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Finding guide to terms in these glossaries Site
Map Related glossaries include
Applications Biomarkers
Bioprocessing & manufacturing Drug
discovery & development Molecular
Diagnostics Molecular
Medicine Proteomics
Informatics Algorithms
& data management Bioinformatics
Information management & interpretation
Technologies Metabolic engineering &
profiling Microarrays &
protein arrays Sequencing
Biology Sequences,
DNA & beyond Functional
Genomics Genomics
-Omes &
-omics Phylogenomics
This Expression glossary seems to have a number of terms
which could be synonymous (i.e. expression, gene expression, various profiling
terms) Are there subtle differences and/ or ambiguities?
alternative transcripts:
Demands on Microarray Design for the evaluation of gene
regulation, Genomatix http://www.genomatix.de/download/documents/AltPromoterMicroarrays.pdf
Google = about 959 Aug. 12, 2002;
about 4,610 Aug. 22, 2003; about 11,500 Apr. 27, 2005, including academic
transcripts.
analysis - gene expression:
Large- scale
methods for analyzing gene expression patterns are needed. The current
challenge is to develop and optimize methods for monitoring these and the
gene products simultaneously. What is needed is genomic scale analysis
of gene expression. Google = about 336,000 Aug. 12, 2002;
about 592,000 Aug. 22, 2003 Related terms: post hoc testing,
statistical analysis; guilt by association Algorithms
glossary cluster analysis, pattern recognition; Microarrays
glossary data analysis, standards
analysis - protein expression:
Remarkable advances are taking place in
protein expression analysis, but major hurdles still loom ahead. 2D gels must be
completely eliminated because they are so cumbersome, and all the steps in
protein expression study must become much more easily reproducible and more
affordable before they will enable researchers to significantly further our
knowledge of protein expression. Another major challenge is to improve
quantification of proteins. It is not sufficient to find a protein is expressed;
one must also know how much is expressed to be able to identify important
patterns. Google = about 38,000 Aug. 12, 2002;
about 130,000 Aug 22, 2003 [analysis "protein expression"]
artificial transcription factors: Regulated gene expression is
critical for cellular existence, and a disruption in the regulatory network can
result in disease or death. Therefore, a goal of primary importance in the
scientific community has been to discover methods of reprogramming gene
expression in diseased cells while leaving normal cells unaffected. Our
understanding of transcription, an early step in gene expression, has now
reached a sufficiently sophisticated level to allow us to tackle this challenge
from a chemical perspective. Dendritic and polymeric structures designed to
functionally mimic the protein participants in activation and repression of
transcription will be examined through in vitro assays and cell culture
experiments. Organic synthesis will play a critical role in this effort. By
varying the synthetic approaches to the artificial transcription factors, their
overall function as activators and/ or repressors can be controlled and important
characteristics such as cell membrane permeability and tissue- type specificity
can be addressed. Anna K. Mapp "Chemistry at the Univ. of Michigan, 2001 http://www.umich.edu/~michchem/faculty/mapp/
Google = about 49 Aug. 12, 2002;
about 347 Aug. 22, 2003 Broader term: transcription factor
basal transcription factors:
Typically defined as the minimal complement of proteins necessary to reconstitute accurate transcription from
a minimal promoter (such as a TATA element or initiator sequence). They are distinct from the regulatory transcription factors, which bind to
sequences farther away from the initiation site and serve to modulate levels of transcription. This regulation presumably occurs through
interactions between the regulatory and basal transcription factors, although there is a great deal of controversy about the identity of the
regulatory factors' "target(s)" The basal transcription complex assembles through an extensive series of protein-protein interactions. Although the basal factors can assemble
on the promoter in a step- wise manner in vitro, there is some evidence that many of the factor interactions can occur in the absence of DNA and
that some of the factors may pre- assemble into a "holoenzyme". Steve Buratowski,
Basal Transcription Factor Information, Harvard Medical School, 1999] http://tfiib.med.harvard.edu/transcription/basaltx.html
Google = about 795 Aug. 12, 2002;
about 2,070 Aug. 22, 2003
biological
networks: We are amongst the first groups to
describe how many weak functional genomic features could be systematically
integrated with data mining techniques to predict protein networks (comprising
protein interactions and other functional linkages). Some of the features
integrated were obviously related to protein interactions (e.g. expression
correlations) but many others such as (e.g. essentiality) were less so. We have
had a number of localization and interaction predictions experimentally
verified. In more recent work, we were able to calibrate the degree to which the
data quality and the specific mining approach is associated with the strength of
the predictions. In addition, we have studied the structure of protein networks,
both on a large-scale in terms of global statistics (e.g. the diameter) and on a
small-scale in terms of local network motifs (e.g. hubs). In particular, we have
correlated network hubs with gene essentiality. Most importantly, we were the
first to study the dynamics of regulatory networks. This allowed us to discover
changing transient hubs and systematic patterns of connectivity rewiring in the
yeast regulatory network. We were able to show for the first time that network
dramatically changes in different conditions. Gerstein Lab Publications, Yale
University, 2007 http://papers.gersteinlab.org/papers/subject/interactions/
Google
= about 4,740 Aug. 22, 2003; about 293,000 June 11, 2007
cell expression profiles: Cell biology glossary
Google = about 31 Aug. 12, 2002;
about 45 Aug. 22, 2003
cell- specific gene expression:
The essence of multicellularity is the ability to express only certain portions
of the genome
in particular cells at particular times. This is done by the synthesis and
assembly of transcription
factors that turn on (and off) specific genes as required. John W. Kimball,
Detecting Cell Specific Gene Expression, Kimball's Biology Pages, 2005 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/ReporterGenes.html
Google = about 681 Aug. 12, 2002;
about 1,660 Aug. 22, 2003; about 5,120 Apr. 27, 2005; about 66,000 June 11, 2007
clinical profiling - gene expression:
Gene
expression profiling has the potential to be used for differentiating types
of cancer (and other diseases) that appear identical to pathologists today.
