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Glossary

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 0-9

3' primer

Small complementary sequence of DNA that is complementary to the 3' and binds to the 3' end of the DNA sequence under study. ie. The end of the DNA molecule which terminates in a 3' hydroxyl group. (see probe).

 

5' primer

Small complementary sequence of DNA that is complementary to and binds to the 5' end of the DNA sequence under study. ie. The end of the DNA molecule which terminates in a 5' phosphate group. (see probe).

 

accession ID

A unique identifier used to identify a piece of information in a database. Technically, unique IDs are used to distinguish different instances of data. For example, each database entry has a unique ID, similarly, each gene, each probe, etc has it's own ID. Different databases can utilise unique IDs to cross-reference genes, probes, etc. Thus, the GUDMAP database can be searched for gene expression patterns using the Mouse Genome Informatics (MGI) gene ID for a gene, e.g. Wnt4.

 

adjacent to

Next to another structure. (see location).

 

anatomy

The study of structures of organisms.

 

anatomy tree

Anatomical structures from the developing mouse GU system and their relationships are displayed as a tree. (see group term).

 

anchor gene

Anchor genes are defined as genes whose expression is restricted to one temporospatial anatomical compartment.

 

annotate

Here we refer to annotation of gene expression patterns. To list, using a standard vocabulary, those structures in which gene expression is present or not detected in a particular assay. In some cases, it is not clear if signal from the assay is present or undetectable and in these cases gene expression is annotated as 'uncertain'.

 

annotation

Here, annotation refers to a record of the presence or absence of signal for a given structure.

 

antisense

A probe that is complementary to mRNA. This probe binds to the mRNA, giving a signal in an in situ hybridisation assay. (see probe type).

 

bissection

A single dissection which cuts the tissue or specimen in to two parts.

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caudal view

A caudal view is a view from the tail end. Because the embryo is curved in a U shape, a caudal view of the head region is a view from the rump. 'Posterior' is broadly synonymous with 'caudal'. (see specimen view).

 

caudal

Closest to the tail mouse, i.e. in a posterior direction. (see location).

 

CEL file

CEL files contain information about where each probe is on the chip and the fluorescence intensity values (ie. signal strength) for each probe. (see supplemental data files).

 

CHP file

CHP files contain the results of the experiment including the average signal values for each probe. Normalisation of the average signal values against internal control standard probe sets determines if gene expression is either present, absent or marginal. (see supplemental data files).

 

clone name

The name of DNA clone used to generate the probe under study. (see probe).

 

component sampled

Tissue or structure taken from the urogenital system for gene expression analysis using, for example, a microarray assay.

 

control probe

A control probe is used to eliminate experimental artifacts and establish the efficacy of the experimental probe used to determine gene expression.

 

deep

closest to the inside of the organ or structure or core. (see location).

 

dissection

Dissection involves the cutting or separating of the tissues of an organism for study. (see frontal; see sagittal; see transverse).

 

distal

Away from the attachment or point of reference of the organ or structure. (see location).

 

dorsal

towards the back of the mouse. (see location).

 

dpc

Days Post Coitum (dpc) is used to age the developing embryo and is the number of days following the parental mating. Notice that, as a result of biological variation, embryos of the same age (dpc) may be at somewhat different stages (Theiler Stages) of development. This is true even for embryos of the same litter. It is for this reason that the database uses developmental stage rather than age as its primary temporal measure. (see embryonic age).

The following table gives an approximate colleration between dpc and Theiler Stage.

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early reproductive system

The early reproductive system in the developing mouse embryo consists of the early gonad and mesonephros. At Theiler Stage (TS)17-TS19 the sex of the developing mouse embryo is not distinguished anatomically. (see focus group).

 

embedding

The tissue under study is placed in a supporting medium so that it can be cut in to thin sections using a microtome. eg. paraffin wax embedding.

 

embryonic age

Age of the developing embryo after mating (often estimated). (see dpc).

 

EXP file

EXP files contain information about the experimental conditions & protocols. (see supplemental data files).

 

expression pattern

Gene expression may not be uniform for a given structure suggesting that expression may be limited to a group of cells or discreet areas of that structure. (see graded; see regional; see restricted; see single cell; see spotted; see ubiquitous).

 

expression strength

(see strong; see moderate; see weak).

 

expression mapping

(see present; see uncertain; see not detected; see not examined).

