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Biopharmaceutical Maps, genomic & genetic glossary & taxonomy
Evolving terminologies for emerging technologies

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Last revised October 30, 2013 

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Of Exactitude in Science
...In that Empire, the craft of Cartography attained such Perfection that the Map of a Single province covered the  space of an entire City, and the Map of the Empire itself an entire Province. In the course of Time, these Extensive maps were found somehow wanting, and so the College of Cartographers evolved a Map of the Empire that was of the same Scale as the Empire and that coincided with it point for point. Less attentive to the Study of Cartography, succeeding Generations came to judge a map of such Magnitude cumbersome, and, not without Irreverence, they abandoned it to the Rigours of sun and Rain. In the western Deserts, tattered Fragments of the Map are still to be found, Sheltering an occasional Beast or beggar; in the whole Nation, no other relic is left of the Discipline of Geography.   From Travels of Praiseworthy Men (1658) by J. A. Suarez Miranda.  The piece was written by Jorge Luis Borges and Adolfo Bioy Casares. English translation quoted from J. L. Borges, A Universal History of Infamy, Penguin Books, London, 1975.  http://www.kyb.tuebingen.mpg.de/bu/people/bs/borges.html

Finding guide to terms in these glossaries  Biology & chemistry map      Site Map  Related glossaries include  Genomics   Technologies  Genomic Technologies  Genomic Informatics  Sequencing  Biology SNPs & Genetic Variations

2D gel maps: Used in expression mapping.

BAC maps: Bacterial artificial chromosome maps, a type of physical map. Google = about 2,560, Aug. 26, 2002; about 4,480 June 23, 2004 Related terms: genome fingerprint maps;  Cell biology 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] 

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

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   Google = about 53, Aug. 26, 2002; about 266 June 23, 2004  Related term: cDNA Gene definitions

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]  Google = about 2,110, Aug. 26, 2002; about 3,200 June 23, 2004

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/industrial/2001/caims/Kearney.html 

Google = about 777, Aug. 26, 2002; about 8,320 June 23, 2004

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; Gene amplification & PCR FISH;  Narrower term: Radiation Hybrid RH maps

chromosome mapping: Any method used for determining the location of and relative distances between genes on a chromosome. MeSH, 1967
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]  Related term: Cell biology clone

CNV map: We have constructed a first-generation CNV map of the human genome through  the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia. ... A total of 1,447 copy number variable regions (CNVRs) which can encompass overlapping of adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations...Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. Richard Redon et. al, Global Variaiton in copy number in the human genome, Nature 2006 Nov 23;444 (7118): 444- 454   

  The new global CNV map will transform medical research in four areas. The first and most important area is in hunting for genes underlying common diseases. To date, attempts to identify these genes have not really considered the role CNVs may play in human health. Second, the CNV map is being used to study familial genetic conditions. Third, there are thousands of severe developmental defects caused by chromosomal rearrangements. The CNV map is being used to exclude variation found in unaffected individuals, helping researchers to target the region that might be involved. The data generated will also contribute to a more accurate and complete human genome reference sequence used by all biomedical scientists. http://www.gene-quantification.de/cnv.html Google = about 723 Dec 8, 2006

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     Google = about 423, Aug. 26, 2002; about 735 June 23, 2004

contig mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.  MeSH, 1999 Google = about 1,830 June 23, 2004  Related terms: high- resolution physical mapping; Sequencing: contig

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 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

disease maps: Ontologies to represent the terminological relationships among concepts necessary to construct a knowledge- base of neurological disorders. A. Gupta, B Ludascher, JS Grethe, ME Martone,  Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Netw. 2003 Nov;16 (9): 1277- 1292.

