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Related glossaries are Applications  Functional Genomics, Genomics, Proteomics, Sequencing, Informatics Algorithms & data management Bioinformatics, Technologies Microarrays,  Biology Sequences, DNA & beyond.

analysis - gene expression analysis: 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. [CHI Gene Expression] 

Related terms post hoc testing, statistical analysis; cluster analysis, pattern recognition, In-depth guilt by association Algorithms glossary data analysis, standards Microarrays glossary

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. [CHI Bioinformatics]

alternative transcripts: When a gene is expressed in different tissues, the cells frequently create variations in mRNAs. Processes such as alternative initiation, splicing and polyadenylation generates transcripts that may be unique to (or enriched in) specific tissues. These alternative transcripts sometimes encode an alternative form of the protein or may encode an identical protein, depending upon whether or not the sequence variation affects the reading frame. This diversity provides the opportunity to make drugs that bind to the region of RNA unique to the desired tissue and not affect the RNA in other tissues.  This opportunity for an additional level of drug specificity generally is not available targeting proteins. An analogous opportunity for specificity at the protein level might be post- translational modifications of proteins that are tissue specific. In practice, however, this is variation in proteins has been difficult to exploit or even understand due to the lack of good analytical tools to sort out tissue- specific protein modifications. In contrast, finding alternative transcript forms in RNA is accomplished by straightforward sequencing of cDNA libraries obtained from different tissues. The potential to find alternative transcript forms is one of the unappreciated strategic advantages of RNA as a drug target. [Ibis Therapeutics "Small molecule drugs that bind RNA" 2000] http://www.ibisrna.com/darpa_ii/overview.html

cluster analysis: Algorithms & data management glossary

clinical profiling of 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  large potential markets for diagnostics, choosing appropriate therapies and ongoing monitoring.

conditional gene expression: When gene expression is activated or suppressed at will. [CHI Functional Genomics]

co-regulation: 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. [CHI Functional Genomics].

differential display: Use of quantitative reverse transcription- polymerase chain reaction (QRT-PCR) to amplify differences in gene expression between different cells or tissues. Specifically, individual dinucleotides, coupled to oligo- dT primers (polymers of 12-18 deoxythymnidine residues), are used to initiate first- strand cDNA synthesis with reverse transcriptase. These single- strand cDNAs are then amplified using PCR in such a manner as to randomly visualize the mRNA products. Researchers then resolve the radioactive products from two experimental samples on long denaturing polyacrylamide sequencing gels and look for quantitative differences (intensities) in the signals These differences are assumed to reflect variations in the starting amounts of RNA. [CHI Gene Expression] 

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] 

Related terms In-depth EVGs; exon arrays Microarrays glossary

In disease … the up- or downregulation of gene activity can either be the cause of the pathophysiology or the result of the disease. ..The opportunity to compare the expression of thousands of genes between ‘disease’ and ‘normal’ tissues and cells will allow the identification of multiple potential targets.  [C Debouck “DNA microarrays in drug discovery and development” Nature Genetics 21 (1s): 48-50 Jan 1999]

Differential Protein Expression DPE: Great anticipation surrounds the area of protein expression analysis. Currently, these studies use difficult- to- standardize two- dimensional (2D) gels and expensive mass spectrometry. As a result, this field is highly specialized and mainly involves academics or others working on very focused projects, as well as a handful of large- scale efforts. [CHI Target Validation]

downregulation: Process that decreases ligand/ receptor interactions due to a reduction in the number of available receptors … Classically the concept referred to hormone receptors but contemporary usage includes other cell surface receptors. [MeSH/Metathesaurus]

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] 

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 Software See Databases & software directory

expression mapping, Maps genomic & genetic 

expression maps Maps genomic & genetic  Narrower terms: protein expression map, self- organizing maps, transcript maps Related terms:EST maps, genome control maps

expression pharmacogenomics: Pharmacogenomics glossary

expression product: Related term gene product Gene definitions

expression profiling, expression profiles: Narrower terms gene expression profiling,  protein expression profiling, transcript profiling.  Related terms gene expression, protein expression, RNA expression, transcript expression.

expression profiling sensitivity: Discussions about the limits of sensitivity of these methods is often confused … Performance is generally stated as the minimal (relative) abundance of mRNA that can be detected, i.e. 1/300,000 or “one copy per cell”  (assuming a mammalian cell contains 300,000 individual mRNA molecules). This abundance must be related, however, to the probe concentration, and ultimately, to the size of the starting biological sample that is the experimentally relevant (and often limiting parameter … We feel that a realistic evaluation of sensitivity can be expressed ass the minimum number of molecules of one particular sequence species in the sample needed to obtain a measurable signal on the corresponding target after hybridisation. [S Granjeaud “Expression profiling: DNA arrays in many guises” BioEssays 21: 781-790,  Sept. 1999]

expression proteomics: Large- scale measurements of protein expression.  [CHI 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]

expression technologies: Chromatography & electrophoresis, Gene amplification & PCR  Microarrays have been a breakthrough technology for studying gene expression. 