Once the technologies are capable of high throughput and sufficient specificity and reproducibility this
will represent significant potential markets for diagnostics, choosing
appropriate therapies, and ongoing monitoring. Google = about 15 Aug. 12, 2002;
about 26, Aug. 22, 2003
conditional gene expression:
When
gene expression is activated or suppressed at will. Google = about 236 Aug. 12, 2002;
about 558 Aug. 22, 2003, about 21,800 Sept 7, 2007
co-regulation - expression: Correlated change(s)
in gene or protein expression
diauxic shift:
A shift in gene expression
that occurs when cells are transferred from a rich medium to a poorer medium,
or when cells in a rich medium grow and deplete their medium of nutrients.
Google = about 1,420 Aug. 12, 2002;
about 1,930 Aug. 22, 2003
differential display:
A theoretically powerful approach in which
researchers use multiplex quantitative reverse transcription- polymerase chain
reaction (QRT- PCR) to amplify – and illuminate – differences in gene
expression between healthy and diseased tissue or between treated versus
nontreated tissue. ... a single gel
can "sample" a significant portion of the expressed complement of
genes in a given tissue, under different physiological/ pharmacological
conditions. This technology has
not been universally successful and has not gained widespread acceptance due to
technical complexities. Differential display is an attractive approach, because it (a) searches for differences in gene expression in the
absence of preconceived biases; and (b) does not require extensive preexisting
knowledge concerning genes of interest. As such, this technique is especially
useful for identifying novel gene- disease associations. Google = about
22,700 Aug. 22, 2003; about 692,000 June 11, 2007 Related term: RT-PCR
Gene
amplification & PCR glossary
Differential Gene Expression DGE:
DGE and
proteomics are screening technologies that are widely used for target validation.
They detect different levels and/or patterns of gene and protein expression
in tissues, which may be used to imply a relationship to a disease affecting
that tissue … the proof- of- concept experiments to demonstrate that differences
in the tissue expression of a particular gene are related to disease expression
(two very different meanings to ‘expression’) have not been performed in
any common disease with known susceptibility genes. Allen D. Roses” Pharmacogenetics
and the practice of medicine” Nature 405: 857- 865 June 15, 2000 An important tool for assembling exons into genes.
D. Shoemaker et. al.
"Experimental annotation of the human genome using microarray
technology" Nature 6822: 925, 15 Feb. 2001
differential protein expression profiling: http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2006/5/i05/abs/pr050455t.html
Google
= about 24 Aug. 22, 2003; about 3,080 June 11, 2007
DNA
profiling techniques
Wikipedia http://en.wikipedia.org/wiki/DNA_profiling
notes "not to be confused with full genome sequencing" accessed
Feb 24 2011
wikipedia http://en.wikipedia.org/wiki/
Category:DNA_profiling_
techniques
downregulation:
A negative regulatory effect on physiological
processes at the molecular, cellular, or systemic level. At the molecular level,
the major regulatory sites include membrane receptors, genes (GENE EXPRESSION
REGULATION), mRNAs (RNA, MESSENGER), and proteins. MeSH, 2002
Wikipedia http://en.wikipedia.org/wiki/Downregulation
Downregulation and upregulation
EVGs Expression Verified Genes:
Co- regulated exons, from Chromosome 22 (the first human chromosome to be
completely sequenced) and used as a benchmark for computational and experimental
analytical methods. Expression data can define gene boundaries because adjacent
exons that are co- regulated across many conditions are likely to be from the
same transcript. Hybridization data defining EVGs could be useful to
"train" next generation gene prediction algorithms. D. Shoemaker et.
al. "Experimental annotation of the human genome using microarray
technology" Nature 6822: 922- 927, 15 Feb. 2001 Google = about 5 Aug. 12, 2002;
about 53 Aug. 22, 2003, about 64 Sept 7, 2007
epigenetic imprinting: A key component of future genomic research and
drug development will be the study of epigenetic imprinting (drug- or
environment-induced changes in gene expression) indicative of disease and/or
pharmacological or environmental exposure. Google = about 48 Aug. 12, 2002;
about 101 Aug. 22, 2003; about 619 June 11, 2007
expression:
The cellular production
of the protein encoded by a particular gene. The process includes
transcription of DNA, processing of the resulting mRNA product and its
translation into an active protein. N.B. A recombinant gene inserted
into a host cell by means of a vector is said to be expressed if the synthesis
of the encoded polypeptide can be demonstrated. [IUPAC Bioinorganic,
IUPAC Compendium]
A description as to how a gene demonstrates
a phenotype. This can range from production of a mRNA to a disease.
If a disease gene carrier shows signs of the disease gene, then that gene
is expressed. Note that an individual must carry the disease gene
and be penetrant for it before the term expression is utilized.
[NHLBI] Narrower terms: gene expression, protein expression, mRNA
expression, RNA expression, transcript expression Expression databases
Databases & software
directory
expression genomics: Genome-wide
expression microarray studies have revealed that the biological and clinical
heterogeneity of breast cancer can be partly explained by information embedded
within a complex but ordered transcriptional architecture. Comprising this
architecture are gene expression networks, or signatures, reflecting biochemical
and behavioral properties of tumors that might be harnessed to improve disease
subtyping, patient prognosis and prediction of therapeutic response. Miller,
Lance D, Liu, Edison T, Expression
genomics in breast cancer research: microarrays at the crossroads of biology and
medicine Breast Cancer Research 2007, 9:206 doi:10.1186/bcr1662, March 2007
Google
= about 1,330 Aug. 22, 2003; about 39,400 June 11, 2007
expression mapping: Maps genomic & genetic
Google = about 1,130 Aug. 12, 2002;
about 2,390 Aug. 22, 2003; about 68,900 June 11, 2007
expression maps: Maps genomic & genetic
Narrower terms: gene expression maps, expression imbalance map, protein expression map, self- organizing maps, transcript maps
Related terms: EST maps, genome control maps Google = about 452 Aug. 12, 2002;
about 733 Aug. 22, 2003; about 23,000 June 11, 2007
expression pharmacogenomics: Pharmacogenomics
glossary Google = about 42 Aug. 12, 2002;
about 58 Aug. 22, 2003; about 218 June 11, 200, about 584 Apr 6, 2009
expression product: Related term Gene
definitions gene product Google = about 1,290 Aug. 12, 2002;
about 2,680 Aug. 22, 2003, about 91, 200 Apr 6, 2009
expression profiling:
In an attempt to avoid expensive late-stage candidate failures,
pharmaceutical companies apply increasingly stringent compound characterization
and selection processes. Gene expression profiling is becoming increasingly
adopted in small molecule drug development programs to characterize
pharmacological and toxicological activity.
