The document discusses various "omics" fields of study including genomics, proteomics, metabolomics, and others. It provides definitions and descriptions of each type of omics, focusing on the large sets of biological molecules they each study such as genomes, proteomes, metabolomes, etc. It explains that omics fields examine biological data on a large scale and provide insights into biological processes, functions, and interactions on a systems-wide level.
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Applications of genomics and proteomics pptIbad khan
Applications of genomics and proteomics ppt
genomics and proteomics ppt
in the field of health genomics and proteomics ppt
oncology ppt
biomedical application of genomics and proteomics ppt
agriculture application of genomics and proteomics ppt
proteomics in agriculture ppt
diagnosis of infectious disease ppt
personalized medicine ppt
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Applications of genomics and proteomics pptIbad khan
Applications of genomics and proteomics ppt
genomics and proteomics ppt
in the field of health genomics and proteomics ppt
oncology ppt
biomedical application of genomics and proteomics ppt
agriculture application of genomics and proteomics ppt
proteomics in agriculture ppt
diagnosis of infectious disease ppt
personalized medicine ppt
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
Personalized Medicine and the Omics Revolution by Professor Mike SnyderThe Hive
Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.
Meet the speaker, Professor Michael Snyder (Stanford):
Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. from the California Institute of Technology and postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has launched many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include; the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-of–the-art omics technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a co-founder of several biotechnology companies including; Protometrix (now part of Life Technologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
Personalized Medicine and the Omics Revolution by Professor Mike SnyderThe Hive
Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.
Meet the speaker, Professor Michael Snyder (Stanford):
Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. from the California Institute of Technology and postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has launched many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include; the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-of–the-art omics technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a co-founder of several biotechnology companies including; Protometrix (now part of Life Technologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.
Data analysis & integration challenges in genomicsmikaelhuss
Presentation given at the Genomics Today and Tomorrow event in Uppsala, Sweden, 19 March 2015. (http://connectuppsala.se/events/genomics-today-and-tomorrow/) Topics include APIs, "querying by data set", machine learning.
Resolving Ambiguity in Target ID Screens - CRISPR-Cas9 Based Essentiality Pro...Candy Smellie
Pathfinder Target Essentiality Assay Service
A new CRISPR─Cas9 based medium throughput assay service for validation of target gene essentiality
Can be used to resolve ambiguous screening results
Can also provide information on drug target suitability
This assay developed at Horizon will enable you to identify genes essential for the growth of specific cancer cell lines.
It can be used to definitively resolve ambiguous screening results.
Or to provide information on target suitability – by testing essentiality in “normal” cells, or in cancer subtypes different to the proposed patient population
Different omics platforms—genomics, transcriptomics, proteomics, metabolomics and fluxomics—are generating new insights into how biological systems work at a molecular level. Although each individual omics approach provides a global view of a specific cellular process, this view is limited to only one aspect. In order to gain a comprehensive understanding of the system as a whole, researchers are faced with the challenge of merging these different types of results.
PathVisio is an open source tool for drawing and editing biological pathways and visualizing and analyzing data. In order to make multi omics data visualization more intuitive we developed new add ons for the software to enable visualization of multiple data sets that can be about data of different types. This also allows visualization of data on the lines that symbolize interactions and reactions in the pathways, essentially adding edge visualization for network biology. In this way we can for instance show results of fluxomics studies or from dynamic system biology models.
Blueprints to blue sky – analyzing the challenges and solutions for IHC compa...Candy Smellie
Manual assessment of biomarker expression is associated with significant inter- and intra reader variability. In some cases there are also limitations when it comes to sensitivity and specificity of manual biomarker assessment.
In one example to the left, the “pure” contribution of inter-reader variability associated with Ki67 assessment was quantified across 20 tumors and 126 participating labs. In that study, it was demonstrated how image analysis can be used to significantly reduce inter-reader variability.
In a another study, the National Danish Validation study of Her2, it was demonstrated how improved sensitivity/specificity of quantitative HER2 protein expression wrt gene amplification lead to significant cost savings in reflex testing.
By automating aspects of stain quality control, it will become scalable to he point where EQA organizations may be able and willing to offer more frequent – perhaps even on-demand – proficiency testing and calibration services.
It is possible that objective and quantitative standards will contribute to improve compliance with protocol recommendations.
In clinical multi-center trials it will be easier to standardize and monitor data from each center.