Narrower terms differential display, SAGE, subtraction cloning, TOGA.

GEML Gene Expression Markup Language: An Extensible Markup Language (XML) based tag set, was developed by Rosetta Inpharmatics and others in the GEML community to provide a standard method of exchanging gene expression data along with the associated gene and experiment annotation.   http://www.geml.org  

Related terms analysis- gene expression; data analysis, standards Microarrays glossary

gene clustering: Related terms Algorithms glossary cluster analysis, hierarchical clustering, self organizing maps; Microarrays glossary k- means clustering; 

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 transcription and processing of an mRNA or the transcription and translation of RNA in order to produce a functional protein. [CHI Gene Expression]

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]http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/ng_paper.html  

Broader terms expression, genome expression.

Gene expression databases see Databases & software directory.

gene expression arrays: Used in drug development to screen drug candidates against cell lines and compare the effects of drug candidates with those of existing "gold standard" drugs on gene expression.  Also used to monitor patients on clinical trials. [CHI Gene Expression]

gene expression monitoring: Significant challenges are to be met in understanding the pathways that exist in gene regulation and the expression and utility of proteins. More robust computational methods are required to analyze gene expression data for higher accuracy and predictive value. Integrative Bioinformatics High- throughput interpretation of pathways and biology Jan. 16 - 18, 2002 Zurich, Switzerland

gene expression profiling: 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.  [CHI Target Validation]  

The determination of the pattern of genes expressed i.e., transcribed, under specific circumstances or in a specific cell. [MeSH]

Related terms expression profile, expression profiling. Related term protein expression, 

gene shaving: A statistical method, which we have called 'gene shaving'. The method 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]

gene transcription: See transcription.

genetic profile, 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. [OED]

Also known as genetic fingerprinting [Oxford Biochem] 

genome expression,: Gene expression at the whole- genome level. Related term global gene expression. Or are these equivalent?

genomic profile, genomic profiling: 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

global gene expression: From experiments on global gene expression, we may obtain data for thousands of genes, often forcing us to consider processes, function and mechanisms about which we know very little. Thus, there is a need for more sophisticated systems of knowledge representation (or ‘knowledge bases’) that organize the data, facts, observations, relationships and even hypotheses that form the basis of our current scientific understanding … Unfortunately the fact that the scientific literature has been somewhat haphazardly built, without the benefit of a controlled or restricted vocabulary and a well defined semantic and grammar.  To take full advantage of the abilities of the new technologies and the rapidly increasing amount of sequence information it is absolutely essential to incorporate the facts, ideas, connections, observations and so forth, which exist in the scientific literature and in the minds of scientists, into a form that is systematic, organized, linked, visualized and searchable. 

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]   http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/ng_paper.html

Related (or equivalent?) term genome expression

guilt by association method: For assessing gene function, although not logically rigorous, the utility has been demonstrated, as genes already known to be related do, in fact, tend to cluster together based on their experimentally determined expression patterns.  The approach is made more systematic and statistically sound by calculating the probability that the observed functional distribution of differentially expressed genes could have happened by chance. [David J. Lockhart & Elizabeth A Winzeler “Genomics, gene expression and DNA arrays” Nature 405: 827-836 June 15, 2000

influence-based data mining: Algorithms & data management glossary

Laser Capture Microdissection: Cell biology glossary

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

metabolic profiling: Metabolic Profiling Dec. 3-4, 2001 Chapel Hill, NC See also Functional genomics glossary

metabolite expression: The availability of expression data is expected to have a significant impact on the understanding of basic cellular processes and the various mechanisms by which cells control these processes. Conversely, the interpretation of expression measurements often requires knowledge about biological networks. We have built upon the PathDB project ( http://www.ncgr.org/pathdb/) to create a database and tools for constructing, visualizing, and analyzing cellular networks. This system is being used to interpret large- scale gene, protein, and metabolite expression data through an integration system (ISYS) synchronized with other publicly available databases and tools. Jeffrey Blanchard "A Platform for the Interpretation of Gene, Protein, and Metabolite Expression Data in the Context of Cellular Interactions" Metabolic Profiling Dec. 3-4, 2001 Chapel Hill, NC

