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Related glossaries include Applications Genomic Sequencing. Biology Genetic Variations

2D gel maps: Used in expression mapping.

BAC maps: Bacterial artificial chromosome maps, a type of physical map. Related term Cell biology In- depth BAC 

biological atlas: Maps describing different aspects of protein function should be compiled into a "biological atlas" By integrating the information contained in the atlas, increasingly meaningful biological hypotheses could be formulated. However, it should be kept in mind that these hypotheses will still need to be tested back in the context of relevant biological settings, perhaps using more refined approaches. Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001] http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11239391&dopt=Abstract

bottom-up: See contig maps, high- resolution physical mapping: Does this relate in some way to bottom-up research? Research glossary

cDNA maps: Shows the locations of expressed DNA regions (exons) on the chromosomal map. Because they represent expressed genomic regions, cDNAs are thought to identify the parts of the genome with the most biological and medical significance. A cDNA map can provide the chromosomal location for genes whose functions are currently unknown. For disease- gene hunters, the map can also suggest a set of candidate genes to test when the approximate location of a disease gene has been mapped by genetic linkage techniques. [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1   Related term cDNA Sequences, DNA & beyond

cell mapping: The determination of the subcellular location of proteins and of protein- protein interactions by the purification of organelles or protein complexes followed by mass- spectrometric identification of the components.  Most proteins are thought to exist in the cell not as free entities but as part of  ‘cellular machines’ which perform cellular functions cooperatively.  Systematic identification of protein  complexes would permit these machines to be defined and allow ‘physical maps’ to be created for a variety of cell types and states.  Such information is of great value for the assignment of protein function.  [Blackstock & Weir “Proteomics” Trends in Biotechnology: 121-134 Mar 1999] 

cell maps: A cell map specifies the proteins that constitute a given organelle within a given cell type. Cell maps for normal and diseased cells can be constructed which give insight into the role proteins have in disease and can guide the drug development process. [Paul Kearney "Mapping and navigating the human Proteome" Annual Meeting of the Canadian Applied and Industrial Mathematics Society, June 7-9, 2001, Victoria, B.C. Canada]  http://www.pims.math.ca/caims/Kearney.html

chromosomal maps: Genes or other identifiable DNA fragments are assigned to their respective chromosomes, with distances measured in base pairs. These markers can be physically associated with particular bands (identified by cytogenetic staining)  primarily by in situ hybridization, a technique that involves tagging the DNA marker with an observable label (e.g., one that fluoresces or is radioactive). The location of the labeled probe can be detected after it binds to its complementary DNA [cDNA] strand in an intact chromosome. 

As with genetic linkage mapping, chromosomal mapping can be used to locate genetic markers defined by traits observable only in whole organisms. Because chromosomal maps are based on estimates of physical distance, they are considered to be physical maps. The number of base pairs within a band can only be estimated.  [Primer on Molecular Genetics, Oak Ridge National Lab, US]  http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1   Related terms cDNA map, cytogenetic map Radiation Hybrid RH maps; FISH Gene amplification & PCR

chromosome mapping: Any method used for determining the location of and relative distances between genes on a chromosome. [MeSH]

Chromosome mapping resources, Oak Ridge National Laboratory, US http://www.ornl.gov/hgmis/research/mapping.html

clone-based maps: The physical map of the human genome published by Nature is a clone- based physical map of 3.2 gigabases (25 times larger than any previously mapped genome). This approach involved generating an overlapping series of clones for the whole genome. With a fingerprinted BAC map clones could be selected for sequencing ensuring comprehensive coverage of the genome. [International Human Genome Mapping Consortium "A physical map of the human genome" Nature 409: 934-941, 15 Feb. 2001]

comparative genome mapping: Comparative genome mapping in the sequence-based era: early experience with human chromosome 7, JW Thomas et. al. Genome Research 10(5):624-33, May 2000 http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10810084&dopt=Abstract

contig mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.  [MeSH] Related term high- resolution physical mapping

contig maps: Contig maps are important because they provide the ability to study a complete, and often large segment of the genome by examining a series of overlapping clones which then provide an unbroken succession of  information about that region. [NHGRI]  

The bottom- up approach involves cutting the chromosome into small pieces, each of which is cloned and ordered. The ordered fragments form contiguous DNA blocks (contigs). Currently, the resulting library of clones varies in size from 10,000 bp to 1 Mb. An advantage of this approach is the accessibility of these stable clones to other researchers Contig construction can be verified by FISH [fluorescence in situ hybridization], which localizes cosmids to specific regions within chromosomal bands.