 

FACS

Fluorescent-activated cell sorting (also known as flow cytometry). Flow cytometry is a technique for counting, examining, and sorting microscopic particles suspended in a stream of fluid. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus (ref. http://en.wikipedia.org/wiki/Flow_cytometry).

 

female reproductive system

Female sex organs which are involved in sexual reproduction. eg. ovary, uterus. Sexual differentiation is seen at Theiler Stage (TS)20 in the developing mouse embryo. (see focus group).

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fixation method

Fixation is a technique employed to preserve the form of the tissue or structure under study by the use of chemicals eg. 4% paraformaldehyde.

 

focus group

The division of the genitourinary system into sub-parts for the convenience of people using the GUDMAP database who have a specific interest in one part of the system. Only experimental data for that division is made available. (see metanephros; see lower urinary system; see early reproductive system; see male reproductive system; see female reproductive system).

 

frontal

The tissue is cut in a plane that includes the medio-lateral and antero-posterior axes. (see dissection).

 

gene expression database

Database containing data that documents where and when genes are expressed in the tissues of an organism.

 

gene name

The name given to a gene. Eg. wingless-related MMTV integration site 1.

 

gene symbol

Symbol used for gene identification. Eg. Wnt1.

 

genitourinary (GU)

The genitourinary system is the organ system containing both the reproductive and urinary systems. The reproductive system comprises testis, ovary, male reproductive tract (Wolffian duct derivatives: epididymis and prostate), gubernaculum (involved in testicular descent), female reproductive tract (Müllerian duct derivatives: oviduct, uterus, upper vagina), and external genitalia (genital tubercle derivatives: penis and scrotum in males, vulva, labia, clitoris in females). The urinary system comprises kidneys, ureter, bladder & urethra.

 

genotype

An organism's genetic information. (see wild type; see non-wild type).

 

GEO

Gene Expression Omnibus (GEO) is a repository where microarray gene expression data from any organism is stored and is made publicly available (http://www.ncbi.nlm.nih.gov/geo/). This data can be retrieved and used for gene expression analysis. (see GEO ID).

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GEO ID

A unique number given by the NCBI Gene Expression Omnibus (GEO) to identify individual microarray experiments and their datasets. (see GEO).

 

global

The entire specimen or tissue under study. (see specimen view).

 

graded

A gradient of strength of expression in the structure. (see expression pattern).

 

group term

A term denoting a structural unit comprising several sub-structures, such as the nephron and juxtaglomerular complex. (see anatomy tree).

 

GU organogenesis

The processes involved in the differentiation, growth and development of organs in the genitourinary system.

 

GUDMAP

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories generating gene expression pattern data, using in situ hybridisation and microarray techniques, of the genitourinary system of the mouse.

 

IHC

Immunohistochemistry (IHC) is a molecular technique used to detect local patterns of gene expression within cells and tissues by assaying the net amounts of protein encoded by a specific gene at a given time.

 

in situ

In situ refers here to assays that detect gene expression in situ, i.e. wherever gene expression occurs in the intact tissue. This is in contrast to sample-based assays which detect expression in selected and homogenized samples of tissues or cells. In situ assays include in situ hybridisation (ISH), immunohistochemistry, and transgenic reporter assays.

 

ISH

In situ hybridisation (ISH) is a molecular technique used to detect local patterns of gene expression within cells and tissues by assaying the net amounts of mRNA encoded by a specific gene at a given time.

 

Inferred Annotation

If an anatomical term is annotated with 'present' expression then, as a consequence, all anatomical terms that it is 'part of' (its parent terms) will have 'inferred present' expression (even though they have not been directly annotated). Equally, if an anatomical term is annotated with 'not detected' expression, then its parts (or child terms) would have 'inferred not detected' expression.

For example, if the anatomical term 'superficial cellular layer' has been annotated as expression 'present' for a particular gene, as a consequence, the anatomical term 'urothelium' will have 'inferred present' annotation (even though it has not been annotated directly) because 'superficial cellular layer' is a part of the 'urothelium'. Equally, if 'urothelium' was annotated as 'not detected' then its parts, including 'superficial cellular layer' would have 'inferred not detected' annotation.

 

labelled with

Probes can be labelled with either radioactive or non-radioactive compounds to enable their detection in the tissues or structures under study.

 

lateral

Away from the median axis, i.e. towards the left or right side of the mouse. (see location).

 

LCD

Laser Capture Dissection where a portion of tissue is cut from a specimen by laser and captured. Repeated Laser captured pieces are pooled, homogenised and the RNA extracted for microarray analysis.