EST maps: Related term expression mapping

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

epigenome maps: Through the Epigenomics Mapping Centers and Data Coordinating Center, the Epigenomics Roadmap Program will provide high resolution maps of epigenetic marks across the full human genome for a representative selection of cell and tissue types. The mapping centers will begin with established methodologies and the purpose of the Discovery RFAs is to develop and validate additional marks which would be incorporated into the comprehensive mapping strategies of the Centers. Epigenomics, NIH Roadmap for Medical Research, 2008 http://nihroadmap.nih.gov/epigenomics/faq.asp 

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, 1995] See also definition in  IUPAC Provisional glossary Biomolecular Screening  Google = about 3,390, Aug. 26, 2002; about 17,600 May 10, 2004  Related terms: Pharmaceutical biology antibody, epitope

evolutionary genetics:  Evolutionary study of genes has been purely theoretical, but it can provide useful information for guiding gene mapping. People are now finding, for example, that a lot of things are not true associations; instead, they are an artifact of association. You can make such mistakes when you are looking at two individuals who share a common ancestry. Understanding the phylogeny helps us, for example, understand horizontal gene transfer between microorganisms. For humans or other sexually reproducing organisms, the use of phylogenetic information improves resolution for making associations by helping to avoid type I errors - that is, finding an association that is actually merely due to sharing a recent common ancestor, or, in other words, being closely related.   Related terms: Phylogenomics

exon mapping: Obtaining gene structure through the assembly of information from different peptides.  Confirmant, Science, Exon Mapping  http://www.confirmant.com/

expression map: See expression imbalance map, gene expression map, protein expression maps. See also under transcript maps

expression imbalance map EIM: A new visualization method, for detecting mRNA expression imbalance regions, reflecting genomic losses and gains at a much higher resolution than conventional technologies such as comparative genomic hybridization (CGH). Simple spatial mapping of the microarray expression profiles on chromosomal location provides little information about genomic structure, because mRNA expression levels do not completely reflect genomic copy number and some microarray probes would be of low quality. The EIM, which does not employ arbitrary selection of thresholds in conjunction with hypergeometric distribution- based algorithm, has a high tolerance of these complex factors. M. Kano et. al, "Expression imbalance map: a new visualization method for detection of mRNA expression imbalance regions" Physiological Genomics 13(1): 31-46, Mar. 18, 2003

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 gene & protein; Narrower term protein expression maps.

fingerprint mapping: 

Google = about 82, Aug. 26, 2002; about 200 June 23, 2004  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 connectivity map: The Connectivity Map is an effort to discover and demonstrate the linkages between diseases, drug candidates, and genetic manipulation. New Roadmap Emphasis areas for 2008, NIH Roadmap, http://nihroadmap.nih.gov/2008initiatives.asp 

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.  Starting genetic maps is easier than finishing them. Related terms: Functional genomics  positional cloning;  Sequencing  finished sequence,  "working draft"  Google = about 26, 900, Aug. 26, 2002; about 145,000 June 23, 2004

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 

Google = about 9, Aug. 26, 2002; about 27, June 23, 2004

genome map: Physical map of the human genome, Nature 409, 934-941 (15 February 2001) | doi:10.1038/35057157 http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html

Genetic, physical and/or transcript maps. Google = about 29,000 June 23, 2004; about 1,530,000 Aug 8, 2007

genome mapping: http://link.bubl.ac.uk/genomemapping/  Google = about 37,500 Aug. 26, 2002; about 45,500 June 23, 2004

genomic cartography: http://acg.media.mit.edu/people/fry/chromosomes/13-icp/ 
Interimbook
, Benjamin Fry, MIT http://acg.media.mit.edu/people/fry/interimbook/

genomic maps: Gene Indices - Genomics Maps, TIGR http://www.tigr.org/tdb/tgi/map.shtml 
Genomic Maps - specification, Object Management Group http://www.omg.org/cgi-bin/doc?formal/2002-02-01  Google = about  1,220 Aug. 26, 2002; about 5,770 June 23, 2004, about 21,900 Jan. 11, 2006; about 648,000 Aug 8, 2007

genomic mapping:  While a few technologies for functional analysis on a genomic basis are being developed at present, additional approaches and technologies for genomic interpretation that can be applied efficiently and economically at the level of an entire genome will be required for comprehensive analyses. Informatics will continue to play an important role in achieving all of these goals, as well as in ensuring the maintenance and accessibility of the forthcoming data. The development and application of new technologies for acquisition, management, analysis, and dissemination of genomic data are still required. TECHNOLOGIES FOR GENOMIC MAPPING, SEQUENCING, AND ANALYSIS NIH GUIDE, Vol. 26, Number 8, March 14, 1997 PA NUMBER: PA-97-044 http://grants.nih.gov/grants/guide/pa-files/PA-97-044.html  Google = about 2,720 Aug. 26, 2002; about 13,200 June 23, 2004, about 61,100 Jan. 11, 2006; about 98,700 AUg 8, 2007