Refers to the expression
values for a single gene across many experimental conditions, or for many
genes under a single condition. In the terminology of cluster format [Algorithms
glossary], the first case amounts to looking at a row of the data table,
and the second case a column. Google = about 14,200 Aug. 12, 2002;
about 51,500 Aug. 22, 2003; about 120,000 Sept. 16, 2004, about 1,470,000 Apr 6,
2009 Narrower terms: gene
expression profiling, protein expression profiling, transcript
profiling. Related terms: gene expression, molecular indexing, protein expression, RNA
expression, transcript expression
PEPR
Public Expression Profiling Resource,
Children's National Medical Center, Microarray Center http://microarray.cnmcresearch.org/pgagoals.asp
expression proteomics:
The ability to measure protein- level changes
directly would seem to carry inherent advantages and it seems likely that
expression proteomics will be a useful tool in drug target discovery and
in studying the effects of various biological stimuli on the cell. Weir
& Blackstock “Proteomics” Trends in Biotechnology: 121-134 Mar
1999
Large- scale
measurements of protein expression. Google = about 668 July 10, 2002;
about 1,250 Aug. 22, 2003
expression systems: include cell free, transient, microbial,
stable cell lines, mammalian cell lines, plants and transgenic animals.
expression technologies: Chromatography
& electrophoresis, Gene
amplification & PCR Microarrays
have been a breakthrough
technology for studying gene expression.
Google = about 1,140 Aug. 12, 2002;
about 1,630 Aug. 22, 2003, about 42,600 Sept 7, 2007 Narrower terms: differential display, RAGE, SAGE, subtraction cloning, TOGA.
gene clustering:
Cluster methods include: finding
genes similar to the current selected gene within a "distance"
threshold; K-means-like clustering where you specify a seed gene and the
number of clusters; and hierarchical clustering with clustergram and
dendrogram graphics. National Cancer Institute, MicroArray Explorer http://www.lecb.ncifcrf.gov/MaeRefMan/hmaeDoc2.4.5.html#clusterPlots
Related terms: Algorithms
glossary cluster analysis, hierarchical clustering, k- means
clustering, self organizing maps
Google = about 604 Aug. 12, 2002;
about 1,630 Aug. 22, 2003
Eisen
Lab, Lawrence
Berkeley National Lab, US http://rana.lbl.gov/
gene expression:
The process by
which a gene’s coded information is converted into the structures present
and operating in the cell. Expressed genes include those that are
transcribed into mRNA and then translated into protein and those that are
transcribed into RNA but not translated into protein (e.g. transfer [tRNA]
and ribosomal [rRNA] RNAs). [DOE]
The phenotypic manifestation of a gene or genes by the processes of gene action.
MeSH, 1990
The transcription of a gene and its processing to yield a
mature messenger RNA (mRNA). (Note that in proteomic studies, the same
term also includes the translation of the mRNA to produce a functional protein.)
In studies of differential gene expression, one looks for genes whose expression
levels differ significantly under different experimental conditions, for example
in normal versus diseased states or in untreated versus treated subjects. This
application is perhaps the most obvious use of microarrays.
Our modern concept of gene expression dates
back to 1961 when messenger RNA was discovered, the genetic code was deciphered,
and the theory of genetic regulation of protein synthesis was described. [O
Ermolaeva et al “Data Management and analysis for gene expression arrays”
Nature Genetics 20: 19- 23,1998
Google = about 592,000 Aug. 12, 2002;
about 1,100,000 Aug. 22, 2003 Broader terms: expression,
genome expression.
Glossary
of gene expression terms,
Wikipedia http://en.wikipedia.org/wiki/Glossary_of_gene_expression_terms
Trends and Challenges in Gene Expression Data Collection and Analysis:
Commentary from Gene Logic,
CHI's GenomeLink 16.2 http://www.chidb.com/newsarticles/issue16_2.asp
Gene expression databases Databases
& software directory
gene expression informatics:
"Gene expression informatics- it's
all in your mine" Douglas E. Bassett Jr. , Nature Genetics 21(1 Supplement): 51- 55,
Jan 1999. http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/full/ng0199supp_51.html
Google = about 262 Aug. 12, 2002;
about 416, Aug. 22, 2003 Related terms: gene expression database mining; Microarrays
data analysis - microarrays
gene expression profiling:
Biology is not static –
neither are the tools and technologies that support genomic discovery for basic
and pharmaceutical research. Gene expression profiling is preferred,
providing common language for finding relationships between health and disease;
genetic changes as a result of therapy; markers for toxicology and drug safety;
and even potentially leading to personalized medicine. Additionally,
it may be possible to capture these revealing expression profiles with as few as
a thousand transcripts. Advances
in Gene Expression Profiling: Technologies Transcripts Therapies Nov 2009
Philadelphia PA order CD
The determination of the pattern of genes expressed i.e., transcribed, under specific circumstances or in a specific cell.
