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

Suggestions? Comments? Questions?
Mary Chitty MSLS
mchitty@healthtech.com
Last revised July 08, 2019 



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.  https://en.wikipedia.org/wiki/On_Exactitude_in_Science  Many thanks to bioinformatician Gustavo Stolovitzky who told me about this story.

Biology term index  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.  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

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: comprehensive schematics of the genetic and physical interactions among genes and their products (primarily proteins) in any cell and help us understand how these interactions are impacted by alterations in the genes.  Cancer Cell Map Initiative http://ccmi.org/cell-maps/view-cell-maps

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.  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

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   

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    

contig mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.  MeSH, 1999   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.

epigenome mapping: Producing the original sequence of the human genome was a landmark achievement. Yet, it posed a new challenge: the genome sequence was an endless stream of As, Cs, Gs, and Ts, devoid of functional interpretation. So beyond protein-coding genes, which constitute only 1% of the genome, we were unable to decode the functions of the other sequences. Epigenomic maps provide an opportunity to identify and understand the sequences, interacting proteins, and chromosomal structures that act throughout the other 99% of the genome to control gene activity. We use DNA sequencing-based mapping technologies such as ChIP-Seq, Bisulfite-Seq, MINT-Chip, RNA-Seq, and chromatin conformation capture assays to annotate the genome and advance our understanding of how it functions. Broad Institute, Epigenome Mapping https://www.broadinstitute.org/epigenomics/epigenome-mapping

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

Identification and localization of the specific regions of protein molecules that are recognized by the immune system IUPAC Glossary of Biomolecular Screening   Related terms: Pharmaceutical biology antibody, epitope

EST maps: Related term expression mapping

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

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 maps: Fingerprint maps have been used for various purposes such as sequencing of entire genomes and genomic regions of special interest. Optimally, a finished map of a genome is available to guide the sequencing of that genome  British Columbia Cancer Agency poster http://mkweb.bcgsc.ca/rat/mapview/images/poster/poster.pdf  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

Researchers begin a genetic map by collecting samples of blood or tissue from family members that carry a prominent disease or trait and family members that don't. Scientists then isolate DNA from the samples and closely examine it, looking for unique patterns in the DNA of the family members who do carry the disease that the DNA of those who don't carry the disease don't have. These unique molecular patterns in the DNA are referred to as polymorphisms, or markers.[3] The first steps of building a genetic map are the development of genetic markers and a mapping population. The closer two markers are on the chromosome, the more likely they are to be passed on to the next generation together. Therefore, the "co-segregation" patterns of all markers can be used to reconstruct their order. With this in mind, the genotypes of each genetic marker are recorded for both parents and each individual in the following generations. The quality of the genetic maps is largely dependent upon these factors: the number of genetic markers on the map and the size of the mapping population. The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map being "saturated". In gene mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. Genes, in this regard, are represented by "traits" that can be faithfully distinguished between two parents. Their linkage with other genetic markers are calculated in the same way as if they are common markers and the actual gene loci are then bracketed in a region between the two nearest neighbouring markers. The entire process is then repeated by looking at more markers which target that region to map the gene neighbourhood to a higher resolution until a specific causative locus can be identified. This process is often referred to as "positional cloning", and it is used extensively in the study of plant species The great advantage of genetic mapping is that it can identify the relative position of genes based solely on their phenotypic effect.  Wikipedia accessed 2018 Nov 9 https://en.wikipedia.org/wiki/Gene_mapping#Gene_mapping

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" 

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 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.

genome mapping: assigning/locating of a specific gene to particular region of a chromosome and determining the location of and relative distances between genes on the chromosome.  NCBI Genome mapping https://www.ncbi.nlm.nih.gov/probe/docs/applmapping/

genomic cartography:  The completion of a genome sequencing project is often followed by the publication of a paper detailing the process and notable observations that can be made of the newly acquired data set...In many such cases, the editors have seen fit to publish an image of the data itself, ostensibly to provide the reader with a high level understanding of how the new data set fits together, as a large-format figure to accompany the paper. Of course these are also meant to be subjectively enjoyed, since they often take the form of a wall poster, which might find a place on the wall of the reader's office or lab. Not so much as a day-to-day research tool, but an image that provides a feel for the data—a sense of what a genome 'looks' like. ...However, there has been a lack of analysis of its implementation. It would appear that the same level of rigor that is applied to the content of the magazine has not been applied to these images. Ben Fry, http://benfry.com/cartography/

genomic maps: Genomic Maps - specification, Object Management Group http://www.omg.org/cgi-bin/doc?formal/2002-02-01 