metabolite systems biology: An important part of  metabolic system biology is focussed on the profiling of body fluids in terms of small molecules. This enables the integration of knowledge bi- directional from the genome as well as the metabolome side. This gives a tremendous clearer view on all aspects of importance not the least by starting up front by disease phenotyping and integrating all aspects in target validation. Jan van der Greef "Metabolite Systems Biology: A New Vision on Drug Discovery" Metabolic Profiling Dec. 3-4, 2001 Chapel Hill, NC    

molecular profile, molecular profiling: 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] 

Related terms transcript profile, transcript profiling. 

CGAP [Cancer Genome Anatomy Project) Molecular Profiling Initiative, National Cancer Institute  http://cgap.nci.nih.gov/

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.

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]  Related term pathways Functional Genomics,

pattern recognition: Algorithms glossary

post hoc testing: 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. [CHI Microarrays] 

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 and mRNA data: Proteomics glossary

protein expression: One of the key challenges in functional genomics today is the assessment of protein expression in the cell. Changes in protein expression in response to disease or environment may provide valuable clues as to which protein may serve as therapeutic targets.  Because of the technical difficulties in obtaining accurate information on protein levels, researchers have relied on mRNA expression as an approximation. [CHI Summit Proteomics]

Protein expression analysis is undergoing a technological revolution, which will change the fundamental nature of the data available. ... Current methods for measuring protein expression are very different from those for measuring gene expression. Typically, 2D gels are used to separate the proteins from one another, and mass spectrometry (MS) is then applied to identify the proteins. MS provides remarkably specific identification of protein fragments, based on their masses. The masses are then compared with lists of computed masses for identification. More and more groups are now seeking to bypass 2D gels, using combinations of protein chips, liquid chromatography, capillary electrophoresis, and mass spectrometry for protein analysis. [CHI Bioinformatics]

Great anticipation surrounds the area of protein expression analysis. Currently, these studies use difficult- to- standardize 2D gels and expensive mass spectrometry. [CHI Target Validation]

Protein expression, as monitored by in situ cellular and subcellular localization, has become exceedingly important in the post genome sequencing era. Immunohistochemistry, coupled with traditional molecular and biochemical techniques, continues to be a powerful tool for studying gene expression. [Promega eNotes, 2000-2001] http://www.promega.com/enotes/features/fe0008a_tabs.htm

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]    

Identifying and quantifying the proteins expressed … Levels of protein(s) in a biological sample (including gene fraction studies).  Area of great commercial interest [CHI Proteomics] 

protein expression profile, protein expression profiling: 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. [CHI Summit Proteomics] 

The vast number of candidate proteins generated from genomics programs is creating enormous opportunities for biologists.  However, efficient and rapid expression of genes in homologous and heterologous expression systems and rapid purification steps are major bottlenecks.  The practical and cost- effective expression of these novel proteins in amounts large enough to allow for their proper characterization and evaluation and, finally, for the scale- up for large- scale production of these proteins presents many difficulties.  Protein Expression: PepTalk  Jan. 7- 8, 2002  *  San Diego CA. 

The expression pattern of a protein. Related (equivalent?) term protein profiling.

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). [CHI Summit Proteomics] 

Related (equivalent?) term protein expression profiling.

quantitative RT-PCR reverse transcription- polymerase chain reaction QRT- PCR: Gene amplification & PCR glossary  

Related term differential display.

quantum resonance interferometry: Expression amplification middleware for enhancing the detection and quantitation of hybridized microarray signals by orders of magnitude over current techniques is presented. The technological principle underlying quantum resonance interferometry is analogous to speckle interferometry and active radar imaging, which have enabled dramatic improvements in ultraweak signal imaging and spectral informatics over the past decade. Specifically, gene expression amplification is achieved by inducing "interference" between a mathematically transformed, hybridized, digitized microarray output and an external designer stimulus. In a molecular diagnostic context, the external synthetic stimulus is designed based on a mutation or a target sequence of interest. Alternately, in a gene expression application for drug target discovery, the microarray "inherent noise response" statistics are used to construct the external synthetic stimulus. This presents an attempt to get an over 100- to 10,000- fold quantitative improvement in detection sensitivity over classic state- of- the- art bioinformatics. The resulting enhancement is enabling to microarray-based drug target discovery and diagnostic applications. Expression detection performance results comparing classic bioinformatics techniques and quantum interferometry will be presented for several classes of standard and spotted arrays. Dr. Sandeep Gulati, ViaLogy Corp. Integrative Bioinformatics: High-Throughput Interpretation of Pathways and Biology Jan. 16-18, 2002  Zurich, Switzerland 