MeSH, 2000
Involves
studying the expression (as mRNA) of thousands of genes in a cell or tissue, and
how gene expression changes under various conditions. ... A major goal of
expression- profiling studies is to gain evidence for coordinate control of the
expression of sets of genes. In studying a disease process, one is interested in
how the expression of large sets of genes may covary in health and disease. Such
analysis is expected to help elucidate gene regulatory networks (e.g.,
molecular networks within the cell by which groups of genes are coordinately
controlled) and biochemical pathways. It is also expected to help
researchers determine how intracellular networks and pathways may be disrupted
in disease processes or altered by drugs. Google = about 7,630 Aug. 12, 2002'
about 31, 500 Aug. 22, 2003, about 4,610,000 Apr 6, 2009
Related terms: expression
profile, expression profiling. Related term protein expression
Wikipedia
http://en.wikipedia.org/wiki/Expression_profiling
gene expression regulation:
Any of the processes by which nuclear,
cytoplasmic, or intercellular factors influence the differential control of gene
action at the level of transcription or translation. These processes include
gene activation and genetic induction. MeSH, 1981 Google = "gene expression regulation" about
2,900 "gene expression" regulation about 230,000 Aug. 12, 2002; "gene expression regulation"
about 62,900 Aug. 22, 2003; about 212,000 May 25, 2005 Related terms Omes & omics glossary regulome,
regulomics; Proteins glossary
protein regulation; Proteomics glossary:
protein- protein interactions
Gene regulation in eukaryotes, Kimball's
Biology Pages http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html
Wikipedia
http://en.wikipedia.org/wiki/Regulation_of_gene_expression
Gene regulation in prokaryotes: See
Gene definitions: operon
gene
shaving:
A statistical method, which ... identifies subsets of genes with coherent expression patterns and large
variation across conditions. Gene shaving differs from hierarchical clustering
and other widely used methods for analyzing gene expression studies in that
genes may belong to more than one cluster, and the clustering may be supervised
by an outcome measure. The technique can be 'unsupervised', that is, the genes
and samples are treated as unlabeled, or partially or fully supervised by using
known properties of the genes or samples to assist in finding meaningful
groupings. [Trevor Hastie et. al. "'Gene shaving' as a method for
identifying distinct sets of genes with similar expression patterns" Genome
Biology 1(2): 003, 2000 Google = about 377 Aug. 12, 2002;
about 611 Aug. 22, 2003, about 3,930 Apr 6, 2009 gene silencing: Gene
definitions
Has effect upon gene expression Google = about 11,000 Aug. 12, 2002;
about 26,700 Aug. 22, 2003, about 1, 101,000 Apr 6, 2009
Wikipedia http://en.wikipedia.org/wiki/Gene_silencing
genetic profiling:
The
description of an individual which lists the significant genetic characteristics
of an individual to establish identify, relationship, genetic predisposition
to certain traits or diseases and other genetic specifics. Oxford English
Dictionary Sometimes
known as genetic fingerprinting. [Oxford Biochem] Google = "genetic profiling" about
1,820; "genetic fingerprinting" about 4,960 Aug. 12, 2002; "genetic profiling" about
3,800; "genetic fingerprinting" about 6,400 Aug. 22, 2003 genome control maps: Maps
& mapping glossary Google = about 12 Aug. 12, 2002;
about 14, Aug. 22, 2003
genome expression,: Gene expression
at the whole- genome level. Related term global gene expression.
Or are these equivalent? Google = about 2,400 Aug. 12, 2002;
about 4,770 Aug. 22, 2003, about 71,100 Apr 6, 2009
genomic profiling:
Refers to testing for genotypes at multiple loci for
susceptibility to common diseases and the subsequent targeting of behavioral and
medical interventions. CHA Cambridge
Healthtech Advisors, Clinical
Genomics: The Impact of Genomics on Clinical Trials and Medical Practice
report, 2004
The recent development of genome- wide expression profiling (chip, microarray or Serial
Analysis of Gene Expression [SAGE] technologies) allows a comprehensive
high- throughput screening of the effects of an insult (genetic, physiologic,
pathologic, etc.) on gene expression in tissues and specific cell populations
of interest. These techniques may aid in determining the function
of a newly discovered gene or discovering new biomarkers and therapeutics
for patients with disease. [NIDDK Biotechnology Centers, Release Date:
September 23, 1999, RFA: DK-00-002, National Institute of Diabetes and
Digestive and Kidney Diseases, US] http://grants.nih.gov/grants/guide/rfa-files/RFA-DK-00-002.html
Google = about 625 Aug. 12, 2002;
about 989 Aug. 22, 2003; about 2,580 June 21, 2004, about 53,600 Apr 6, 2009
global gene expression:
An often overlooked aspect of measurements
of global gene expression is that the sequence or even the origin of the
arrayed probes does not need to be known to make interesting observations ... The basic idea is
that if a drug interacts with and inactivates a specific cellular protein,
the phenotype of the drug- treated cell should be very similar to the phenotype
of a cell in which the gene encoding the protein has been genetically inactivated,
usually through mutation. David J. Lockhart & Elizabeth A Winzeler
“Genomics, gene expression and DNA arrays” Nature 405: 827-836 June 15, 2000
The first attempts at global surveys of gene expression were undertaken
in the mid- 1970s … The serial methods involve direct, large scale sequencing
of cDNAs … the parallel approaches are based upon hybridization to
cDNAs immobilized on glass (microarrays) or to synthetic oligonucleotides
immobilized on silica wafers or "chips". . We note that bioinformatics
needs are similar and equally essential for all methods. O
Ermolaeva et al “Data Management and analysis for gene expression arrays”
Nature Genetics 20: 19-23, 1998
Google = about 2,060 Aug. 12, 2002;
about 6,210 Aug. 22, 2003; about 13,600 June 10, 2004, about 177,000 Apr 6, 2009
Related (or equivalent?) term: genome expression
global regulators- expression:
The loosely- defined term "global regulator" refers to a relatively small number
