]> http://dumontierlab.com en September 1, 2007 sgd ontology Natalia Villanueva-Rosales SGD Ontology (primitive) 2.0 An ontology for biological data obtained from the Saccharomyces Genome Database (SGD). Michel Dumontier rdf/xml has outcome has perturbation has reference has source has status is outcome of is perturbation of is reference for is source of is status of consensus sequence of an automomously replicating sequence The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS. ACS affinity capture A physical interaction experiment where a "bait" protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by some method. affinity capture MS An affinity capture experiment in which an interaction is inferred when a "bait" protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods. affinity capture RNA An affinity capture where a "bait" protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by specific RNA binding. affinity capture western An affinity capture where a "bait" protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by Western blotting with a specific polyclonal antibody or second epitope tag. affinity chromatography An affinity capture in which chromatographic purification is used to detect the interaction. affinity precipitation An affinity capture in which a "bait" protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by immunoblot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. autonomously replicating sequence Autonomously Replicating Sequence (ARS) is a region of DNA involved in the replication on extrachromosomal circular DNA molecules. ARS elements correspond to chromosomal origins of replication (ORIs), tend to be A/T rich, and have been implicated in the binding of the primosome complex. ARS biochemical activity experiment A physical interaction experiment where the biochemical effect of one protein is compared to another, for example, GTP-GDP exchange activity or phosphorylation of a substrate by a kinase. centromere A region of a chromosome where the kinetochore assembles, and where the kinetochore attaches chromosomes to mitotic and meiotic spindles. centromere DNA element CDE centromere DNA element I CDE I The centromere DNA Element I is the smallest of three adjacent centromeric domains, CDEI is an 8-11 bp consensus sequence that is bound by centromere binding factor 1 (Cbf1p). centromere DNA element II Central of three adjacent centromeric domains, CDEII is AT-rich and ~ 75-100 bp in length. CDE II centromere DNA element III Most essential of three adjacent centromeric domains, CDEIII consists of a 25-bp consensus sequence and provides the binding site for the centromere DNA binding factor 3 (CBF3) complex. CDE III chromosome region A region that is located on a chromosome. chromosome strand A single strand of DNA that is part of a chrosomome. co-crystollagraphy A physical interaction experiment that is directly demonstrated at the atomic level by X-ray crystallography. co-fractionation A physical interaction experiment in which molecules are partially purified. co-localization A physical interaction experiment where two molecules are co-localized by some means. co-purification A physical interaction experiment where two or more molecules are purified in a complex. coding exon An exon that directs the production of a peptide sequence. coding sequence CDS CoDing Sequence, region of nucleotides that corresponds to the sequence of amino acids in the predicted protein. The CDS includes start and stop codons, therefore coding sequences begin with an "ATG" and end with a stop codon. In SGD, unexpressed sequences, including the 5'-UTR, the 3'-UTR, introns, or bases not expressed due to frameshifting, are not included within a CDS. Note that the CDS does not correspond to the actual mRNA sequence. complex A reversible association of molecules, atoms, or ions through weak non-covalent chemical bonds complex purification A physical interaction experiment in which proteins are co-purified. crick strand The sense DNA strand. database source The database source of some object. dna A type of molecule that consists of a linear polymer of deoxy nucleotides. DNA binding site A DNA region by which other molecules may bind to. DNA region The extended spatial location of some thing. DNA transposon ds dna Double stranded DNA. dosage growth defect A dosage outcome where the overexpression or increased dosage of one gene causes a growth defect in a strain that is mutated or deleted for another gene. dosage growth defect experiment dosage interaction experiment A genetic interaction experiment in which the amount of gene/protein is increased. dosage lethality A dosage outcome where the overexpression or increased dosage of one gene rescues the lethality or growth defect of a strain that is mutated or deleted for another gene. dosage lethality experiment dosage outcome dosage rescue A dosage outcome where the overexpression or increased dosage of one gene rescues the lethality or growth defect of a strain that is mutated or deleted for another gene. dosage rescue experiment dubious enzyme A protein that exhibits catalytic activity. epistatic mini array profile A genetic interaction experiment in which observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. exon A portion of a split gene that is included in the transcript of a gene and survives processing of the RNA to become part of the spliced messenger of a structural RNA. Exons generally occupy three distinct regions of genes that encode proteins. Exons in the first region are not translated into protein, but signal the beginning of RNA transcription and contain sequences that direct the mRNA to ribosomes for protein synthesis. Exons in the second region contain the information that is translated into the amino acid sequence of the protein, and are sometimes referred to as coding exons. Exons in the third region are transcribed into the part of the mRNA that contains the signals for the termination of translation and for the addition of a polyadenylate tail. experiment An experiment is a