Consist of a linked library of small overlapping clones representing a complete chromosomal segment. While useful for finding genes localized to a small area (under 2 Mb), contig maps are difficult to extend over large stretches of a chromosome because all regions are not clonable. DNA probe techniques can be used to fill in the gaps, but they are time consuming. [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1   Related terms macrorestriction maps, physical maps; Sequencing glossary 'contig'.

cosmid maps:  "Constructing chromosome- and region-specific cosmid maps of the  human genome" Carrano AV, de Jong PJ, Branscomb E, Slezak T, Watkins BW Genome 31(2):1059-65, 1989

cytogenetic maps: The visual appearance of a chromosome when stained and examined under a microscope. Particularly important are visually distinct regions, called light and dark bands, which give each of the chromosomes a unique appearance. This feature allows a person's chromosomes to be studied in a clinical test known as a karyotype, which allows scientists to look for chromosomal alterations. [NHGRI] The lowest resolution physical map.

DNA maps: See genetic maps.

EST maps: Related term expression mapping

ESTs Expressed Sequence Tags: See Sequences, DNA & beyond glossary  Markers, useful for mapping.  Related term STS Sequence tagged Sites.

epitope mapping: Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of  immunochemistry.  [MeSH] Related terms Pharmaceutical biology glossary

expression mapping: The creation of quantitative maps of protein expression from cell or tissue extracts, akin to the EST maps commercially available.  This approach relies on 2D gel maps and image analysis, and opens up the possibility of studying cellular pathways and their perturbation by disease, drug action or other biological stimuli at the whole- proteome level … Expression mapping is a valuable tool in the discovery of disease markers and its use in gaining information in toxicological and drug- action studies seems assured. It is unclear at present how successful this approach will be in elucidating cellular pathways and their importance in disease processes, and how much the precise measurement of protein levels matters when compared with the rough guide provided by the measurement of mRNA levels … 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] 

Related terms transcript maps; Expression glossary; Narrower term protein expression maps.

fingerprint mapping: Related term: genome fingerprint map

functional maps: In addition to the raw data, it will be important to design the proper visualization tools to graphically represent the functional relationships contained in different maps ... Finally, it will be important to consider the possibility that functional maps need to be related back to particular tissues or even cell types. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001] 

gene expression maps: Stuart K. Kim et. al. "A gene expression map for C. elegans" Science, 293: 2087- 2092, Sept. 14, 2001

gene map: Gene Map of the Human Genome, International RH Mapping Consortium http://www.ncbi.nlm.nih.gov/genemap99/    Includes locations of more than 30,000 genes and provides an early glimpse of some of the most important pieces of the genome.

gene mapping: Determination of the relative positions of genes on a DNA molecule (chromosome or plasmid) and of the distance, in linkage units or physical units, between them. [DOE]

genetic linkage map: Shows the relative locations of specific DNA markers along the chromosome. Any inherited physical or molecular characteristic that differs among individuals and is easily detectable in the laboratory is a potential genetic marker.  [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1  Related term linkage maps.

genetic maps: Also known as a linkage map. A chromosome map of a species that shows the  position of its known genes and/ or markers relative to each other, rather than as specific physical points on each chromosome. [NHGRI]

The value of the genetic map is that an inherited disease can be located on the map by  following the inheritance of a DNA marker present in affected individuals (but absent in unaffected individuals), even though the molecular basis of the disease may not yet be understood nor the responsible gene identified. Genetic maps have been used to find the exact chromosomal location of several important disease genes, including cystic fibrosis, sickle cell disease, Tay- Sachs disease, fragile X syndrome, and myotonic dystrophy.  [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1