of genes whose products have a wide- ranging influence on the state of the
cell. One mechanism of action of these regulators is that their products
bind the DNA slightly upstream of the
coding region of the gene whose expression they influence. Thus there is information in both gene expression
and genome sequence measurements regarding the identities of the global regulators. I will discuss a
graph- structured probability model for identifying global regulators. Kerby A Shedden,
Univ. of Michigan "Two Problems in Genomics that can be Addressed by Statistical Modeling and
Simulation" UCLA Dept. of Statistics Department Seminar, Nov. 6, 2001
http://lists.stat.ucla.edu/pipermail/uclastat/2001-October/000058.html
Google = about 378 Aug. 12, 2002;
about 1,150 Aug. 22, 2003; about 3,180 June 10, 2004
Related
terms: mixed cell populations- expression signals Pharmacogenomics
glossary
in silico transcriptomics : Omes & omics
glossary Google = about 12 Aug. 12, 2002;
about 14, Aug. 22, 2003, about 138 Apr 6, 2009
high- throughput protein expression: One
of the key steps of structural genomics and proteomics is high-throughput
expression of many target proteins. Gene cloning, especially by ligation-
independent cloning techniques, and recombinant protein expression using
microbial hosts such as Escherichia coli and the yeast Pichia pastoris
are well optimized and further robotized. Cell- free protein synthesis systems
have been developed for large- scale production of protein samples for NMR
(stable- isotope labeling) and X-ray crystallography (selenomethionine
substitution). Protein folding is still a major bottleneck in protein
expression. Cell- based and cell- free methods for screening of suitable samples
for structure determination have been developed for achieving a high success
rate. S. Yokoyama, Protein expression systems for
structural genomics and proteomics, Current Opinion in Chemical Biology 7(1):
39-43, Feb. 2003
Google
= about 574 Aug. 22, 2003, about 6,660 Apr 6, 2009
layered expression scanning:
uses a layered array of capture membranes coupled to
antibodies or DNA sequences to perform multiplex protein or mRNA analysis Englert
CR, Baibakov GV, Emmert- Buck MR, "Layered expression scanning: rapid
molecular profiling of tumor samples" Cancer Research 60(6): 1526-
1530, Mar. 15, 2000
Google = about 21 Aug. 12, 2002;
about 54 Aug. 22, 2003 Related terms: expression microdissection; Cell
biology glossary Laser Capture Microdissection LCM
mesoscopic
biology: looks between the
macroscopic and microscopic (single cell) realms. Using quantitative
RT-PCR, and sampling variable numbers of cells, we were able to
demonstrate that steady state gene expression does, in fact, obey
Poisson statistics (Mar et al., 2006 ).
The beauty of this approach is that it can provide experimental
measurements even for genes expressed at very low levels. It further
suggests that other stochastic events occurring in single cells, even
complex interactions in pathways, may reveal themselves through the
analysis of samples of mesoscopic size. John Quackenbush, Extracting
biology from high dimensional data, First published online April 20, 2007
Journal of Experimental Biology 210, 1507-1517 (2007) Published by The
Company of Biologists 2007 doi: 10.1242/jeb.004432 http://jeb.biologists.org/cgi/content/full/210/9/1507
mesoscopic
expression:
John Quackenbush http://dash.harvard.edu/handle/1/4515107
metabolic engineering, metabolic fingerprinting, metabolic pathways: Metabolic
engineering glossary
metabolic
phenomics: Omes & omics glossary Google = about 45 Aug. 12, 2002;
about 65 Aug. 22, 2003, about 310 Apr 6, 2009
metabolic profiling: Metabolic
engineering glossary Google = about 1,570 Aug. 12, 2002;
about 2,900 Aug. 22, 2003, about 57,300 Apr 4, 2009
metabolite, metabolite expression, metabolite profiling, metabolism, metabolite systems biology: Metabolic
engineering glossary
metagenes:
Aggregate patterns of gene expression
(metagenes) that associate with lymph node status and recurrence, and that are
capable of predicting outcomes in individual patients with about 90% accuracy.
The metagenes defined distinct groups of genes, suggesting different biological
processes underlying these two characteristics of breast cancer. E. Huang et.al,
Gene
expression predictors of breast cancer outcomes, Gene expression predictors of
breast cancer outcomes, Lancet 361(9369): 1590- 1596, May 10, 2003
mRNA expression:
If messenger RNA
is only an intermediate on the way to production of the functional protein
products, why measure mRNA at all? One reason is simply that protein-
based
approaches are generally more difficult, less sensitive and have a lower
throughput than RNA- based ones. But more importantly, mRNA levels are immensely
informative about cell state and the activity of genes, and for most genes,
changes in mRNA abundance are related to changes in protein abundance. David J. Lockhart & Elizabeth A Winzeler “Genomics, gene expression
and DNA arrays” Nature 405: 827- 836 June 15, 2000 Related (equivalent?)
term: RNA expression Google = about 28,700 Aug. 12, 2002;
about 125,000 Aug. 22, 2003
mRNA
expression arrays: Messenger RNA
expression arrays immobilize stretches of mRNA and are used to measure the
concentration of mRNA species in a sample as a function of tissue type, cell
cycle and other environmental conditions. Andrej Sali et. al, From words
to literature in structural proteomics, Nature 442 (6928): 13 Mar. 2003 http://www.nature.com/nature/journal/v422/n6928/box/nature01513_bx2.html
Google = about 23 May 15, 2003;
about 42 Aug. 22, 2003 Related
terms: gene expression arrays, protein expression arrays; Are RNA expression
arrays equivalent to mRNA expression arrays?
molecular indexing:
A technique to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). By this technique, 3' end cDNA fragments are divided into 16 fractions by selective ligation of adapters and subsequent PCR amplification. Each fraction is used as a hybridization target for microarray hybridization. This fractionated target has a relatively lower nucleic acid complexity, including more fractions for rare transcripts, and is useful for their detection.