And it is our hope tha larger diagnostic pathology labs will be able to benefit from such a method by closely monitoring drift in staining quality for biomarkers.
Challenges and opportunities in personal omics profilingSenthil Natesan
The term ‘‘omic’’ is derived from the Latin suffix ‘‘ome’’ meaning mass or many. Thus, OMICS involve a mass (large number) of measurements per endpoint. (Jackson et al., 2006)
The functional state of a cell can be explained by the integrated set of different OMICS data, called molecular signature or biomarker.The same fact can be exploited to find out difference between diseased and normal.
For diagnosis of a diseases in future, personal OMICS profiling (POP) is indispensible.
The POP further confer advantage to produce personal drugs, based on POP.
Biosimilar is the term coined for protein drugs that are similar, but not identical to, an existing product. Copies of biopharmaceuticals (proteins) that can be made after the patent on the original product has expired Example: Epoetin, G-CSF, insulin, somatropin
In interactome, basically for interaction of proteins there is certain key elements requited, they are: Interactomics and Proteomics, Complementation groups, Modifier screens 1. Interactomics and Proteomics
Field of interactomics is concerned with interactions between genes or proteins. They can be genetic interactions, in which two genes are mainly involved in the same functional pathway (leading to a particular phenotype), or physical interactions, in which there is direct physical contact between two proteins (or between protein and DNA) (Janga et al.,2008). 2. Complementation groups Using forward saturation genetics, one may recover several independent mutants with the same (or similar) phenotype (Hernández et al., 2007). There are two possibilities: a) Mutations are in the same gene b) Mutations are in different genes involved in the same pathway. Scenario
(b) Can be tested genetically with a complementation test:
Cross two homozygous mutants (samples) and observe heterozygous offspring phenotypes(samples)
Mutations in the same gene will not complement
offspring have mutant phenotype
Mutations in different genes will complement
offspring have wild
Type phenotype
Do pairwise crosses for all mutants to identify complementation groups
Typically each complementation group represents a different gene
If many mutations are recovered in the same genes, this implies saturation
Proteomics and its applications in phytopathologyAbhijeet Kashyap
Dear friends, I Abhijeet kashyap presenting the basics of proteomics to you all . Proteomics is the large-scale study of proteins, particularly their structures and functions.Proteomics helps in understanding the structure and function of different proteins as well as protein-protein interactions of an organism.
DOI:10.21276/ijlssr.2016.2.4.11
ABSTRACT- Every year more than 13 million deaths worldwide are due to environmental pollutants, and
approximately 24% of diseases are caused by environmental exposures that might be averted through preventive
measures. Out of all these environmental chemicals, effects of air pollution is responsible for death of 3.3 million people
prematurely worldwide - a figure that could double by 2050 if emissions continue to rise at the current rate. Increasing
number of evidences has linked environmental pollutants with epigenetic variations, including changes in DNA
methylation status, histone modifications and other factors like incorporation of miRNAs, nucleosome remodeling, etc.
These entire mechanisms are likely to play important roles in disease aetiology, and their modifications, thus providing
further understanding of disease aetiology, as well as biomarkers for these exposures to environmental chemicals and/or
prediction of the risk for the disease. In this, we had tried to summarize the different epigenetic alterations related to
environmental chemical exposures, and propose the probable mechanisms of action behind such epigenetic changes. We
will also focus onopportunities, challenges and further directions for future epidemiology research in environmental
epigenomics. Further studies are needed in this regard to solve methodological and practical challenges, including
uncertainties about stability over time of epigenomic changes induced by the environment, tissue specificity of epigenetic
alterations, validation of laboratory methods, and adaptation of bioinformatic and biostatistical methods to
high-throughput epigenomics. Moreover, there are several reports of epigenetic modifications arising from environmental
chemical exposures, but most have not been directly linked to disease endpoints. Key-words- Environmental chemicals, Epigenetics, Disease susceptibility
Interactomics, Integromics to Systems Biology: Next Animal Biotechnology Fron...Varij Nayan
“Organisms function in an integrated manner-our senses, our muscles, our metabolism and our minds work together seamlessly. But biologists have historically studied organisms part by part and celebrated the modern ability to study them molecule by molecule, gene by gene. Systems biology is critical science of future that seeks to understand the integration of the pieces to form biological
systems”
(David Baltimore, Nobel Laureate)
Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome.