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.  Google = about 503, Aug. 26, 2002; about 4,830 June 23, 2004, about 30,700 Jan. 11, 2006; about 55,200 Dec 8, 2006; about 69,500 Aug 8, 2007

Haplotype map project, National Human Genome Research Institute, NIH, US http://www.genome.gov/page.cfm?pageID=10001688

HapMap: See International HapMap

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  Google = about 176, Aug. 26, 2002; about 866 June 23, 2004; about 14,700 Jan. 11, 2006

heat map: Algorithms

high density maps: Genetic maps with (many) markers at relatively short intervals.  

high dimensional brain mapping: High- dimensional brain mapping is a new analytic method that quantitatively characterizes the shape as well as volume of a brain structure. In this study, high- dimensional brain mapping was used to evaluate hippocampal shape and volume in patients with major depressive disorder and healthy comparison subjects. JA Poesner et. al, High- dimensional mapping of the hippocampus in depression,  American Journal of Psychiatry 160(1): 83 8-9, Jan. 2004

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/  Google = about 4,670, Aug. 26, 2002; about 1,770 June 23, 2004  Related terms: Functional genomics

interactome map: -Omes & -omics Google = about 10, Aug. 26, 2002; about 135 June 23, 2004

International HapMap project The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. http://www.hapmap.org/ 

The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors. The information produced by the Project will be made freely available. International HapMap Project   http://www.hapmap.org/abouthapmap.html 

The goal of the International HapMap Project is to produce a resource that describes the haplotypes in the human genome and the SNPs that tag them. It is estimated that roughly 300,000 to 500,000 tag SNPs can be chosen that contain most of the information on the patterns of variation of the 10 million common SNPs in the human genome. By using the HapMap tag SNPs, researchers will be able to examine candidate regions or even the entire genome for association with a phenotype in an efficient and comprehensive way. Additional genotyping for the Human Haplotype Map, Apr. 16, 2004 RFA Number: RFA-HG-04-005  http://grants1.nih.gov/grants/guide/rfa-files/RFA-HG-04-005.html 

The HapMap Project, Nature 7064 , 27 Oct. 2005 http://www.nature.com/nature/journal/v437/n7063/edsumm/e051027-01.html 
NHGRI, NIH International HapMap Project  http://www.genome.gov/10001688  
Google = about 13,200 June 23, 2004; about 272,000 Jan. 11, 2006; about 706,000 Dec 8, 2006  Related term: haplotype Sequencing

Guidelines for referring to the HapMap populations in publications and presentations, International HapMap Project, 2005  http://snp.cshl.org/citinghapmap.html.en 
International SNP Map Working Group:
Identifies and localizes 1.42 millions SNPs in the human genome. ["A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms" International SNP Map Working Group Nature 409: 928- 933, 15 Feb. 2001] http://www.nature.com/cgi-taf/DynaPage.taf?
file=/nature/journal/v409/n6822/full/409928a0_fs.html

interologs: Proteomics

linkage disequilibrium: See SNPs & genetic variations. 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; -Omes & -omics localizome

locus: 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: 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 Biomarkers and SNPs & other Genetic variations  for more extended definitions.

memory mapped data structures: Bioinformatics

microsatellite markers: Genetic variations  Most existing genetic maps are based on microsatellite markers.

molecular interaction maps: Are becoming the equivalent of an anatomy atlas to map specific measurements in a functional context; e.g. QTLs, expression profiles, etc. MAGNet Center: Andrea Califano, NCIBI: Brian Athey, Simbios: Russ Altman, Creating a DBP Community to Enhance the NCBC Biomedical Impact, NCBC Work Group Report, 18 July 2006
http://www.na-mic.org/Wiki/images/5/52/Systems_WG7.pptRelated terms: -Omes & -Omics interactome, resourceome

nucleotide mapping: Two- dimensional separation and analysis of nucleotides. MeSH, 1987 Related terms:  electrophoresis Chromatography & electrophoresis; Northern blotting, Southern blotting Microarrays.