 In 1913, Alfred Sturtevant, a member of Thomas Hunt Morgan's fly group at Columbia University, drew the first genetic map - "The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association". Ever since, the map of the genes has been, in fact, the map of gene defects. Only about fifteen years ago, when DNA sequencing and the art of locating genes on chromosomes began to be practical, were geneticists able to isolate a gene sequence and then reason forward to what it specifies. [Horace Freeland Judson "Talking about the genome" Nature 409: 769, 15 Feb. 2001]

Can be cytogenetic, linkage, or physical maps. Also called DNA maps. Related term positional cloning Functional genomics glossary Starting genetic maps is easier than finishing them. Sequencing glossary  finished sequence,  "working draft"

genome control maps: Would identify all the components of the transcriptional machinery that have roles at any particular promoter and the contribution that specific components make to coordinate regulation of genes. The map will facilitate modeling of the molecular mechanisms that regulate gene expression and implicate components of the transcription apparatus in functional interactions with gene-specific regulators. [R. Young et al “Dissecting the regulatory circuitry of a eukaryotic genome” Cell 95:717-728 Nov. 25 1998]

genome fingerprint map : The collection of all fingerprint clone contigs placed in a genome- wide map. (Nickname "BAC map" or "FPC map".) [UC-Santa Cruz, US, Human Genome Project Working Draft Terminology, 2001] http://genome.ucsc.edu/goldenPath/term.html 

genome maps: This document describes a data representation (or schema) for genome maps intended to support the exchange of such maps among programs and databases. We intend the representation to be general enough to accommodate many common types of maps including cytogenetic, genetic linkage, radiation hybrid, clone contig (e.g., STS/YAC contig), and restriction maps, as well as integrated maps that are combinations of these. Though intended for data exchange, the representation may also be useful for data management.

The scope of this work is limited to geometric or spatial aspects of maps. We do not consider the experimental data underlying a map, nor the biological import of a map or its elements. The scope is further limited to finished maps, as opposed to maps that in the process of being constructed. The main difference is that finished maps are (or should be) consistent, while maps that are under construction are generally contradictory. Some aspects of our treatment may apply to the under- construction case, but we have not analyzed this in detail. [Nat Goodman "A Schema for the Exchange of Genome Maps Revision 2.0 Genome Informatics Workshop, UCSD Supercomputer Center, August 24-26, 1995, Sept. 1995] http://www-genome.wi.mit.edu/~nat/map_schema.rev2.0.html

genome scale metabolic maps: Annotated genomic data, along with legacy data on the cell's biochemistry and physiology, can be used to construct genome-scale metabolic maps. The challenge now is to formulate reliable mathematical descriptions of the integrated function of these maps. It has proven difficult, if not impossible, to formulate detailed theory-based models of these genome-scale maps. An alternative approach that is data driven and constraints based will be described. It is an iterative model-building process. Bernhard Palsson "Constraints- Based Data- Driven Models of Complex Biological Reaction Networks" Metabolic Profiling Dec. 3-4, 2001 Chapel Hill, NC  

haplotype map: Francis Collins, director of the NHGRI, speaking at BIO 2001 (San Diego CA, US, June 2001) announced plans for a public- private effort to create a human haplotype map.  Creators hope this so- called haplotype map will be a tool for pinning down the genes that contribute to the development of complex diseases such as cancer, diabetes, and mental illness. [L. Helmuth "Map of the Human Genome 3.0" Science 293 (5530) :583-5 July 27, 2001]  Agreeing on a definition of haplotype is only one of the challenges.  

