Genome Database

The Genome Database (GDB) is the official central repository for genomic mapping data resulting from the Human Genome Initiative. It was
established at Johns Hopkins University in Baltimore, Maryland, USA in 1990. In 1999, the Bioinformatics Supercomputing Centre (BiSC) at
The Hospital for Sick Children in Toronto, Ontario, Canada, assumed the management of GDB. The Human Genome Initiative is a worldwide
research effort to analyze the structure of human DNA and determine the location and sequence of the estimated 100,000 human genes. In
support of this project, GDB stores and curates data generated worldwide by those researchers engaged in the mapping effort of the Human
Genome Project (HGP).
GDB's mission is to make available to scientists an encyclopedia of the human genome that is being constantly revised and updated to reflect the
current state of scientific knowledge. Although GDB has historically focused on gene mapping, as the Genome Project moves from mapping to
sequence to functional analysis, GDB's focus will be broadened. Extensions are under development in the representation of sequence-level
genome content, including DNA sequence variations, along with richer descriptions of function and phenotype.
The task of curating the content of this genomic encyclopedia and maintaining its correctness and currency is enormous. Members of the
scientific community participate by submitting their data, adding annotations to existing data, and adding links from objects in GDB to related
objects in other databases. GDB is, in a sense, an experiment in a new form of collaborative scientific publication, a community-curated
database.
Genomics
Genomics is an area within genetics that concerns the sequencing and analysis of an organism’s genome. The genome is the entire DNA content
that is present within one cell of an organism. Experts in genomics strive to determine complete DNA sequences and perform genetic mapping to
help understand disease.
Genomics also involves the study of intragenomic processes such as epistasis, heterocyst and pleiotropic as well as the interactions between loci
and alleles within the genome. The fields of molecular biology and genetics are mainly concerned with the study of the role and function of
single genes, a major topic in today’s biomedical research. By contrast, genomics does not involve single gene research unless the purpose is to
understand a single gene’s effects in context of the entire genome. As per the definition from the United States Environmental Protection
Agency, genomics concerns a wider line of scientific inquiry and associated techniques than it did initially. Genomics involves the study of all
genes at the DNA, mRNA, and proteome level as well as the cellular or tissue level Genomics is a concept that was first developed by Fred
Sanger who first sequenced the complete genome of a virus and of a mitochondrion. He initiated the practice of sequencing and genome
mapping as well as developing bioinformatics and data storage in the 1970s and 1980s.The knowledge about genes that has so far been gathered
has led to the emergence of functional genomics, a field concerned with trying to understand the pattern of gene expression, especially across
different environmental conditions.
The term genomics was first coined in 1986 by Tom Roderick, a geneticist at the Jackson Laboratory in Maine, during a meeting about the
mapping of the human genome.
Genomic expression
Gene expression is the process by which the instructions in our DNA are converted into a functional product, such as a protein.

 When the information stored in our DNA Is converted into instructions for making proteins Or other molecules, it is called gene
expression
 Gene expression is a tightly regulated process that allows a cell to respond to its changing environment.
 It acts as both an on/off switch to control when proteins are made and also a volume control that increases or decreases the amount of
proteins made.
There are two key steps involved in making a protein, transcription and translation.
Transcription

 Transcription is when the DNA in a gene is copied to produce an RNA Transcript called messenger RNA (mRNA).
 This is carried out by an enzyme Called RNA polymerase which uses available bases from the nucleus of the cell to form the mRNA.
 RNA is a chemical similar in structure and properties to DNA, but it only has a single strand of bases and instead of the base thymine (T),
RNA has a base called uracil (U).
Translation