peptide mapping: Two- dimensional separation and analysis of peptides. MeSH, 1987

The characteristic pattern of fragments formed by the separation of a mixture of peptides resulting from hydrolysis of a protein or peptide.  AKA peptide finger- printing. Thomas J. Wiese, Biochemistry Glossary, Chemistry Dept. Fort Hays State Univ. http://www.fhsu.edu/chemistry/twiese/glossary/biochemglossary.htm#P

Google = about 5,580, Aug. 26, 2002; about 21,800 June 23, 2004  Related terms: electrophoresis; Microarrays Western blotting

peptide maps: One way to research the structure of a protein is to seek to identify the specific sequence of amino acids which form the protein. Tr. at 202-3. An initial approach is to cut the protein into fragments, called peptides, using enzymes or chemicals which reliably divide the chain at predictable points. Tr. at 523. These fragments can be isolated and analyzed to create "peptide maps," which show the pattern of pieces from these breaks as a unique "fingerprint." ... A peptide map does not disclose the precise order of the amino acids in a protein, although it may point to areas of difference between similar proteins. Tr. at 493, 506-7; ORI Scientific Terms at 2. Additional work must be done to determine the amino acid sequence of a particular peptide, and then to determine the order of the sequence within the protein as a whole. RESEARCH INTEGRITY ADJUDICATIONS PANEL SUBJECT: Aug. 6, 1993 Docket http://www.os.dhhs.gov/dab/decisions/dab1431.txt

Google = about 783, Aug. 26, 2002; about 5,850 June 23, 2004

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  

Google = about 11, Aug.. 26, 2002; about 55 June 23, 2004

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

Google = about 7, Aug. 26, 2002; about 24 June 23, 2004  Related terms: interactome maps, localizome maps, transcriptome maps; Omes & omics phenome.

physical mapping:  The determination of the linear positions of genes on a DNA molecule; distances are measured in physical units, i.e., base pairs, kilobases, and megabases. Genetic Glossary, Judith Hall, M.D. and William Horton, M.D., Growth, Genetics and Hormones Journal, June 1997 http://www.kumc.edu/gec/gloss.html 

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]  Related terms: clone- based maps, contig maps, cosmid maps, cytogenetic maps, restriction mapping. Narrower term: BAC maps. See also Human Genome Project Genomics

positional cloning: See Functional genomics. 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 Google = about 22, Aug. 26, 2002; about 190 June 23, 2004

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  Google = about 36, Aug. 26, 2002; about 92 June 23, 2004

protein interaction mapping: Methods for determining interaction between proteins. MeSH, 2002  Google = about 419, Aug. 26, 2002; about 2,090 June 23, 2004

protein interaction maps:  Hybrigenics" comprehensive protein interaction maps using automated yeast- two- hybrid methodology in pathogens and in cDNA of normal and diseased tissues. "Moving up a dimension: Proteomics deal making" CHI's GenomeLink 5.2  http://www.chidb.com/newsarticles/issue5-2.ASP   Google = about 645, Aug. 26, 2002; about 4,820 June 23, 2004

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.  Google = about 58, Aug. 26, 2002; about 422 June 23, 2004

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  Google = about 151, Aug. 26, 2002; about 757 June 23, 2004

QTL mapping Quantitative Trait Loci mapping: A phenotype driven approach to gene function. As such it permits the discovery of new genes and can be contrasted with gene- driven approaches such knock-out and knock-in mice which allow for the study of known genes. QTL reflect natural genetic variations as they exist in the mouse strains under study. We are limited to detecting those genes that vary among the available strains. However the natural variations among mouse strains are vast and largely untapped.  Gary Churchill's Statistical Genetics Group QTL mapping, Jackson Laboratory, 2000   http://www.jax.org/research/churchill/research/qtl/

RFLP (Restriction Fragment Length Polymorphism): See Genetic variations & SNPs    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 & SNPs 

