in the genome. RNA profiling provides
clues to functional differences between tissues and cell
types, function and interaction between genes, ex-
pressed sequences and genes of a genome, gene regula-
tion and regulatory sequences and identification of
candidate genes for any condition or disease [23, 24].
DNA microarray technology is used for the study of
transcriptomics or expression profiling which examines
mRNA expression levels. Transcriptomics aims to
catalogue all species of transcripts, to assess transcrip-
tional structures and to quantify the changing expres-
sion levels during growth and under different states
such as disease [24].
Methods for transcriptomics are gene expression ar-
rays (quantification of transcript abundance, sin-
gle/multiple 3’ probes), genome tiling arrays (identifi-
cation of transcribed sequences, multiple probes along
the genome), alternative splicing arrays (quantification
of different RNA isoforms and probes in exons and
exon-exon junctions), RNA-tag sequencing (quantifica-
tion of transcript abundance and single end reads of
each RNA species) and whole RNA sequencing (iden-
tification of transcribed sequences and multiple reads
Bensu Karahalil
along each RNA species). ENCyclopedia Of DNA
Elements (ENCODE) project identifies all functional
elements in genome and gives comprehensive informa-
tion. It composes of 2 phase program namely Pilot
Phase (2003-2007) which is identification of all func-
tional components in 1% of genome and Production
Phase (2007-2012) which is identification of all func-
tional components in the whole genome (ENCODE
project).
Transcriptomics has many benefits. It determines
the gene expression responses to xenobiotic exposures
and drug therapy and the analysis of functional rela-
tionships between modulated genes and furthermore, it
may help to identify the major pathways involved in
drug response and toxicity. It is an advantage that inter
laboratory studies show good reproducibility of gene
expression profiles induced by exposure to different
toxicants. Transcriptomics/RNA-sequence provides
analysis of the complete transcriptome; however, post-
translational modifications can influence the protein
expression; therefore transcriptome cannot be consid-
ered as the last step. Posttranslational modifications
keep continue as an intermediate step [23]. The major
alterations of proteins are estimated by changes in gene
expression. However, despite gene expression, a func-
tional protein may not be produced. Thus, changes in
the transcriptome are not able to show a variation in the
pattern of “end- products” [25].
Various technologies have been developed for the
transcriptome analysis, including hybridization or se-
quence-based approaches. Hybridization-based ap-
proaches typically involve incubating fluorescently
labelled cDNA with custom-made microarrays or
commercial high-density oligomicroarrays [24].
3.1. Microarrays
Microarrays analyze thousands of genes in one ex-
periment. Not only the change in gene expressions but
also mutations in DNA are measured. . Gene expres-
sion profiles can be compared between 2 different
samples. It provides clarification of the underlying
mechanism of the disease such as cancer (comparison
of cancerous and noncancerous samples). Microarrays
are commercially available for different model species,
such as human and mouse. Microarrays are constructed
by enclosing specific DNA sequences to a solid surface
such as glass, silicon, or nylon, often a glass micro-
scope slide. The microarrays are often called “chips”.
Each probe corresponds to a spot for a different gene.
A probe can be a cDNA fragment or a synthetic oli-
gonucleotide. Probes can either be attached by robotic
System Biology and Technologies
means or by a method similar to making silicon chips
for computers. There are many benefits of microarray.
Pre-made chips are commercially available and easy to
use. They are relatively affordable for arrays and scan-
ner setup. Plates are suitable for work due to their small
sizes Method is very fast and thousands of genes can be
analyzed at once. Many comparisons and replicates can
be performed since it is cost-effective. The major chal-
lenges when performing assay are cross-contamination
and printing consistency. It only detects whether a gene
is up or down. Cross-contamination and the integrity of
the microarray should be checked. Determination only
is made in case whether a gene is opened or closed. It
may be difficult to be interpreted and to statistically
evaluate the massive amount of data from transcrip-
tomics. Microarray gives relative abundance; does not
measure absolute [26, 27].