"Microarray hybridization with fractionated cDNA: enhanced identification of differentially expressed
genes" K. Sakai, H. Higuchi, K. Matsubara, K. Kato, Analytical Biochemistry
287 (1): 32- 37, Dec. 1, 2000 Google = about 88 Aug. 12, 2002;
about 137 Aug. 22, 2003; about 341 Feb. 17, 2005, about 1,390 Apr 6, 2009 Related terms: differential display, expression profiling
molecular profiling:
Drug & disease
targets Google = about 1,160 Aug. 12, 2002;
about 7,660 Aug. 22, 2003, about 249,000 Sept 7, 2007, about 108,000 Apr 6, 2009
Related terms: transcript profile, transcript profiling; Cell
biology cellular resolution,
FACS, laser capture microdissection.
CGAP [Cancer Genome Anatomy Project] Molecular
Profiling Initiative,
National Cancer Institute http://cgap.nci.nih.gov/
nucleome: -Omes & -omics glossary
overexpressed
proteins: Are often insoluble, and can be
recalcitrant to conventional solubilization techniques such as refolding.
Directed evolution methods, in which protein diversity libraries are screened
for soluble variants, offer an alternative route to obtaining soluble proteins.
Recently, several new protein solubility screens have been developed that do not
require structural or functional information about the target protein. Soluble
protein can be detected in vivo and in vitro by fusion reporter
tags. Protein misfolding can be measured in vivo using the bacterial
response to protein misfolding. Finally, soluble protein can be monitored by
immunological detection. Efficient, well- established strategies for generating
and recombining genetic diversity, driven by new screening and selection
methods, can furnish correctly folded, soluble protein. GS Waldo, Genetic
screens and directed evolution for protein solubility, Current Opinion in
Chemical Biology 7(1): 33- 38, Feb. 2003 Google
= about 834 Aug. 22, 2003
overexpression, underexpression:
Comparison of expression levels of normal tissues with diseased tissue
may be useful for prognostics. Overexpression of a gene can be used
to produce proteins on an industrial scale. Google = overexpression about 74,200 Aug. 12, 2002;
about 300,000 Sept. 16, 2004
pathways
databases:
: Electronic databases
of pathway information are currently limited in scope, computability, or
both. A major focus of infrastructure development to support large- scale
gene expression studies will be in the area of electronic biological pathway
databases and resources. D Bassett et al “Gene expression informatics
– it’s all in your mine” Nature Genetics 21 (1supp): 51-56 Jan 1999 Google = about 224 Aug. 12, 2002;
about 253 Aug. 22, 2003; about 580 Sept. 16, 2004 Related terms: Metabolic engineering
pathways
phylogenomic profiling: Phylogenomics
glossary
post hoc testing- expression:
The need for post hoc testing deserves special
mention. Because arrays measure a large number of genes simultaneously and
independently, false positives can occur. With false positives, certain genes’
expression appears to change, but the change is a not a result of underlying
biology but random chance. This phenomenon is especially common in biological
systems in which the changes are small in magnitude. The smaller the magnitude
of the change seen on a hybridization array, the more likely that it is a
spurious result.
Google = about 94 Aug. 12, 2002;
about 578 Aug. 22, 2003 Related term: statistical
analysis.
profile:
A table that lists the frequencies of each amino acid in each position of
protein sequence. Frequencies are calculated from multiple alignments of sequences containing a domain of interest
[NCBI Bioinformatics] How does this relate to the other profiling terms?
Narrower terms: clinical profiling, expression profiling,
expression profiling - sensitivity, gene expression profiling, genetic profiling,
genomic profiling, molecular profile, protein expression profiling, tissue
profiling, transcript profiling.
protein correlation profiling:
Overcomes
the problem in proteomics of distinguishing proteins that are part of a complex
from contaminating proteins. This method could be applied to the analysis of any
protein complex. For example, a team led by Matthias Mann, a professor in the
department of biochemistry and molecular biology at the University of Southern
Denmark in Odense, and Erich A. Nigg, director of the cell biology department at
Max Planck Institute for Biochemistry in Martinsried, Germany, has applied the
method to characterize the centrosome Nature, 426, 570 (2003)]. New proteomic
method, Chemical & Engineering News, Dec. 4, 2003 Related/synonymous
term: protein profiling
protein expression:
Just because a gene is overexpressed doesn’t
necessarily mean the protein will be. Sometimes we find the accompanying protein
to be downregulated even though the gene is upregulated: That is because there
are a lot of steps between gene expression and protein expression. Better
Understanding of Diseases and Drug Targets Through Systems Biology: An Interview with N. Stephen Ober of Beyond
Genomics, CHI's GenomeLink 17.2 http://www.chidb.com/newsarticles/issue17_2.asp
The importance
of the protein- based methods is that they measure the final expression
product rather than an intermediate. In addition, some of them enable the
detection of post- translational protein modifications (for example, phosphorylation
and glycosylation) and protein complexes, and in some cases, yield information
about protein localization … There is no question that protein - and
RNA- based
measurements are complementary, and that protein- based methods are important
as they measure observable that are not readily detected in other ways. David J. Lockhart & Elizabeth A Winzeler “Genomics, gene expression
and DNA arrays” Nature 405: 827-836 June 15, 2000 Google = about 69,100 Aug. 12, 2002;
about 197,000 Aug. 22, 2003; about 2,680,000 June 11, 2007 Narrower terms: cell-free protein expression,
difficult to express proteins, high- throughput protein expression
protein
expression arrays: Microarrays
glossary protein chips Google = about 27 May 15, 2003;
about 38 Aug. 22, 2003; about 54 June 10, 2004; about 3,450 June 11, 2007
protein expression profile:
Similar to gene expression profiling,
protein expression can also be profiled using a two- color assay. This assay
provides an indication of the relative levels of protein expression between two
different conditions, whether they are disease vs. health, tissue vs. tissue,
or normal vs. drug treated. The antibodies can be used to tag the profiled
proteins, or the proteins themselves can be hapten derivatized, which in
turn become targets for the immuno- RCA signal amplification complex.