Radiation Hybrid RH map: A genome map in which STSs are positioned relative to one another on the basis of the frequency with which they are separated by radiation-induced breaks. The frequency is assayed by analyzing a panel of human–hamster hybrid cell lines. These hybrids are produced by irradiating human cells, which damages the cells and fragments the DNA. The dying human cells are fused with thymidine kinase negative (TK−) live hamster cells. The fused cells are grown under conditions that select against hamster cells and favor the growth of hybrid cells that have taken up the human TK gene. In the RH maps, the unit of distance is centirays (cR), denoting a 1% chance of a break occurring between two loci. NCBI Handbook, NLM US, 2002, 2003    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.glossary.1237   Google = about 1,200 Aug. 26, 2002; about 8,060 June 23, 2004; about 27,500 June 14, 2007  Broader term: chromosome maps

radiation hybrid mapping: A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA. MeSH, 2001 Google = about 6, 590, Aug. 26, 2002; about 14,800 June 23, 2004

Radiation Hybrid Mapping Information Page, Rutgers Univ., 2008  http://compgen.rutgers.edu/old/rhmap/ 

receptor mapping: In silico & Molecular modeling  Google = about 416, Aug. 26, 2002; about 790 June 23, 2004

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 endonucleases: Cell biology

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, 1989  Google = about 5,770, Aug. 26, 2002; about 31,300 June 23, 2004; about 610,000 Aug 8, 2007

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]  Google = about 451, Aug. 26, 2002; about 4,030 June 23, 2004

SSR Simple Sequence Repeats: Genetic variations & SNPs  Often used as a mapping marker

STS Sequence-Tagged Sites:  See also SNPs & Genetic variations 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 map: See STS- content mapping

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

syntenic Map: Chromosomal maps showing the collinear relationships between the genomes of different organisms. Often these chromosomal regions from related organisms (such as various grass species) contain corresponding genetic information and similar gene order.  Glossary, National Plant Genome Initiative, Interagency Working Group on Plant Genomes, 1999 http://www.ostp.gov/html/genome/genome_6.html 

tandem repeats: See SNPs & Genetic variations  Useful as a marker in physical mapping.

telomere maps: Telomeres are the tips of the chromosomes. They are crucial in maintaining the chromosomes' stability and are important in the cell cycle and ageing. Because of the way the physical maps are constructed, many telomeres of chromosomes are left out. Riethman et al. used a special way of capturing the ends of all the telomeres to ensure that the whole- genome map stretches all the way to the tips of the chromosomes. The authors also show from their computational analysis that these areas are not boring junk DNA but contain many interesting gene sequences likely to be important to our cells. Nature Genome Gateway Press Releases, Human Genome issue, 15 Feb. 2001  http://www.nature.com/genomics/human/overview/press-releases.html

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

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. Mark S Boguski and Gregory D Schuler “ESTablishing a Human Transcript Map” Nature Genetics 10:369-371, 1995

Expression map of the genome.  Google = about 359, Aug. 26, 2002; about 6,330 June 23, 2004  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   Google = about 33, Aug. 26, 2002; about 534 June 23, 2004  Related terms: interactome maps, localizome maps, phenome maps.

whole genome clone- based maps: In their paper, the International Human Genome Mapping Consortium describe how they constructed the first whole- genome physical map, how they created the templates from which the genome was sequenced and demonstrated how the map was essential for the accurate assembly of the human genome by the publicly funded effort.

Four short reports accompanying the whole- genome mapping paper (Bruls; Bentley; Kucherlaparti; Page), describe alternative mapping strategies that were implemented for chromosomes 12, 14 and Y, as well as a host of other chromosomes. Information from all these papers were integrated into the whole- genome paper and demonstrate how a rich resource of mapping information can be generated by the cooperation of international independent efforts. Nature Genome Gateway Press Releases, Human Genome issue, 15 Feb. 2001 http://www.nature.com/genomics/human/overview/press-releases.html

whole genome maps: See whole genome clone- based maps

YAC maps: Yeast artificial chromosome maps, a type of physical map. Google = about 106, Aug. 26, 2002; about 6,300 June 23, 2004

Bibliography

Alpha glossary index

How to look for other unfamiliar  terms

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

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