3.2. Other Methods
In contrast to microarray methods, sequence-based
approaches directly define the cDNA sequence. Ini-
tially, Sanger sequencing of cDNA or EST libraries
was used, but they provide relatively low data, they are
not cheap and do not give quantitative results. To over-
come these problems tag-based methods were devel-
oped:serial analysis of gene expression (SAGE), cap
analysis of gene expression (CAGE). These approaches
give large scale results and enable precise, ‘digital’
gene expression levels. However, mostly, they are ex-
pensive [24].
3.3. Expressed Sequence Taqs (EST) Sequencing
mRNA is reverse-transcribed into cDNA, followed
by sequencing of cDNAs. Typically, the full-length of
the mRNA is not reverse-transcribed and and parallelly
whole cDNA is not sequenced . Thus, the resulting se-
quence fragments are referred to as ESTs. There are 2
major advantages. a. Prediction of absolute mRNA
abundance b. Useful for gene discovery. Nevertheless,
it is expensive, time-consuming and required to make
large-scale sequencing. Much of the sequencing is re-
dundant since ESTs from highly-expressed genes are
sequenced many times. A hundred thousand of ESTs
should be sequenced to provide representation of genes
that expressed at low levels. . Genes expressed in spe-
cific tissues, cells, developmental stages, etc. may be
missed since the ESTs only reveal gene expression lev-
els in the particular tissue or sample [28].
3.4. Serial Analysis of Gene Expression (SAGE)
It is another method and similar to EST sequencing.
This method is more efficient since only short “tags” (~
Current Medicinal Chemistry, 2016, Vol. 23, No. 36 7
15 bases) are sequenced from each cDNA. Before se-
quencing, connecting of tags can provide sequencing of
them in a single sequencing reaction. Having good se-
quence and annotation is essential, so that the tags can
be accurately mapped back to their corresponding
genes. SAGE is more efficient than large-scale EST
sequencing and gives a prediction of absolute transcript
abundance. Otherwise, much sequencing is re-
quired; however it may not be cheap and not precise for
rare transcripts; furthermore, it is difficult to map tags
to genes. For different states such as tissue, gender,
it must be repeated.
3.5. RNA-Seq
There have been various technologies to understand
and quantify the transcriptome; for example, hybridiza-
tion-or sequence-based approaches, taq –based meth-
ods. These methods have several limitations such as
cross-hybridization. Especially sequence based ap-
proaches are relatively low throughput, qualitative
andnot cheap . To accomplish these disadvantages, taq-
based methods (SAGE; Cap Analysis of Gene Expres-
sion; CAGE, Massively Parallel Signature Sequencing
MPSS) were developed. They are high throughput and
give precise “digital” gene expression level however
they are expensive and have some problems during
analyzing procedure; for example, separation isoforms
from each other. It is difficult to separate. RNA-seq,
Whole Transcriptome Shotgun Sequencing; WTSS are
new methods and use next-generation sequencing
(NGS) methods. They have advantages compared to
previous techniques such as revealing new transcrip-
tomic views, accuracy of transcription level, etc. RNA-
seq provides survey of quantitatively entire transcrip-
tome in high throughput [24].
4. PROTEOMICS
Proteomics is important to make comprehensive in-
vestigation into proteins since it gives information on
the actual enzymes of the metabolic process. However,
unlike genomics or transcriptomics, proteomics and its
techniques and strategies are still largely in develop-
ment [29].
Abundance of proteins and protein-protein interac-
tions are dynamic. These properties can change rapidly
during cell proliferation and migration. Therefore, elu-
cidating protein structure–function associations is es-
sential and provides identification and analysis of pro-
teins. Single fundamental parameter, such as protein
abundance or post-translational modifications, is used
for analysis due to dynamic behavior of the proteome.
8 Current Medicinal Chemistry, 2016, Vol. 23, No. 36
Although such single dimension analyses are precious,
they cause the loss of biological information through
the averaging of quantitative data from the different
cellular pools of a protein [30].