Related term haplotype Genetic variations glossary

haplotype mapping: is often carried out as part of a genome scan. In a population isolate, the appearance of a rare Mendelian disease is almost always attributable to a single founder gene or mutation. The disease allele can be identified by searching for a common haplotype signature shared among patients. As the ancestral haplotype signature is passed from generation to generation, it is disrupted by recombination. Partial conservation of the haplotype signature in a patient strongly suggests that the disease locus resides in the conserved region of the haplotype. [L. Peltonen et. al, "USE OF POPULATION ISOLATES FOR MAPPING COMPLEX TRAITS" Nature Reviews Genetics 1; 182-190 (2000) http://www.nature.com/nrg/journal/v1/n3/slideshow/nrg1200_182a_bx4.html

high density maps: Genetic maps with (many) markers at relatively short intervals.  [CHI SNPs]

high-resolution genetic maps: 2-5 cM [centiMorgans]. Genetic mapping resolution has been increased through the application of  recombinant DNA technology, including in vitro radiation- induced chromosome fragmentation and cell fusions (joining human cells with those of other species to form hybrid cells) to create panels of cells with specific and varied human chromosomal components. [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1  Related term macrorestriction maps.

high- resolution physical mapping: The two current approaches are termed top- down (producing a macrorestriction map) and bottom- up (resulting in a contig map). With either strategy the maps represent ordered sets of DNA fragments that are generated by cutting genomic DNA with restriction enzymes. The fragments are then amplified by cloning or by polymerase chain reaction (PCR) methods. Electrophoretic techniques are used to separate the fragments according to size into different bands, which can be visualized by direct DNA staining or by hybridization with DNA probes of interest. The use of purified chromosomes separated either by flow sorting from human cell lines or in hybrid cell lines allows a single chromosome to be mapped. [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1

homology map: The Davis Human/ Mouse Homology Map, a table comparing genes in homologous segments of DNA from human and mouse sources, sorted by position in each genome. A total of 1793 loci are presented, most of which are genes. The authors did not include pseudogenes, members of multigene families where specific homology relationships could not be determined, nor any other genes for which homology was in doubt. In addition, for 568 of the loci there are provisional assignments of markers that link the homology map with that of the Gene Map of the Human Genome. These links also provide a rough approximation of the position of markers in the Genethon linkage map. In constructing this table, the authors first ordered genes so as to best maintain order according to both human cytogenetic position and mouse genetic map position. Within these homologous regions, genes were ordered according to the mouse genetic mapping data. [NCBI, US "Human Mouse Homology Map] http://www.ncbi.nlm.nih.gov/Omim/Homology/

interactome map: Omes & omics glossary

International SNP Map Working Group: Genetic variations glossary In-depth

interologs: Proteomics glossary

linkage disequilibrium: See Genetic variations glossary. Evidence for linkage disequilibrium can be helpful in mapping disease genes since it suggests that the two [alleles] may be very close to one another. [NHLBI]

linkage maps: A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together. Distance is measured in centimorgans (cM). [DOE]

Also known as a genetic map or genetic linkage map.

localizome mapping: One can imagine comprehensive mapping projects of the "localizome", with the goal of recording not only where all proteins of a proteome can be found but also when. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001]  Related terms interactome maps, phenome maps, transcriptome maps.

locus: See Gene definitions. Any genomic site, whether functional or not, that can be mapped through formal genetic analysis.  [NHLBI] Related term markers.

macrorestriction map: Describes the order and distance between enzyme cutting (cleavage) sites ... In top- down mapping, a single chromosome is cut (with rare- cutter restriction enzymes) into large pieces, which are ordered and subdivided; the smaller pieces are then mapped further. The resulting macro- restriction maps depict the order of and distance between sites at which rare- cutter enzymes cleave. This approach yields maps with more continuity and fewer gaps between fragments than contig maps, but map resolution is lower and may not be useful in finding particular genes; in  addition, this strategy generally does not produce long stretches of mapped sites. Currently, this approach allows DNA pieces to be located in regions measuring about 100,000 bp to 1 Mb. [Primer on Molecular Genetics, Oak Ridge National Lab, US] http://www.ornl.gov/hgmis/publicat/primer/prim2.html#1    Related term high-resolution physical mapping.

mapping: The determination of the relative positions of genes within the chromosomes or of restriction sites along a DNA molecule. [IUPAC Biotech, IUPAC Compendium]

The process of determining the position of a locus on the chromosome relative to other loci. [NHLBI]

