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Of Exactitude in Science
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 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/
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 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.ppt.
Related
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 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 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
How
to look for other unfamiliar terms
.IUPAC definitions are reprinted with
the permission of the International Union of Pure and Applied Chemistry
Evolving terminologies for emerging
technologies
Suggestions? Comments? Questions?
Mary Chitty MSLS mchitty@healthtech.com
Last revised
July 08, 2019
...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.
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
genomic maps:
Genomic Maps - specification, Object
Management Group http://www.omg.org/cgi-bin/doc?formal/2002-02-01
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]
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.
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
NCBI Genomes and Maps
https://www.ncbi.nlm.nih.gov/guide/genomes-maps/
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