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
How to Split Bills in the Odoo 17 POS ModuleCeline George
Bills have a main role in point of sale procedure. It will help to track sales, handling payments and giving receipts to customers. Bill splitting also has an important role in POS. For example, If some friends come together for dinner and if they want to divide the bill then it is possible by POS bill splitting. This slide will show how to split bills in odoo 17 POS.
Students, digital devices and success - Andreas Schleicher - 27 May 2024..pptxEduSkills OECD
Andreas Schleicher presents at the OECD webinar ‘Digital devices in schools: detrimental distraction or secret to success?’ on 27 May 2024. The presentation was based on findings from PISA 2022 results and the webinar helped launch the PISA in Focus ‘Managing screen time: How to protect and equip students against distraction’ https://www.oecd-ilibrary.org/education/managing-screen-time_7c225af4-en and the OECD Education Policy Perspective ‘Students, digital devices and success’ can be found here - https://oe.cd/il/5yV
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
This is a presentation by Dada Robert in a Your Skill Boost masterclass organised by the Excellence Foundation for South Sudan (EFSS) on Saturday, the 25th and Sunday, the 26th of May 2024.
He discussed the concept of quality improvement, emphasizing its applicability to various aspects of life, including personal, project, and program improvements. He defined quality as doing the right thing at the right time in the right way to achieve the best possible results and discussed the concept of the "gap" between what we know and what we do, and how this gap represents the areas we need to improve. He explained the scientific approach to quality improvement, which involves systematic performance analysis, testing and learning, and implementing change ideas. He also highlighted the importance of client focus and a team approach to quality improvement.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Ethnobotany and Ethnopharmacology:
Ethnobotany in herbal drug evaluation,
Impact of Ethnobotany in traditional medicine,
New development in herbals,
Bio-prospecting tools for drug discovery,
Role of Ethnopharmacology in drug evaluation,
Reverse Pharmacology.
1. OMICS ERA
Dr. Hetalkumar Panchal
Associate Professor
Gujarat Agricultural Biotechnology Institute (GABI)
Navsari Agriculture University,
Athwa Farm, Surat – 395007
swamihetal@gmail.com
29th Refresher Course :Bio-Sciences and Bio-Enginering (ID)
(02/06/2014 to 2/06/2014)
UGC-Academic Staff College,
Sardar Patel University,
Vallbh Vidyangar -38120, Dist. Anand, (Gujarat)
2. • OMICS
– The term ‘‘omic’’ is derived from the Latin suffix
‘‘ome’’ meaning mass or many. Thus, OMICS
involve a mass (large number) of measurements
per endpoint. (Jackson et al., 2006)
• Integration of OMICS data
– Efficient integration of data from different OMICS
can greatly facilitate the discovery of true causes
and states of disease, mostly done by softwares
(Andrew et al., 2006).
What is ‘omics’?
3. What is ‘omics’?
• In biological context , suffix –omics is used to
refer to the study of large sets of biological
molecules (Smith et al., 2005)
• The realization that DNA is not alone regulate
complex biological processes (as a result of
HGP, 2001), triggered the rapid development of
several fields in molecular biology that together
are described with the term OMICS.
• The OMICS field ranges from
– Genomics (focused on the genome)
– Proteomics (focused on large sets of proteins, the
proteome)
– Metabolomics (focused on large sets of small
molecules, the metabolome).
4. TYPES OF OMICS
Genomics
Computational genomics
Epigenomics
Functional genomics
Immunomics
Metagenomics
Pathogenomics
Regenomics
Personal genomics
Proteomics
Psychogenomics
4
5. GENOMICS
• The field of genomics has been divided into 3 major
categories.
– Genotyping (focused on the genome sequence),
• The physiological function of genes and the elucidation of the
role of specific genes in disease susceptibility (Syvanen, 2001)
– Transcriptomics (focused on genomic expression)
• The abundance of specific mRNA transcripts in a biological
sample is a reflection of the expression levels of the
corresponding genes (Manning et al., 2007)
– Epigenomics (focused on epigenetic regulation of
genome expression)
• Study of epigenetic processes (expression activities not involving
DNA) on a large (ultimately genome-wide) scale (Feinberg, 2007)
6. GENOTYPING
• Goal
– Identification of the physiological function of genes
– Role of specific genes in disease susceptibility (syvanen et al., 2001)
• Common Parameter used
– Among different variations (insertions, deletions, SNPs, etc.), single
nucleotide polymorphisms (SNPs) are the most commonly investigated
(Sachidanandam et al., 2001) and can be used as markers for diseases.