procedure that is carried out and repeated under controlled conditions in order to discover, demonstrate, or test a hypothesis. experiment participant A participant in some experiment. external transcribed spacer ETS The ETS is a region of DNA in the rDNA repeat which flanks the 18S-5.8S-25S gene cluster and is included as part of its transcription unit. The 5' ETS is immediately upstream of the 18S gene and includes the A0 processing site. The 3' ETS is immediately downstream of the 25S gene. fret A physical interaction experiment in which the close proximity of interaction partners is detected by fluorescence resonance energy transfer between pairs of fluorophore-labeled molecules. far western A physical interaction experiment that involves the immobilization of a protein on a membrane and identified usinga probe. fast growth Growth at a faster than normal rate. frameshift gene Genes are regions of DNA that are transcribed into RNA. gene deletion A perturbation in which a gene is deleted. gene expression outcome gene insertion A gene perturbation in which a new copy of a gene is inserted. gene overexpression An outcome in which the natural levels of a gene message or product are increased. gene perturbation The perturbation of a gene. gene underexpression An outcome in which the natural levels of a gene message or product are decreased. genetic interaction experiment An interaction experiment where that includes the perturbation of a gene. genetic interaction participant A participant in a genetic interaction. growth The quality of creating biomass. growth defect growth defect heterozygous gene deletion A whole gene deletion in which a single copy of a gene exists is deleted in a diploid organism. homozygous gene deletion A whole gene deletion in which both copies of a gene are deleted from a diploid organism. interaction experiment An experiment to support or falsify an interaction between one or more entities. interaction experiment participant A participant in an interaction experiment. internal transcribed spacer The ITS is a region of DNA in the rDNA repeat which flanks the 5.8S gene and is included as part of the transcription unit of the 18S-5.8S-25S gene cluster. ITS1 is immediately upstream of the 5.8S gene and ITS2 is immediately downstream of the 5.8S gene. ITS intron A portion of a split gene that is transcribed into RNA, but subsequently removed from within the transcript prior to translation. long terminal repeat LTR Identical sequences, typically several hundred nucleotides in length, that are located both at the ends of intact Ty retrotransposons and as solo elements present in multiple copies throughout the genome. There are several types of LTR elements in yeast: delta, tau, sigma and omega. molecule no growth no growth non coding exon An exon that does not direct the production of a peptide sequence. non transcribed region non viable The quality of not showing characteristics of life especially the capacity to sustain life. normal growth Growth at an expected or anticipated rate. not physically mapped feature not sensitive The quality of not being responsive to some stimulus. null perturbation A null perturbation is a perturbation that results in the complete loss of function of a gene product. Often used to refer to the complete deletion of a protein-coding sequence; however, point mutations, partial deletions, and insertions may also result in a null phenotype. null phenotype A phenotype that results in the complete loss of function. orf status The status of an Open Reading Frame. open reading frame ORF An ORF (Open Reading Frame) corresponds to a stretch of DNA that could potentially be translated into a polypeptide or RNA; i.e., it begins with an ATG "start" codon and terminates with one of the 3 "stop" codons. For an ORF to be considered as a good candidate for coding a bona fide cellular protein, a minimum size requirement is often set, e.g., many of the systematic sequencing groups define an ORF as a stretch of DNA that would code for a protein of 100 amino acids or more. An ORF is not usually considered equivalent to a gene or locus until there has been shown to be a phenotype associated with a mutation in the ORF, and/or an mRNA transcript or a gene product generated from the ORF's DNA has been detected. See ORF naming conventions for how ORFs are named in Saccharomyces cerevisiae. outcome A characteristic obtained as of the result of some process. overexpression perturbation partial gene deletion Partial gene deletion is a gene deletion in which only part of the gene is deleted. pathway participant A participant in some biological pathway perturbation A perturbation is a modification of some entity. phage display A protein peptide interaction experiment that tests protein peptide interactions using phages. phenotype phenotypic enhancement A phenotypic outcome in which a mutation or overexpression of one gene results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation or overexpression of another gene. phenotypic enhancement experiment phenotypic experiment A genetic interaction experiment in which a mutation or overexpression of one gene results in enhancement/suppression of any phenotype (other than lethality/growth defect) associated with mutation or overexpression of another gene. phenotypic suppression A phenotypic outcome in which a mutation or overexpression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation or overexpression of another gene. phenotypic suppression experiment physical interaction experiment An interaction experiment that involves direct or indirect physical interaction between objects. physical interaction participant A participant in a physical interaction experiment. point mutation A perturbation in which a single residue (DNA or Protein) has been changed. process participant An object participant in some process protein A molecule that consists of a linear polymer of amino acids. protein peptide interaction experiment A physical interaction experiment between a protein and a peptide. protein rna