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

HapMap: See International HapMap  now retired and archived

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

interactome map: -Omes & -omics

International HapMap project: The original mission statement of the International HapMap Project was to develop a haplotype map of the human genome, HapMap, which would describe the common patterns of human DNA sequence variation. Through this research millions of SNPs were discovered and many GWAS studies used this dataset in research for disease association. This project was a necessary stepping stone for the 1KG project which utilizes many of the same populations.  While this project was an impactful start for the scientific community, the HapMap Project has lost momentum in research. This statement from Buchanan et al. 2012 seems to have come to pass. The number of novel variants is constantly increasing and many believe that the 1000 Genomes Project could potentially overshadow the utility of HapMap.” Please visit the 1000 Genomes Project resources for access to current and best data (genotypes, sequences and genome mapping) at http://www.1000genomes.org/, or through the NCBI Browser: https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/. The archived HapMap data will continue to be available via FTP from ftp://ftp.ncbi.nlm.nih.gov/hapmap  NCBI retiring HapMap Resource 2016 https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/    Related term: haplotype Sequencing

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, 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: SNPs & 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

Peptide mapping is a critical workflow in biotherapeutic protein characterization and is essential for elucidating the primary amino acid structure of proteins. For recombinant protein pharmaceuticals, such as monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs), peptide mapping is used for proof of identity, primary structural characterization and quality assurance/quality control (QA/QC). Global regulatory agencies, including US Food and Drug Administration (US FDA) and European Medicines Agency (EMA), look to harmonized guidelines from the International Council for Harmonisation (ICH). ICH Q6B  covers the test procedures and acceptance criteria for biologic drug products and specifies the use of peptide mapping as a critical quality test procedure for drug characterization used to confirm desired product structure for lot release purposes. Thermo fisher, Peptide Mapping Information https://www.thermofisher.com/us/en/home/industrial/pharma-biopharma/pharma-biopharma-learning-center/biopharmaceutical-characterization-information/peptide-mapping-information.html    Related terms: electrophoresis; Microarrays Western blotting

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 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 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 

protein interaction mapping: Methods for determining interaction between proteins. MeSH, 2002 

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. 

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 

proteome mapping: Mapping the proteome Valda Vinson  26 May 2017: Vol. 356, Issue 6340, pp. 816-818 DOI: 10.1126/science.356.6340.816-k

QTL mapping Quantitative Trait Loci mapping: For organisms whose genomes are known, one might now try to exclude genes in the identified region whose function is known with some certainty not to be connected with the trait in question. If the genome is not available, it may be an option to sequence the identified region and determine the putative functions of genes by their similarity to genes with known function, usually in other genomes. This can be done using BLAST, an online tool that allows users to enter a primary sequence and search for similar sequences within the BLAST database of genes from various organisms. It is often not the actual gene underlying the phenotypic trait, but rather a region of DNA that is closely linked with the gene[14].[citation needed] Another interest of statistical geneticists using QTL mapping is to determine the complexity of the genetic architecture underlying a phenotypic trait. For example, they may be interested in knowing whether a phenotype is shaped by many independent loci, or by a few loci, and do those loci interact. This can provide information on how the phenotype may be evolving.[citation needed] In a recent development, classical QTL analyses were combined with gene expression profiling i.e. by DNA microarrays.  Wikipedia accessed 2018 Oct 26 https://en.wikipedia.org/wiki/Quantitative_trait_locus#QTL_mapping

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 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

receptor mapping:
  A method used to guess at (determine) the three-dimensional structure of a receptor binding site extrapolating from the known structure of the molecule binding to it. This approach can be carried out because of the complementary shape of the receptor and the binding molecule. Functionally, the researcher projects the (guessed-at) properties of the receptor ligands into a mathematical model in which the profile of the receptor is predicted by complementariness (to known chemical molecular structures). The receptor mapping process requires repetitive refinement of the mathematical model to fit properties continually being discovered via the use/interaction of chemical reagents bearing the known molecular structures.  Biotech terms.org  http://biotechterms.org/sourcebook/savetermretrieve.php3?Receptor%Mapping%(RM)

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: Wikipedia https://en.wikipedia.org/wiki/Restriction_map

restriction mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA. MeSH, 1989 

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 & 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 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

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

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.  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.

Mapping resources
NCBI Genomes and Maps https://www.ncbi.nlm.nih.gov/guide/genomes-maps/

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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