– Tag SNPs (informative subset of SNPs) and fine mapping are further
used to identify true cause of phenotype (patil et al., 2001).
• Application
– Identification of genes associated with disease
• Recent improvement in genotyping
– Array-based genotyping techniques, allowing the simultaneous
assessment (up to 1 million SNPs) per assay, leads to the genotyping of
entire genome known as genome-wide association studies (GWAS)
Jelly et al., 2010)
7. TRANSCRIPTOMICS
• Gene expression profiling
– The identification and characterization of the mixture of mRNA that is
present in a specific sample.
• Principle
– The abundance of specific mRNA transcripts in a biological sample
is a reflection of the expression levels of the corresponding genes
(Manning et al., 2007).
• Application
– To associate differences in mRNA mixtures originating from different
groups of individuals to phenotypic differences between the groups
(Nachtomy et al., 2007).
• Challenge
– The transcriptome in contrast to the genome is highly variable over
time, between cell types and environmental changes (Celis et al.,
2000).
8. EPIGENOMICS
• Epigenetic processes
– Mechanisms other than changes in DNA sequence that cause
effect in gene transcription and gene silencing30-32.
– Number of mechanisms of epigenomics but is mainly based on
two mechanisms, DNA methylation and histone modification28 33-
39.
– Recently RNAi has acquired considerable attention31 40 41.
• Goal
– The focus of epigenomics is to study epigenetic processes on a
large (ultimately genome-wide) scale to assess the effect on
disease28 29.
• Association with disease
– Hypermethylation of CpG islands located in promoter regions of
genes is related to gene silencing. 28 36. Altered gene silencing
plays a causal role in human disease31 34 37 38 42.
– Histone proteins are involved in the structural packaging of DNA
in the chromatin complex. Post translational histone
modifications such as acetylation and methylation are believed
to regulate chromatin structure and therefore gene expression34
37
9. PROTEOMICS
• Proteomics provides insights into the role proteins in biological systems. The
proteome consists of all proteins present in specific cell types or tissue and
highly variable over time, between cell types and will change in response to
changes in its environment, a major challenge (Fliser et al., 2007).
• The overall function of cells can be described by the proteins (intra- and inter-
cellular )and the abundance of these proteins (Sellers et al., 2003)
• Although all proteins are directly correlated to mRNA (transcriptome) , post
translational modifications (PTM) and environmental interactions impede to
predict from gene expression analysis alone (Hanash et al., 2008)
• Tools for proteomics
– Mainly two different approaches that are based on detection by
• mass spectrometry (MS) and
• protein microarrays using capturing agents such as antibodies.
• Major focuses
– the identification of proteins and proteins interacting in protein-complexes
– Then the quantification of the protein abundance. The abundance of a specific protein is
related to its role in cell function (Fliser et al., 2007)
10. METABOLOMICS
• The metabolome consists of small molecules (e.g.
lipids or vitamins) that are also known as metabolites
(Claudino et al., 2007).
• Metabolites are involved in the energy transmission in
cells (metabolism) by interacting with other biological
molecules following metabolic pathways.
• Metabolic phenotypes are the by-products of
interactions between genetic, environmental, lifestyle
and other factors (Holmes et al., 2008).
• The metabolome is highly variable and time
dependent, and it consists of a wide range of chemical
structures.
• An important challenge of metabolomics is to acquire
qualitative and quantitative information with
preturbance of environment (Jelly et al., 2010)
11. METABOLITES, METABOLOME & METABONOMICS
Metabolites are the intermediates and products of metabolism.
Within the context of metabolomics, a metabolite is usually
defined as any molecule less than 1 kDa in size.
Metabolome refers to the complete set of small-molecule
metabolites (such as metabolic intermediates, hormones and
other signaling molecules, and secondary metabolites) to be
found within a biological sample.
The word was coined in analogy with transcriptomics and
proteomics; like the transcriptome and the proteome, the
metabolome is dynamic, i.e. changing from second to second.
Metabonomics is defined as "the quantitative measurement of
the dynamic multiparametric metabolic response of living
systems to pathophysiological stimuli or genetic modification".
11
12. METAGENOMICS,
Metagenomics is the study of
metagenomes, genetic material recovered
directly from environmental samples. The
broad field may also be referred to as
environmental genomics, ecogenomics or
community genomics.