The combination of New Mass Spectrometry (MS)-
based proteomic approaches with the instrumentation
and analytical procedures provide comprehensive bio-
logical knowledge. In most MS-based proteomics, pro-
teins are identified by detecting peptides however there
was a disadvantage since the peptides might not have
all come from a single protein species. Same peptide
can come from multiple protein isoforms and/or from
distinct functional pools and give us little/lack of in-
formation on protein. There may be numerous proteins
uniquely expressed under particular circumstances.
This helps to learn link between proteomic pattern and
disease. For example, when normal and squamous cell
carcinoma are compared to each other, a set of protein
spots unique to the disease and were observed only in
squamous cell carcinoma samples, not control or
healthy cells. Therefore, this protein set could be useful
to discover biomarker [31]. Proteomic technologies are
2-dimensional difference gel electrophoresis (2D
DIGE), matrix-assisted laser desorption/ionization
(MALDI) imaging MS, Electron Transfer Dissociation
– Mass Spectrometry (ETD-MS) and reverse-phase
protein array, Liquid Chromatography MS (LC-MS),
liquid chromatography tandem MS (LC-MS/MS), in-
gel tryptic digestion followed by liquid chromatogra-
phy-tandem MS (geLC-MS/MS. So far, mRNA tran-
scriptomics and protein expressions are considered to
be in direct correspondence.. However, recent investi-
gations have shown that the correlation between them
can be low due to various factors (different half-lives
and post transcription). Thus, a collective analysis can
provide useful information [32]. Furthermore, compari-
sons of proteomic and transcriptomic expressions on
different platforms have some problems. Microarrays
provide an abundance measurement for a finite set of
target transcripts, but typical MS analysis does not.
Common 2-DE practices give preliminary idea about
the detection of soluble proteins, particularly those of
high abundance and non-extreme isoelectric point (pI)
values; on the other hand, LC-MS, even with elaborate
multidimensional LC separations, still suffers from
peptide co-elution (LC limitations), scanning and sensi-
tivity limitations [33].
5. METABOLOMICS
Metabolites are the end products of cellular regula-
tory processes. The levels of metabolites are final re-
Bensu Karahalil
sponse of biological systems against to genetic and en-
vironmental alterations. In parallel to the terms ‘tran-
scriptome’ and ‘proteome’, the set of metabolites is
called “metabolome” [34].
The goal of metabolomics is to analyse all small
molecules in a biological system. There are four main
steps in metabolomics as used in other metabolite
analyses. i. Efficiency ii. Separation ofanalytes, iii. De-
tection of analytes and iv. Identification and quantifica-
tion of analytes There are various separation techniques
which have been used for years such as Gas Chroma-
tography (GC), Capillary Electrophoresis (CE), High
Performance Liquid Chromatography (HPLC). Sensi-
tivity and selectivity increase when two techniques are
used together such as GC-MS and HPLC-MS.
MS and Nuclear Magnetic Resonance (NMR) are also
used for detection. MS and NMR spectroscopy have
their own specific advantages and disadvantages when
conducting metabolomics studies. The main advantage
of MS is sensitivity, their detection levels in the fem-
tomolar to attomolar range. Coupling MS with LC or
GC enables the detection of hundreds of individual
species within a single sample. Quantification is one of
the major disadvantages. The MS signal intensity is
affected by sample preparation method used and its
molecular environment. Adding known amounts of
internal isotope-labeled standards enables accurate
quantification for specific molecules; however, this
is not practical for purely discovery-driven metabolom-
ics research. Although metabolomics is less mature
than genomics and proteomics, metabolomics is better
promising technology than others to find biomarkers of
diseases such as cancer. An ideal biomarker should be
able to be assessed easily noninvasively. Metabolomics
provides discovery of ideal biomarker since small
molecules can distribute quickly all over the body.
Larger proteins and nucleic acids are not secreted into
biofluids thus they cannot distribute all over the body
[35, 36]. Sreekumar et al. used LC-MS and GC-MS to
profile metabolites in tissue, urine and plasma samples
from patients with benign prostate. Except for NMR,
they found a specific metabolite. This metabolite was
found in high concentration in urine during prostate
cancer progression to metastasis [37]. Obtaining good
result in urine provided good benefit for sampling and
furthermore it could be used as a biomarker for prostate
cancer.