Hapten derivatization of the profiled proteins is one way to make this a
universal assay.
The expression pattern of a protein. Related (equivalent?) term protein profiling.
Google = about
122 Aug. 12, 2002; about 396 Aug. 22, 2003; about 761 June 10, 2004; about
33,700 June 11, 2007, about 44,800 Apr 6, 2009
protein
profiling:
Allows one to
find differences in sample spectra very quickly using a small amount of
material. When those differences are noted, one may proceed to identify and
purify larger amounts of material using other types of array. This material can
then be used to characterize the protein and assays can be developed for
research or diagnostic purposes. Protein profiling is typically used for target
discovery, toxicological studies or disease marker discovery (Wright et al.
2000; Paweletz et al. 2000). Google = about 1,180 Aug. 12, 2002;
about 2,840 Aug. 22, 2003; about 6,440 June 10, 2004; about 159,000 June 11,
2007, about 68,200 Apr 6, 2009 Related
(equivalent?) term: protein
expression profiling.
RNA expression:
The focus of most
current array based studies is the monitoring of RNA expression levels.
The tools are most comprehensive for the yeast Saccharomyces cerevisiae…Yeast
geneticists have recently [Jan 1999] begun reporting global expression
studies of such fundamental processes as mitosis and meiosis. The
tools are also quite powerful for mammalian genomes, albeit with room for
improvement. Eric Lander “Array of hope” Nature Genetics 21 (1s): 3-4 Jan
1999 Google = about 5,370 Aug. 12, 2002, about
17,400 Aug. 22, 2003; about 868,000 June 11, 2007, about 1,420,000 Apr 6, 2009
Related (equivalent?) term: mRNA expression
RNA expression arrays: See mRNA expression
arrays
Google = about 41 May 15, 2003;
about 44, Aug. 22, 2003, about 433 Apr 6, 2009
regulomics:
The regulation of specific molecular
interactions that determine gene expression.
reverse transcription:
Sequences,
DNA & beyond Google = about 24,900 Aug. 12, 2002;
about 109,000 Aug. 22, 2003
Serial Analysis of Gene Expression
SAGE:
SAGE is a sequence- based technology for gene identification and quantitation in which
short (10-14 bp) sequences, called tags, are extracted from specific
positions within a transcript. Many transcript tags are concatenated into a
single molecule and then sequenced, revealing the identity of multiple tags
simultaneously. The expression profile is then computed by counting the
abundance of individual tags and identifying the gene corresponding to each tag.
Among the purported advantages of SAGE are that it is highly sensitive and
scaleable and that it detects all genes, including unknowns, and provides
quantitative data. Google = about 3,150 Aug. 12, 2002;
about 6,910 Aug. 22, 2003, about 253,000 Sept. 7, 2007 Related term: RAGE
SAGE homepage
http://www.sagenet.org
sequential regulation: Correlated changes in protein expression.
Google = about 63 Aug. 12, 2002;
about 140 Aug. 22, 2003
spatio
temporal dynamics:
Bioinformatics
glossary
standards - gene expression: Microarrays glossary
Google = 21,500 about Aug. 12, 2002;
about 58,400 Aug. 22, 2003
subtraction cloning:
Uses competitive hybridization of nucleic
acids from two different samples to selectively remove common expressed
sequences. What remains are those sequences uniquely expressed in one sample or
the other. The drawbacks of this approach are that it requires technical
sophistication and is associated with an extremely low throughput rate for target
identification.... On the positive side however, this approach does not
involve proprietary technologies and is generally available to most
investigators, and does not require a large infrastructure investment. Google = about 207 Aug. 12, 2002;
about 413, Aug. 22, 2003, about 4,510 Apr 6, 2009
subtractive hybridization:
Method by which genes expressed in a
tissue- specific manner can be enriched for cloning. Space Studies Board "A
Strategy for Research in Space Biology and Medicine in the New Century"
glossary, 2001 http://www.nationalacademies.org/ssb/csbmapb.htm#s
Google = about 405 Aug. 12, 2002;
about 7,650 Aug. 22, 2003
tissue profiling:
Compares
gene expression in diseased and normal tissues. Useful in the target validation process.