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location

Describes where within a structure gene expression is detected. (see adjacent to; see caudal; see deep; see distal; see dorsal; see lateral; see medial; see proximal; see radial; see rostral; see surface; see ventral).

 

lower urinary system

The lower urinary system is composed of the ureter, bladder and urethra. The ureter connects the kidney to the bladder where urine is stored before being expelled from the body via the urethra. (see focus group).

 

male reproductive system

Male sex organs which are involved in sexual reproduction. eg. testis, epididymis. Sexual differentiation is seen at Theiler Stage (TS)20 in the developing mouse embryo. (see focus group).

 

maprobe number

Unique number given to identify the probe used in an in situ hybridisation experiment in the GUDMAP database. (see probe).

 

marker gene

Marker genes are defined as genes which display a regional or enriched expression pattern and may be useful in identifying one or more particular temporospatial compartment(s).

 

medial

Closest to the median axis or middle along the left/right axis. (see location).

 

metanephros

The permanent kidney. (see focus group).

 

MGI number

Unique identifier for information held within the Mouse Genome Informatics (MGI) database (http://www.informatics.jax.org). The GUDMAP database uses several different MGI Unique IDs: for example, separate IDs for genes and probes. (see probe).

 

microarray

We refer here to expression microarrays as distinct from other array-based techniques. An expression microarray is a tool used to simultaneously detect the expression of many genes in a sample of tissue. An array consists of a small membrane or glass slide containing probes for many genes (usually more than one probe per gene) arranged in a regular pattern. The sample is taken from the tissue and homogenised then assayed on the array. Alternatively, labelled cells are isolated from a tissue (e.g. by fluorescence activated cell sorting, FACS) then assayed on the array. Being a sample-based technique, microarray assays do not resolve differences in expression between different cells within the sample. This contrasts with in situ assays which detect local differences in expression. However, unlike in situ assays which each detect the expression of only one or a few genes, microarrays detect the expression of many thousands of genes in a single assay. (see series).

 

moderate

Probe signal strength is moderate indicating average/fair/medium concentration of gene product for the gene of interest. (see expression strength).

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molecular anatomy

A molecular anatomy domain is a region of tissue defined by the expression of a particular panel of genes. eg. Proximal and distal regions of the renal vesicle.

 

mouse strain

Inbred mice that are genetically uniform.

 

non-wild type

The genotype of wild type mouse has been altered. ie. mutated. (see genotype).

 

not detected

Probe signal is not detected for the gene of interest. Since mRNA may still be present below the limits of detection of the method used, this result does not categorically denote the absence of gene expression. Notice also that what is assayed is the net amount of mRNA (in situ hybridisation) or protein (immunohistochemistry). Since mRNA and protein can be degraded by natural processes in the cell, the assay does not directly measure transcriptional or transcriptional + translational activity. (see expression mapping).

 

not examined

Anatomical structures have not been examined for gene expression. (see expression mapping).

 

ontology

An ontology is a description of what exists. It includes entities (things or processes) and their relationships. An anatomy ontology comprises anatomical structures (e.g. bladder) and their structural (part-of) and type (is-a) relationships. Some anatomy ontologies, including the GUDMAP ontology, also include temporal relationships (exists at stages X to Y). The anatomy ontology facilitates annotation of gene expression patterns by providing standard names for structures. It also facilitates data mining by providing describing the relationships between structures. The GUDMAP ontology is a hierarchy of histologically defined anatomical structures for the embryological stages in the developing mouse genitourinary system.

 

platform

Platform' details describe the type of microarray. This description includes (or refers to manufacturers details of) information about the probes on the array, etc.

 

present

Probe signal is positive indicating that gene expression is present for the gene of interest. (see expression mapping).

 

probe

Here, a molecule (e.g. RNA or a protein antibody) that binds to a gene product and that has been labelled so that it can be detected and visualised. Because the labelled probe binds to a gene expression product (mRNA or protein) it's visualisation can be used to assay gene expression in the tissue or structure of interest. Probes can be used in situ in the tissue or on microarrays. (see clone name; see sequence; see 5' primer; see 3' primer; see MGI number; see maprobe number)

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probe type

(see antisense; see sense).

 

protein

Proteins are composed of amino acid subunits . Proteins carry out the many different biomolecular functions within the cell and organism.

 

proximal

Closest to the attachment or point of reference of the organ or structure. (see location).