The process of deducing schematic representations of DNA. Three types of DNA  maps can be constructed: physical maps, genetic maps, and cytogenetic maps, with the key distinguishing feature among these three types being the landmarks on which they are based. [NHGRI]

Narrower terms include cell mapping, chromosome mapping, comparative genome mapping, contig mapping, epitope mapping, expression mapping, gene mapping, high- resolution physical mapping, nucleotide mapping, optical mapping, Protein Expression Mapping PEM, receptor mapping, restriction mapping, STS- content mapping.

mapping technologies: Include electrophoresis, flow sorting, imaging, in situ hybridization, PCR, scanning, others?

maps: Narrower terms include 2D gel maps, BAC maps, cDNA maps, chromosomal maps, clone- based maps, contig maps, cosmid maps, cytogenetic maps, DNA maps, EST maps, epitope maps, expression maps, gene expression maps, gene map, genetic linkage maps, genetic maps, genome control maps, genome maps, haplotype map, high density maps, high- resolution genetic maps, homology map, linkage maps, macrorestriction map, peptide maps, physical maps, protein expression map, protein linkage maps, radiation hybrid RH maps, restriction map, SNP maps, self- organizing maps, transcript maps, YAC maps. 

markers: Include ESTs, locus, microsatellites, RFLPs, SNPs, STSs, tandem repeats. See also Genetic variations glossary  for more extended definitions.

memory mapped data structures: Bioinformatics glossary

microsatellite markers: Genetic variations glossary  Most existing genetic maps are based on microsatellite markers. [CHI SNPs]

molecular combing: A method ... which can straighten and align molecules of genomic DNA on a solid surface. The technology also includes a battery of novel statistical methods developed for analyzing the large amounts of data obtained from FISH analyses made on individual DNA molecules.

Molecular combing relies on the action of a receding air/ water interface, or meniscus, to uniformly straighten and align DNA molecules on a solid surface. The advantages of this approach reside in the reproducibility of the results, their precision (1 to 4 kb resolution) and the relative ease of analysis afforded by the ability to visualize the molecules directly. Beyond its obvious applications to genomic studies and genetic diseases, it creates new experimental possibilities for research into cancer. Indeed, as a tool, molecular combing is a versatile approach to a wide range of subjects and questions of fundamental interest. This is especially true for the multifaceted domain of DNA replication in eukaryotes. [Aaron Bensimon et. al. "Detection of Genomic Alteration by Molecular Combing" NCI Innovative Molecular Analysis Technologies Programs, July 6-8, 2000, Chantilly VA]    http://otir.nci.nih.gov/cgi-bin/imat_search.cgi?ABSTRACTID=IMAT-00-007

nucleotide mapping: Two- dimensional separation and analysis of nucleotides. [MeSH] Related terms electrophoresis Chromatography & electrophoresis; Northern blotting, Southern blotting Microarrays.

optical mapping: A single molecule approach for the construction of ordered restriction maps. Optical Mapping dispenses with electrophoretic approaches,  and uses light microscopy to directly image individual DNA molecules which are bound to specially derivatized surfaces and then cleaved by restriction enzymes. Importantly, cleaved fragments retain their original order, and cut sites are  flagged by small, visible gaps. Optical Mapping solves the problem of determining fragment order, and in addition, works with only a handful of molecules. By determining the existence of these sequence- specific cut sites and the distances  between them, we can create a landmark map of the DNA sequence. Such restriction enzyme maps also provide a useful scaffold for the alignment and verification of sequence data and are of particular value in assembling sequence from problematic DNA regions.  [David Schwartz "Optical Mapping" Laboratory for Molecular and Computational Genomics, Univ. of Wisconsin, US] http://schwartzlab.biotech.wisc.edu/omm/omm.html

peptide mapping: Two- dimensional separation and analysis of peptides. [MeSH] Related terms electrophoresis; Western blotting Microarrays.