 Translation occurs after the messenger RNA (mRNA) has carried the transcribed ‘message’ from the DNA to protein-making factories in
the cell, called ribosomes
 The message carried by the mRNA is read by a carrier molecule called transfer RNA (tRNA).
  The mRNA is read three letters (a codon) at a time.
 Each codon specifies a particular amino acid. For example, the three bases ‘GGU’ code for an amino acid called glycine.
 As there are only 20 amino acids but 64 potential combinations of codon, more than one codon can code for the same amino acid. For
example, the codons ‘GGU’ and ‘GGC’ both code for glycine.
 Each amino acid is attached specifically to its own tRNA molecule.
 When the mRNA sequence is read, each tRNA molecule delivers its amino acid to the ribosome and binds temporarily to the
corresponding codon on the mRNA molecule.
 Once the tRNA is bound, it releases its amino acid and the adjacent amino acids all join together into a long chain called a polypeptide.
 This process continues until a protein is formed.
 Proteins carry out most of the active functions of a cell.

Proteomics

Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. We
may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not
constant; it differs from cell to cell and changes over time. To some degree, the proteome reflects the underlying transcriptome. However,
protein activity (often assessed by the reaction rate of the processes in which the protein is involved) is also modulated by many factors in
addition to the expression level of the relevant gene.

Proteomics is used to investigate

 when and where proteins are expressed;

 rates of protein production, degradation, and steady-state abundance;
 how proteins are modified (for example, post-translational modifications (PTMs) such as phosphorylation);
 the movement of proteins between subcellular compartments;
 the involvement of proteins in metabolic pathways;
 How proteins interact with one another.
Proteomics can provide significant biological information for many biological problems, such as:
  Which proteins interact with a particular protein of interest (for example, the tumour suppressor protein p53)
 Which proteins are localized to a subcellular compartment (for example, the mitochondrion)
 Which proteins are involved in a biological process (for example, circadian rhythm)

Difference between genomics and proteomics

S.N. Character Genomics Proteomics

Genomics is the study of genomes Proteomics is the branch of molecular

which refers to the complete set of genes biology that studies the set of proteins
1.       Definition
or genetic material present in a cell or expressed by the genome of an
organism. organism.

Genomics is the study of the genes in an Proteomics is the study of the

2.       Study of
organism. all the proteins in a cell.

The study of the function of

3.       Unit under Study The study of the function of genomes
proteomes

4.       Nature of Study The genome is constant. Every cell of an Proteome is dynamic and varies. The
Material organism has the same set of genes. set of proteins produced in different
tissues varies according to the gene

Use of High throughput
5.       the genomics to map, sequence, and
techniques
6.       Techniques involved
7.       Types
High throughput techniques are used in
analyze genomes.
The techniques involved in genomics
include gene sequencing strategies such
as directed gene sequencing, whole
genome shotgun sequencing,
construction of expressed sequence tags
(ESTs), identification of single
nucleotide polymorphisms (SNPs), and
the analysis and interpretation of
sequenced data using different software
and databases.
The two types of genomics are structural
genomics and functional genomics.
expression.
In proteomics, characterization of the
3D structure and the function of
proteins is carried out by the use of
high throughput methods.
Techniques involved in proteomics
include extraction and electrophoretic
separation of proteins, digestion of
proteins with the use of trypsin into
small fragments, determination of the
amino acid sequence by mass
spectrometry, and identification of
proteins using the information in the
protein databases. Moreover, the 3D
structure of the protein can be
predicted using software-based
methods. The expression of proteins
can be studied by protein microarrays.
Protein-network maps can be
developed to determine protein-
protein interactions. 
The three types of proteomics are
structural, functional, and expression

Important Areas Genome sequencing projects such as the
8.       Human Genome Project are the
  important areas of genomics.
Genomic studies are important to
understand the structure, function,
9.       Importance
location, regulation of the genes of an
organism.
Genes in the nucleus may not accurately
portray conditions in the cell due to
10.    Significance regulation at the RNA and protein level
that can not be viewed in Genomics
studies.
proteomics.
Proteome database developments
such as SWISS-2DPAGE and
software development for computer-
aided drug design are the important
areas of proteomics.
The study of the entire set of proteins
produced by a cell type is done in
order to understand its structure and
function.
Proteomics studies are more
beneficial because proteins are the
functional molecules in cells and
represent actual conditions.