interaction experiment A physical interaction experiment between a protein and an RNA molecule. pseudogene A pseudogene is a gene that has lost its protein-coding ability or is otherwise no longer expressed in the cell. publication rna A molecule that consists of a linear chain of ribonucleotides. reconstituted complex experiment A physical interaction experiment to detect interactions from purified proteins. repeat region A region containing some type of tandemly repeated sequence. For example, in the case of the telomeric Y' elements, these are known as "36-bp repeats". retrotransposon Transposable element that mobilizes via an RNA intermediate. Each DNA segment in the host chromosome is transcribed into RNA and then reverse-transcribed via a reverse transcriptase into a DNA segment. This is reinserted into the host genome, usually at a new site. Retroposon is a shortened form of retrotransposon, and also appears in the literature. ss dna Single stranded DNA. sensitive The quality of being responsive to some stimulus. sensitivity The quality of being sensitive or not sensitive to some stimulus. slow growth A slower than normal growth. synthetic genetic experiment A genetic interaction experiment in which mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in some phenotype. synthetic genetic outcome synthetic growth defect A synthetic genetic outcome in which mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in a significant growth defect when combined in the same cell under a given condition. synthetic growth defect experiment synthetic lethality A synthetic genetic outcome in which the interaction of two genetic perturbations (mutations/deletions), each of which alone causes a minimal phenotype, results in lethality when combined in the same cell under a given condition. synthetic lethality experiment synthetic rescue A synthetic genetic outcome in which the mutation/deletion of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene. synthetic rescue experiment telomere The telomeric regions are complex mosaics of several different types of telomeric and subtelomeric elements known as X element core sequences, X element combinatorial repeats, telomeric repeats, and Y' elements. Possible functions include roles in chromosomal segregation, maintenance of chromosome stability, recombinational sequestering, or as a barrier to transcriptional silencing. telomeric repeat The telomeric repeat is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. transcribed spacer translational frameshift transposon Any of the five classes (TY1 through Ty5) of mobile genetic elements in yeast that contain long terminal repeats flanking a central epsilon element that encodes two gene products, TyA (structural component) and TyB (reverse transcriptase). Ty elements are retrotransposons that move about the genome via an RNA intermediate. two hybrid A physical interaction experimetn where a "bait" protein fused to a DNA-binding domain is tested against a "prey" protein fused to a DNA-activating domain. An interaction between the "bait" and "prey" is indicated by transcriptional activation of a test gene. uncharacterized An uncharacterize status is applied to an ORF that is likely to encode an expressed protein, as suggested by the existence of orthologs in one or more other species, but for which there are no specific experimental data demonstrating that a gene product is produced. verified A verified ORF status is one for which experimental evidence exists that a gene product is produced. viability The quality of being able to survive and develop normally. viable The quality of being capable of life or normal growth and development. watson strand The anti-sense DNA strand. whole gene deletion Whole gene deletion is where the whole gene is deleted from a system. x element combinatorial repeat Formerly known as subtelomeric repeats (STRs), X element combinatorial repeats are located between the X element core sequence and the telomere or adjacent Y' element, and are usually present as a combination of one or more of several types of smaller elements (designated A, B, C, or D). X element combinatorial repeats contain Tbf1p binding sites, and possible functions include a role in telomerase-independent telomere maintenance via recombination or as a barrier against transcriptional silencing. subtelomeric repeat STR x element core sequence The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1. Possible functions include roles in chromosomal segregation, maintenance of chromosome stability, recombinational sequestering, or as a barrier to transcriptional silencing. Y' element A repetitive sequence found in many but not all subtelomeric regions, the Y' element is located next to the telomeric repeats, or adjacent X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. Two types of Y' elements are known, Y'-L and Y'-S, and any particular array will consist of only one type, not a combination of both. Y' elements contain helicase-encoding ORFs which are expressed only during meiosis and in telomerase-deficient cells. Possible functions include rescue of telomeres when the telomeric repeats are no longer present and a role in telomere maintenance during meiosis. non coding RNA The non-coding RNA components of ribonucleoproteins (for example see NME1, RPR1, RUF1-8, SCR1 and TLC1). ncRNA ribosomal rna ribosomal RNA RNA that forms the structural and functional components of ribosomes. rRNA gene small nuclear ribonucleotide small nuclear RNA An RNA component of small nuclear ribonucleoproteins (snRNPs) or snurps. They are located in the nucleus and are important for splicing of hnRNAs and telomeric maintenance snRNA gene small nucleolar rna small nucleolar RNA An RNA that is located in the nucleolus and is typically involved in nucleotide modification or rRNA, cleavage of precursor rRNA, rRNA folding and assembly of ribosomal subunits. snoRNA gene transfer RNA Transfer RNA molecule are involved in bonding to and transferring of amino acids to the ribosomes where proteins are translated. tRNA gene