peptide maps: 

phenome mapping: The conceptual matrix for a comprehensive "phenome" mapping project would be as follows: one axis represents all available knockouts while the other represents a large series of standardized phenotypes that can be screened. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001] 

phenome maps: Can be thought of as lists of similar phenotypes that could be referred to as "pheno- clusters"....  [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001]   Related terms interactome maps, localizome maps, transcriptome maps; Omes & omics glossary phenome.

physical mapping:  

physical maps: A map of the locations of identifiable landmarks on DNA (e.g. restriction enzyme cutting sites, genes) regardless of inheritance.  Distance is measured in base pairs.  For the human genome, the lowest- resolution physical map is the banding patterns on the 24 different chromosomes; the highest resolution map would be the complete nucleotide sequence of the chromosomes. [DOE]

A chromosome map of a species that shows the specific physical locations of its genes and/ or markers on each chromosome. Physical maps are particularly important when searching for disease genes by positional cloning strategies and for DNA sequencing. [NHGRI]

The Human Genome Project public consortium announced on Feb. 12, 2001 that it had assembled and published a nearly- completed physical map of the human genome.  It appeared in the Feb. 15 issue of the journal Nature. The public effort to sequence the genome has relied on a map- based approach.  [NHGRI press release "International Human Genome Mapping Consortium Publishes Physical Map of the Human Genome" Feb. 12, 2001] http://www.nhgri.nih.gov/NEWS/physical_map.html  Related terms clone- based maps, contig maps, cosmid maps, cytogenetic maps, restriction mapping. Narrower term BAC maps. See also Human Genome Project Genomics glossary

positional cloning: See Functional genomics glossary. Requires a genetic map with a large number of markers (especially in the region of interest), and the use of physical mapping and DNA sequencing technologies to isolate and sequence the targeted gene.

protein expression map: Since 2D Electrophoresis gel patterns reveal not only the amounts of protein, but is unrivaled in its ability to detect post- translational modifications, the 2DE protein map provides much more relevant information about cellular dynamics than the corresponding expression map at the mRNA level. By comparing the 2DE gel patterns of samples exposed to different physiological conditions or different drug treatments it is possible to identify groups of proteins with related functions or whose expression is interdependent (expression proteomics).  [ John Barrett’s research group, “Parasite proteomics” Aberystwyth University, Wales, UK]  http://www.aber.ac.uk/~mpgwww/Proteome/Proteome.html

Protein Expression Mapping PEM: Details the distribution and abundance of protein in specific samples, under defined physiological conditions. [CHI Proteomics]  Quantitative study of global changes in protein expression in tissues, cells or body fluids using 2D gels and image analysis.  Currently carried out by 2D gel electrophoresis, though alternatives are under investigation. [Blackstock & Weir “Proteomics” Trends in Biotechnology: 121-134 Mar 1999]  

 The researchers (in the laboratory of Marc Vidal [then at] at Massachusetts General Hospital [now at Dana- Farber Cancer Institute]) were able to develop and validate (using known biological information derived from sources other than their two- hybrid assay) a map that reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. The researchers  believe that protein interaction mapping is now feasible for C. elegans on a genome- wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases. [Walhout AJ, Sordella R, Lu X, “Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development.” Science 287(5450):116-122. Jan 7 2000 cited in CHI Functional Genomics]  

protein linkage maps: With respect to a genome- wide use of the two- hybrid assay in the case of yeast, the goal is to find which proteins in the yeast genome interact with every other protein.  This process would generate protein linkage maps, delineating large networks of interacting proteins.  The approximately 6,000 yeast proteins can potentially interact in 18 million pairwise combinations.  [CHI Functional Genomics]

protein localization mapping: 

proteome map: A number of organizations have announced plans to produce a map of the proteome, including Myriad Genetics, Large Scale Biology, CuraGen and others. ["Whether the Human Proteome Will Be Successfully Mapped in Three Years Depends On How You Define "Proteome" Scientific American Aug. 2001] http://www.sciam.com/2001/0801issue/0801scicit7.html

RFLP (Restriction Fragment Length Polymorphism): See Genetic variations glossary   Polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps.  RFLPs are usually caused by mutation at a cutting site. See marker. [DOE] Genetic variations glossary

Radiation Hybrid RH maps: Chromosome maps that are calculated from RH score vectors. An RH score vector is the pattern of assay results of a particular STS (marker) on a particular panel. The vector consists of 1's (did amplify) and 0's (did not amplify). Simplistically speaking, the more similar two score vectors are, the closer the markers are on the chromosome.