 

radial

Ray-like expression, uniformly arranged around a central axis or spreading from a central point. (see location).

 

regional

Localised expression restricted to a region within the structure. (see expression pattern).

 

restricted

(see expression pattern).

 

RNA

Ribonucleic acid (RNA) is a transcript of the genetic code found within the nucleus of the cell. Messenger RNA (mRNA) is translated in to proteins by molecular machinery present in the cytoplasm.

 

rostral view

A rostral view is a view from the head end. 'Anterior' is broadly synonymous with 'rostral'. (see specimen view).

 

rostral

Closest to the head of the mouse. i.e. in an anterior direction. (see location).

 

RPT file

The RPT files includes information about background fluorescence values (ie. 'noise') and the internal hybridisation controls within the microarray chip. (see supplemental data files).

 

sagittal

The tissue is cut in a plane that includes the antero-posterior and dorso-ventral axes. Strictly, the sagittal plane is the single plane passing through the midline, but common usage includes all planes parallel to this. (see dissection).

 

sample

A Sample describes an experimental unit in a microarray experiment. There may be several replicate samples in a Series. Sample details describe the structure under study, the experimental details, the expression values derived from the study and downloadable files for end user analysis.

 

section

A thin section cut from the tissue of study used for a gene expression assay.

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sense

A probe has the same sequence as mRNA. Since this probe is not complementary to mRNA it does not bind to it. Binding of sense probe to the tissue in an in situ hybridisation assay generally indicates non-specific binding (background). Sense probes are therefore sometimes used as 'controls'. One caveat is that sense probes may also bind to naturally occurring antisense RNA. (see probe type).

 

sequence

The order of the nucleotides of in the gene or probe under study.

 

series

A Series is a group of related samples under study. Generally speaking a Series is an Experiment. Series data describes the microarray study including; experimental design, summary & the samples. (see microarray).

 

single cell

Expression in a single cell within the structure (one single cell). (see expression pattern).

 

specimen view

The view of the specimen or tissue under study. (see global; see rostral; see caudal).

 

spotted

Spotted pattern of expression in groups of cells or multiple single cells scattered within the structure. (see expression pattern).

 

strong

Probe signal strength is strong indicating high concentration of gene product for the gene of interest. (see expression strength).

 

supplemental data files

Data files that are generated during & following a microarray experiment by Affymatrix software. (see CEL file; see CHP file; see EXP file; see RPT file; see TXT file).

 

surface

Closest to the outside of the organ or structure or shallow. (see location).

 

Tg

A 'transgenic' mouse that contains stably inherited DNA which has been experimentally inserted into the genome. The inserted gene sequence (the transgene) may or may not be derived from a mouse genetic sequence.

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Theiler stage

A description of the developmental stages of the developing embryo of the laboratory mouse by Karl Theiler. (http://genex.hgu.mrc.ac.uk/Atlas/intro.html). See 'The House Mouse - Atlas of Embryonic Development', Karl Theiler, 178 pages.
Copyright © Springer-Verlag. Second printing 1989. (see TS).

One of the 28 different stages described by Theiler. The arbitrary subdivision of the developing mouse embryo is defined by the presence of characteristic features. The following table gives an approximate colleration between dpc and Theiler Stage.

 

transgenic

A transgenic organism is one that has had it's genetic material modified by the inclusion of external DNA using genetic engineering techniques.

 

transverse

The tissue is cut in a plane that includes the medio-lateral and dorso-ventral axes. (see dissection).

 

TS

Abbreviation of Theiler Stage. One of the 28 different stages described by Theiler. The arbitrary subdivision of the developing mouse embryo is defined by the presence of characteristic features. (see Theiler Stage).

 

TXT file

The expression analysis value from the CHP file is contained in a text file format. (see supplemental data files).

 

ubiquitous

Expression throughout the structure. (see expression pattern).

 

uncertain

Probe signal is ambiguous and gene expression can not be readily determined for the gene of interest. (see expression mapping).

 

ventral

towards the belly of the mouse. (see location).

 

visualisation method

Tissue under study is treated with compounds so that the probe can be visualized.

 

weak

Probe signal strength is weak indicating low concentration of gene product for the gene of interest. (see expression strength).

 

wholemount

An intact organ or embryo used for a gene expression assay, as distinct from histologically sectioned material.

 

wild type

The inherited genotype of the wild type mouse that commonly found in the mouse population. (see genotype).

 
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