12
13. COMPUTATIONAL GENOMICS
Computational genomics (often referred to as
Computational Genetics) refers to the use of
computational and statistical analysis to decipher
biology from genome sequences and related
data,[1] including both DNA and RNA sequence as
well as other "post-genomic" data (i.e. experimental
data obtained with technologies that require the
genome sequence, such as genomic DNA
microarrays). These, in combination with
computational and statistical approaches to
understanding the function of the genes and
statistical association analysis, this field is also often
referred to as Computational and Statistical
Genetics/genomics.
13
14. EPIGENETICS
Genomic modifications that alter gene
expression that cannot be attributed to
modification of the primary DNA sequence
and that are heritable mitotically and
meiotically are classified as epigenetic
modifications. DNA methylation and histone
modification are among the best
characterized epigenetic processes
14
15. FUNCTIONAL GENOMICS
Functional genomics is a field of molecular biology that
attempts to make use of the vast wealth of data
produced by genomic projects (such as genome
sequencing projects) to describe gene (and protein)
functions and interactions. Unlike genomics, functional
genomics focuses on the dynamic aspects such as
gene transcription, translation, and protein–protein
interactions, as opposed to the static aspects of the
genomic information such as DNA sequence or
structures. Functional genomics attempts to answer
questions about the function of DNA at the levels of
genes, RNA transcripts, and protein products. A key
characteristic of functional genomics studies is their
genome-wide approach to these questions, generally
involving high-throughput methods rather than a more
traditional “gene-by-gene” approach.
15
16. IMMUNOMICS
Immunomics is the study of immune system
regulation and response to pathogens using
genome-wide approaches. With the rise of
genomic and proteomic technologies,
scientists have been able to visualize
biological networks and infer interrelationships
between genes and/or proteins; recently, these
technologies have been used to help better
understand how the immune system functions
and how it is regulated.
16
17. PATHOGENOMICS
Pathogen infections are among the leading causes of
infirmity and mortality among humans and other animals
in the world.[1] Until recently, it has been difficult to
compile information to understand the generation of
pathogen virulence factors as well as pathogen
behaviour in a host environment. The study of
Pathogenomics attempts to utilize genomic and
metagenomics data gathered from high through-put
technologies (e.g. sequencing or DNA microarrays), to
understand microbe diversity and interaction as well as
host-microbe interactions involved in disease states.
The bulk of pathogenomics research concerns itself with
pathogens that affect human health; however, studies
also exist for plant and animal infecting microbes.
17
18. REGENOMICS
Regenomics represents the merger of two fields of
scientific endeavor: Regenerative medicine[1] and
genomics.[2][3][4] New technologies to reprogram aged
somatic cells back to pluripotency and to restore
telomere length are currently used in research in
regenerative medicine,[5] though FDA-approved cellular
therapies using reprogrammed cells are currently not
available in the United States.[6] The culture and
banking of somatic cells also allows the parallel
sequencing of their nuclear DNA to provide individuals
with potentially valuable information for guiding them in
lifestyle choices, but also one day, potentially in
preventative strategies where cell types are made in
advance for high risk categories of disease, i.e.
preparing cardiac progenitor cells for individuals at high
risk for heart disease.
18
19. PERSONAL GENOMICS
Personal genomics is the branch of genomics concerned with
the sequencing and analysis of the genome of an individual.
The genotyping stage employs different techniques, including
single-nucleotide polymorphism (SNP) analysis chips (typically
0.02% of the genome), or partial or full genome sequencing.
Once the genotypes are known, the individual's genotype can
be compared with the published literature to determine
likelihood of trait expression and disease risk.
Use of personal genomics in predictive and precision
medicine[edit]
Predictive medicine is the use of the information produced by
personal genomics techniques when deciding what medical
treatments are appropriate for a particular individual. Precision
medicine is focused on "a new taxonomy of human disease
based on molecular biology“.
19
36. II. FAMILY CLASSIFICATION METHODS
Multiple Sequence Alignment and Phylogenetic Analysis
ClustalW Multiple Sequence Alignment
Alignment Editor & Phylogenetic Trees
Searches Based on Family Information
PROSITE Pattern Search
Motif and Profile Search
Hidden Markov Model (HMMs)
36
53. IV. PROTEIN FAMILY DATABASES
Whole Proteins
PIR: Superfamilies and Families
COG (Clusters of Orthologous Groups) of Complete
Genomes
ProtoNet: Automated Hierarchical Classification of Proteins
Protein Domains
Pfam: Alignments and HMM Models of Protein Domains
SMART: Protein Domain Families
Protein Motifs
PROSITE: Protein Patterns and Profiles
BLOCKS: Protein Sequence Motifs and Alignments
PRINTS: Protein Sequence Motifs and Signatures
Integrated Family Databases
iProClass: Superfamilies/Families, Domains, Motifs, Rich
Links
InterPro: Integrate Pfam, PRINTS, PROSITES, ProDom,
SMART
53
56. PROTEIN MOTIFS
56
PROSITE is a database of protein families and domains.