RH maps are an indispensable alternative to genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs.  International collaborative projects are producing numbers of these hybrids for the human genome, the mouse genome, the rat genome and others. This in turn allows the generation of a very precise STS map that is indispensable in the study of multifactorial diseases. [HowTo: RHdb Radiation Hybrid DataBase, CORBA at EBI European Bioinformatics Institute, UK] Broader term chromosome maps http://corba.ebi.ac.uk/RHdb/howto/RHdb_how.html

receptor mapping: Molecular modeling glossary

resolution: Degree of molecular detail on a physical map of DNA, ranging from low to high. [DOE] Related terms genetic maps, high- resolution, physical maps.

restriction map: A description of restriction endonuclease cleavage sites within a piece of DNA. Generating such a map is usually the first step in characterizing an unknown DNA, and a prerequisite to manipulating it for other purposes. Typically, restriction enzymes that cleave DNA infrequently (e.g. those with 6 bp recognition sites) and are relatively inexpensive are used to produce at a map. [L. Augsten, RA Bowen, M Rouge "Restriction Mapping" Biotechnology and Genetic Engineering" 2000] http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/maps.html

restriction mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA. [MeSH]

SNP maps: A collection of SNPs that can be superimposed over the existing genome map, creating greater detail and facilitating further genetic studies. [SNP Consortium]

Current estimates indicate that a very dense marker map (30,000 - 1,000,000 variants) would be required to perform haplotype - based association studies. We have constructed a SNP map of the human genome with sufficient density to study human haplotype structure, enabling future study of human medical and population genetics. [International SNP Map Working Group "A map of human genome sequence variation containing 1.42 millions Single Nucleotide Polymorphisms" Nature 409: 928-934, 15 Feb. 2001]

SSR Simple Sequence Repeats Genetic variations glossary  Often used as a mapping marker

STS Sequence-Tagged Sites:  See also Genetic variations glossary In-depth Useful for orienting the physical mapping and sequence data reported from different laboratories.  [DOE]

PCR- based STSs have been used as landmarks for construction of various types of genomic maps.  [Electronic PCR, NCBI , US]  http://www.ncbi.nlm.nih.gov/STS/

Related term EST Expressed Sequence Tag

STS- content mapping:  A physical mapping method in which the presence of STSs on large- insert clones (e.g. YACs) is used to infer linkage and ordering of the sites. [NCBI]

self-organizing maps: Algorithms & data management

tandem repeats: See Genetic variations glossary  Useful as a marker in physical mapping. [CHI SNPs]

top-down: See high- resolution physical mapping. Any relation to top-down research? (Research glossary)

transcript maps:  In only a year or two, most human genes will be sequence- tagged and placed on various physical maps. Such a ‘transcript map’ (or ‘expression map’) of the genome will be an important part of the sequencing infrastructure, as well as a critical resource for the positional candidate approach to gene cloning. One of the specific goals of the US Human Genome Project is the construction of a  high resolution STS map of the genome. .. One of the early problems with gene- based STSs was that there simply were  not enough unique human gene sequences to bother with. But all of that changed with the advent of EST sequencing, at which time several groups began mapping ESTs albeit on a limited scale and only to the resolution of a chromosome assignment. [Marl S Boguski and Gregory D Schuler “ESTablishing a Human Transcript Map” Nature Genetics 10:369-371, 1995] 

Expression map of the genome. Related term expression mapping.

transcriptome maps: Consist of "expression clusters" of co-regulated genes. Challenges ahead for computational biology include the integration of clusters obtained for the transcriptome, the interactome, the phenome, and the localizome. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001]  Related terms interactome maps, localizome maps, phenome maps.

YAC maps: Yeast artificial chromosome maps, a type of physical map.

Bibliography

Alpha glossary index

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