RAGE Random Activation of Gene Expression: We have developed a proprietary technology, RAGE (Random Activation of Gene Expression), that we believe provides us with the unique ability to express protein from virtually any gene in the human genome, without requiring either the isolation of individual genes or any prior knowledge of gene sequence, function or normal expression characteristics. RAGE enables us to rapidly survey the entire human genome for proteins with specific biological functions and to quickly and accurately correlate protein function with gene structure, addressing one of the most significant bottlenecks in functional genomics. We efficiently create comprehensive, genome- wide protein expression libraries that can be used for many different applications, such as functional characterization of expressed proteins, generation of cell lines expressing validated drug targets, manufacturing of established therapeutic proteins and gene discovery. [Athersys, Inc. website] http://www.athersys.com/products/rage.html

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]  

Related (equivalent?) term mRNA expression

reverse transcription:  Sequences, DNA & beyond

SAGE Serial Analysis of Gene Expression: A method of gene expression analysis involving reverse transcription, restriction enzyme mediated digestion of oligonucleotides, ligations and PCR. Specifically, SAGE converts polyadenylated mRNA into cDNA by reverse transcription. Oligonucleotide "tags" of 10-14 base pairs are then hybridized to the cDNA and reduced by restriction enzymes. The tags are then ligated to form concatemers that are amplified by PCR and then cloned and sequenced. The number of tags present indicates the prevalence of the gene, a powerful tool for gene discovery, but ill suited for high throughput. [CHI Gene Expression] 

SAGE homepage http://www.sagenet.org

sequential regulation:  Correlated changes in protein expression. [CHI Proteomics]

standards, gene expression: Microarrays glossary

statistical analysis, expression data: Still at an early stage of development. See data analysis Microarrays glossary

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. [CHI Gene Expression]

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

TOGA Total Gene Expression Analysis: An automated hybrid of SAGE and differential display, promises to completely elucidate gene expression patterns for a given tissue or cell. It requires a complex series of steps involving multiplex PCR, cDNA cloning, in vitro transcription, cDNA construction, sequencing gel analysis, and quantification. [CHI Gene Expression]

tissue profile, tissue profiling: Compares gene expression in diseased and normal tissues. Useful in the target validation process. 

transcript: An mRNA molecule that encodes a protein. [Schlindwein] Narrower term In-depth alternative transcript

transcript arrays: Microarrays glossary

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]

transcript imaging: See molecular profiles/ molecular profiling.

transcript profile, 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 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.]

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: Sequences, DNA & beyond

transcription machinery:  Sequences, DNA & beyond

transcriptional repression: A network of transcriptional repressors keeps the genome in a quiescent state, unless directed otherwise by transcriptional activators. We have employed DNA microarray analysis in the yeast Saccharomyces cerevisiae to peel back layers of repression and reveal the mechanisms by which each repressor exerts control over gene expression. Surprisingly, our findings indicate that chromatin is highly accessible and that a significant amount of global repression is targeted directly at the general transcription machinery by preventing it from assembling at permissive chromatin. [Dr. Frank Pugh, Pennsylvania State Univ. "Unraveling Genomewide Networks of Transcriptional Repression" Integrative Bioinformatics: High-Throughput Interpretation of Pathways and Biology Jan. 16-18, 2002  Zurich, Switzerland 

transcriptome, transcriptomics: Omes & omics glossary

translatome: Omes & omics glossary

underexpression: See under overexpression; underexpression.

upregulation:  Process that increases ligand/receptor interactions due to an increase in the number of available receptors. [MeSH]

whole genome expression: Narrower terms genome expression, global gene expression.

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

Bibliography

[CHI Gene Expression] Cambridge Healthtech Institute, Kent Vrana and Williard Freeman, Genomic-Scale Gene Expression Analysis: Advancing from DNA to Disease, Report 6,  Nov. 2000.  http://www.chireports.com/content/reports/multiplex.asp

Alpha glossary index