It consists of biologically significant sites, patterns and
profiles. (http://www.expasy.ch/prosite/)
57. INTEGRATED FAMILY CLASSIFICATION
InterPro: An integrated resource unifying PROSITE, PRINTS, ProDom,
Pfam, SMART, and TIGRFAMs, PIRSF.
(http://www.ebi.ac.uk/interpro/search.html)
57
58. V. DATABASES OF PROTEIN FUNCTIONS
Metabolic Pathways, Enzymes, and Compounds
Enzyme Classification: Classification and Nomenclature of Enzyme-Catalysed Reactions (EC-
IUBMB)
KEGG (Kyoto Encyclopedia of Genes and Genomes): Metabolic Pathways
LIGAND (at KEGG): Chemical Compounds, Reactions and
Enzymes
EcoCyc: Encyclopedia of E. coli Genes and Metabolism
MetaCyc: Metabolic Encyclopedia (Metabolic Pathways)
WIT: Functional Curation and Metabolic Models
BRENDA: Enzyme Database
UM-BBD: Microbial Biocatalytic Reactions and Biodegradation Pathways
Klotho: Collection and Categorization of Biological Compounds
Cellular Regulation and Gene Networks
EpoDB: Genes Expressed during Human Erythropoiesis
BIND: Descriptions of interactions, molecular complexes and
pathways
DIP: Catalogs experimentally determined interactions
between proteins
RegulonDB: Escherichia coli Pathways and Regulation
58
59. KEGG METABOLIC & REGULATORY PATHWAYS
59
(http://www.genome.ad.jp/dbget-
bin/show_pathway?hsa00590+874)
KEGG is a suite of databases and associated software, integrating our current
knowledge
on molecular interaction networks, the information of genes and proteins, and of
chemical
compounds and reactions. (http://www.genome.ad.jp/kegg/kegg2.html)
60. BIOCYC (ECOCYC/METACYC METABOLIC PATHWAYS)
60
The BioCyc Knowledge Library is a collection of
Pathway/Genome
Databases (http://biocyc.org/)
64. VI. DATABASES OF PROTEIN STRUCTURES
Protein Structure and Classification
PDB: Structure Determined by X-ray Crystallography and
NMR
CATH: Hierarchical Classification of Protein Domain
Structures
SCOP: Familial and Structural Protein Relationships
FSSP: Protein Fold Family Database
Protein Sequence-Structure Relationship
PIR-NRL3D: Protein Sequence-Structure Database
PIR-RESID: Protein Structure/Post-Translational
Modifications
HSSP: Families and Alignments of Structurally-Conserved
Regions
64
67. 67
PDB: EXPERIMENTAL 3D STRUCTURE
REPOSITORY
(http://www.rcsb.org/pdb/)
Rat gamma-crystallin,
chain A, B.
Can you do a
text search at
PIR to find this?
72. VII. PROTEOMIC RESOURCES
72
GELBANK (http://gelbank.anl.gov): 2D-gel patterns from completed
genomes; SWISS-2DPAGE (http://www.expasy.org/ch2d/)
PEP: Predictions for Entire Proteomes: (http://cubic.bioc.columbia.edu/
pep/): Summarized analyses of protein sequences
Proteome BioKnowledge Library: (http://www.proteome.com): Detailed
information on human, mouse and rat proteomes
Proteome Analysis Database (http://www.ebi.ac.uk/proteome/): Online
application of InterPro and CluSTr for the functional classification of
proteins in whole genomes
Expression Profiling databases: GNF (http://expression.gnf.org/cgi-
bin/index.cgi, human and mouse transcriptome), SMD (http://genome-
www5.stanford.edu/MicroArray/SMD/, Stanford microarray data
analysis), EBI Microarray Informatics (http://www.ebi.ac.uk/microarray/
index.html , managing, storing and analyzing microarray data)