Google = about
57 Aug. 12, 2002; about 102, Aug. 22, 2003, about 4,770 Apr 6, 2009
trans-acting factors:
Trans- acting factors
functionally have two domains. One domain is required for the factor to bind to
DNA, and the second domain is required for the activation of transcription. This
was discovered by studying deletion mutants of the factors. Mutants factors were
found that could bind DNA but could not activate transcription. Other
experiments in which a hybrid protein consisting of the non- DNA binding segment
of one trans- acting factor fused to the DNA- binding region of a second trans-
acting activated transcription defined the second function of trans- acting
factors. Phil McLean "Control of gene expression in eukaryotes" North
Dakota State Univ. 1997 http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/geneexpress/eukaryex6.htm
Google = about 3,050 Aug. 12, 2002;
about 8,030 Aug. 22, 2003
trans-activators:
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
MeSH, 1990 Google = about 285 Aug. 12, 2002;
about 8,390 Aug. 22, 2003
transcript:
An mRNA molecule that
encodes a protein. [Schlindwein] Narrower term alternative
transcript
transcript abundance: Information
about mRNA transcript abundance under different experimental conditions can be
obtained from the analysis of EST sequences. If we assume that ESTs are randomly
selected from non- normalised libraries, then the number of EST sequences
representing each gene is directly proportional to the mRNA abundance in the
tissue from which the library was constructed. Cogeme, UK http://cogeme.ex.ac.uk/transcript.html
Google
= about 3,210 Aug. 22, 2003, about 68,300 Apr 6, 2009
transcript amplification: See under gene
expression profiling Google = about 22 Aug. 12, 2002;
about 114, Aug. 22, 2003, about 873 Sept 7, 2007
transcript arrays: Microarrays glossary
Google = about 35 Aug. 12, 2002;
about 64 Aug. 22, 2003, about 515 Sept 7, 2007
transcript expression:
Advances
[in the study of gene transcription] have not been matched by an
understanding of the transcripts that are actually expressed under different
conditions in cells, tissues, and organisms. The development of methods
to visualize gene expression by hybridization of DNAs carried on chips
promised to help correct that ignorance … In the past few years, the number
of such proteins [lacking a particular transcription associated protein]
has greatly proliferated … and this has been reflected in a burgeoning and
confusing literature….[some results suggest] control of the activity of
individual transcription components – by which extracellular and intra-
cellular
events can affect gene expression. Roger Brent ‘Learning to think about gene
expression data” Current Biology 9: R338-341 May 6 1999 Google = about 642 Aug. 12, 2002;
about 2,730 Aug. 22, 2003, about 57,700 Apr 6, 2009 Related term: tissue- specific/cell- specific gene expression
transcript imaging: See under molecular profiles/ molecular profiling
Google = about 225 Aug. 12, 2002;
about 417, Aug. 22, 2003
transcript profiling:
Four
characteristics of the regulation of gene expression at the level of transcript
abundance account for the great value and appeal of genome- wide surveys
of transcript levels … DNA microarrays make it easy … the tight connection
between the function of a gene product and its expression pattern … promoters
function as transducers … Thus, as we learn what information is transduced
by the promoter of each gene, we can begin to read this information from
the profile of transcripts. [Patrick O. Brown “Exploring the new world of the genome”
Nature Genetics 21 (1s): 33-37 1999]
A set of molecules
in a particular cell or tissue type that exist within a range of values
that are distinct from those in other cell or tissue type that exist within
a range of values. Gene- transcript profiles are particularly appealing
because RNA transcripts represent the primary output of the genome …. This
technique, sometimes referred to as transcript imaging, has been used to
identify genes that vary between diseased and healthy tissues. Although
large changes in expression often attract our greatest attention, subtle
changes can be highly significant…Currently, the significance of the vast
majority of gene expression changes remains unknown … a small change in expression
level could be a valuable diagnostic and prognostic indicator, provided
that it can be accurately detected. [G Zweiger “Knowledge discovery in gene-
expression- microarray data” Trends in Biotechnology 17: 429-436 Nov.
1999]
A pharmacogenomic
application that might enable drugs or other treatments to be tailored
to narrowly defined patient groups, or to be excluded from patients with
a high likelihood of responding adversely. [Zweiger G. “Knowledge discovery
in gene- expression microarray data.” Trends in Biotechnology. November
1999;17:429-436.] Google = about 771 Aug. 12, 2002;
about 1,900 Aug. 22, 2003, about 48,100 Apr 6, 2009 Related term: molecular profile, molecular profiling
transcription:
The process by which the genetic information encoded
in a linear sequence of nucleotides in one strand of DNA is copied into
an exactly complementary sequence of RNA. [IUPAC Biotech]
Can be used to find disease related genes to discover pathways, leading to drug target identification
and test the effect of
drugs on gene expression (which can warn of potential side effects). Useful in
toxicology and pharmacogenomics
studies. More under transcription: Sequences, DNA
& beyond
transcription factors:
Endogenous
substances, usually proteins, which are effective in the initiation, stimulation,
or termination of the genetic transcription process. MeSH, 1977
Wikipedia http://en.wikipedia.org/wiki/Transcription_factor
Google = about 72,600 Aug. 12, 2002;
about 216,000 Aug. 22, 2003, about 2, 170,000 Sept. 7, 2007, about 12, 300, 000
Apr 6, 2009 Narrower terms: artificial transcription factors,
basal transcription factors, regulatory transcription factors
transcription machinery:
Sequences, DNA
& beyond Google = about 49,100 Aug. 12, 2002;
about 91,500 Apr 6, 2009
transcriptome, transcriptomics: Omes & omics
glossary Google = transcriptome about 8,120, transcriptomics about
1,770 Aug. 12, 2002; transcriptome about 32,600, transcriptomics about
4,130 Aug. 22, 2003
translatome: Omes & omics glossary Google = about 106 Aug. 12, 2002;
about 69 Aug. 22, 2003, about 213 Apr 6, 2009
underexpression: See under
overexpression; underexpression.
upregulation:
A positive regulatory effect on physiological
processes at the molecular, cellular, or systemic level. At the molecular level,
the major regulatory sites include membrane receptors, genes (GENE EXPRESSION
REGULATION), mRNAs (RNA, MESSENGER), and proteins. MeSH, 2002 Google = about 19,300 Aug. 12, 2002;
about 77,500 Aug. 22, 2003, about 2,760,000 Apr 6, 2009
Wikipedia http://en.wikipedia.org/wiki/Downregulation
Downregulation and upregulation
whole genome expression:
The current excitement in
bioinformatics - analysis of whole-genome expression data: how does it relate to
protein structure and function? Mark Gerstein, Ronald Jansen. Current Opinion
in Structural Biology 10:(5): 574- 584, 2000 Google = about 626 Aug. 12, 2002;
about 1,810 Aug. 22, 2003, about 20,500 Apr 6, 2009 Narrower terms genome expression, global gene
expression.
IUPAC definitions are reprinted with the
permission of the International Union of Pure and Applied Chemistry.
Bibliography
Chipping Forecast III,
Nature Genetics, 37 (65): June 2005 http://www.nature.com/ng/journal/v37/n6s/index.html
Chipping Forecast II, Nature Genetics 32
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Nature Genome Gateway - Post- Genomics,
Profiling Microarrays, http://www.nature.com/genomics/post-genomics/microarrays.html
Science,
Gene Expression and Function, Oct. 22, 2004 http://www.sciencemag.org/sciext/genome2004/
Science,
Gene Expression Links http://www.sciencemag.org/feature/plus/sfg/resources/res_expression.shtml
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