Metabolomics has more advantages than genomics
and proteomics. Endogenous metabolites are fewer
than genes, transcripts and proteins, so less data is
available to be interpreted. Major changes in endoge-
System Biology and Technologies
nous metabolites reflect changes in biological states,
whilst, differential splicing events result in complexity
of the transcriptome and the proteome. Researchers
have performed different types of studies which enable
the evaluation of biological responses to toxic expo-
sures and clarification of the mechanisms of toxic sub-
stances and their toxicities using omics technologies.
Gene and genome knowledge have produced many
new omics that are very useful for the evaluation of
biological responses to toxic exposures and for the
clarification of the action mechanisms of toxic sub-
stances and their toxicities. García-Sevillano et al.
evaluated the influence of contamination, especially
metal pollution, using omics technologies at Doñana
National Park in Spain. However, in this area there is
metal contamination comes from mining and industrial
activities. Several studies have showed that there was a
metal pollution in sediments and waters as well as bio-
accumulation and effects on plants, other organisms
and human populations. They collected free-living
mice (M. spretus) in five sampling areas from the pos-
sible contaminated and control areas (low contamina-
tion area). Oligonucleotide microarrays were used
since there was gene sequence similarity between clas-
sical M. musculus and M. spretus. Microarrays identi-
fied 1872 spots which were differentially expressed in
animals living in the contaminated sites as compared
with low contaminated sites. 242 out of these spots
showed differential expression in contaminated sites
and 39 of them corresponded to transcript genes that
exhibited ≥10-fold increased or decreased expression in
animals from at least one contaminated site as com-
pared with the control. In mice living in these contami-
nated sites, it was found that there was a high accumu-
lation of toxic metals (Nickel; Ni, Arsenic; As,
Chrome; Cr, Cadmium; Cd and Lead; Pb). Quantifica-
tion was made by Quantitative Real Time –PCR (qRT-
PCR) and Western-blotting. Expressed genes were
classified into functional categories as follows; immune
response; 7 genes, stress response; 3 genes, cell cy-
cle/cell. The up- and –down regulation of these genes
were evaluated and were linked to oxidative stress re-
lated to pollution and the inflammatory response [38].
CONCLUSIONS
Systems biology is a global and detailed quantita-
tive analysis of the manner in which each interaction of
all components in a biological system is included.Such
analysis is made by investigators, who are also able to
develop required technologies and computational tools,
from different disciplines (biology, computer science,
engineering, bioinformatics, physics, immunology, and
Current Medicinal Chemistry, 2016, Vol. 23, No. 36 9
neurobiology). Automated DNA sequencers provide
genome sequence and detection of polymorphisms;
microarrays analyze transcripts and MS enables pro-
teomic and metabolomics profiling. Tremendous
amount of biological data, such as genetic sequences,
cell populations or protein samples, on the functional
and/or structural alterations within the cell is obtained
by these high throughput methods. These huge data are
analyzed by computational method which is a combi-
nation of computational biology and bioinformatics.
All information on genome with these methodologies
provides understanding of cellular functions in biologi-
cal system. Systems biology and omics technologies
together provide global understanding of the mecha-
nisms and give valuable flow information on biological
systems by studying of the interactions between differ-
ent components [7]. A comprehensive understanding of
biological system cannot be predicted by their individ-
ual parts, even with full understanding of the parts
alone. Systems biology and omics technologies with
holistic approach give comprehensive and valuable in-
formation, which assist to solve problems and over-
come challenges in various situations such as diseases
and therapy.
RECOMMENDATIONS
Omics and omics technologies have various advan-
tages and disadvantages. Therefore, to overcome the
challenges arising from different omics, it is better to
perform more than one or two omics together. The im-
portant point is to select a method which can eliminate
the disadvantages of another method. Furthermore, data
integration and interpretation should be meticulously
made.
CONFLICT OF INTEREST
The author(s) confirm that this article content has no
conflict of interest.
ACKNOWLEDGEMENTS
Declared none.
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