Bioinformatics glossary - T

Tentative Consensus (TC)

The identification of a sequence from an EST cluster that represents part or all of a complete gene.  TCs are usually determined by clustering ESTs allowing for sequencing errors, artefacts such as chimeric clones, and naturally occuring biological phenomena such as alternative splicing.  Creation of a cluster allows one to generate a consensus sequence and then identify a long open reading frame which would suggest the possibility of that consensus representing a bona fide gene.

Tentative Human Consensus sequences (THCs)

A consensus sequence generated from human EST fragments. THCs may be validated by comparison against databases of known human gene sequences, human genomic sequences, or by identification of the ORFs or other sequence features contained within the consensus as belonging to a known human gene product.

Tertiary structure

Folding of a protein chain via interactions of its sideschain molecules including formation of disulphide bonds between cysteine residues.

Thymine

A pyrimidine base found in DNA but not in RNA.

Tissue

Section of an organ that consists of a largely homogenous population of cell types. Since many organs are multifunctional, they have developed highly specialized cell types to perform different functions. Identifying the section of an organ that is homogenous for a particular cell type ensures that the gene expression profiles extracted from those cells will accurately resemble the class of cells that make up the tissue.

Transcript

The single-stranded mRNA chain that is assembled from a gene template.

Transcription

The assembly of complementary single-stranded RNA on a DNA template.

Transcription factors

A group of regulatory proteins that are required for transcription in eukaryotes. Transcription factors bind to the promoter region of a gene and facilitate transcription by RNA polymerase.

Transfer RNA (tRNA)

A small RNA molecule that recognizes a specific amino acid, transports it to a specific codon in the mRNA, and positions it properly in the nascent polypeptide chain.

Transformation

A genetic alteration to a cell as a result of the incorporation of DNA from a genetically diferent cell or virus; can also refer to the introduction of DNA into bacterial cells for genetic manipulation.

Transgene

A foreign gene that is introduced into a cell or whole organism (eg.transgenic mice) for therapeutic or experimental purposes.

Translation

The process of converting RNA to protein by the assembly of a polypeptide chain from an mRNA molecule at the ribosome.

Transmembrane region

The region of a transmembrane protein that actually spans the membrane.  Transmembrane regions are usually hydrophobic in order to be thermodynamically compatible with the lipid bilayer portion of the membrane.  They may consist of either alpha-helical or beta-strand secondary structure elements, but in either case the external residues (the ones facing the membrane) are invariably hydrophobic while the internal residues may be hydrophilic (as in the case of a pore or channel) or polar.  One common transmembrane structural domain is the seven-helix bundle seen in numerous channel proteins.

Tissue

Section of an organ that consists of a largely homogenous population of cell types. Since many organs are multifunctional, they have developed highly specialized cell types to perform different functions. Identifying the section of an organ that is homogenous for a particular cell type ensures that the gene expression profiles extracted from those cells will accurately resemble the class of cells that make up the tissue.

Tentative Consensus (TC)

The identification of a sequence from an EST cluster that represents part or all of a complete gene.  TCs are usually determined by clustering ESTs allowing for sequencing errors, artefacts such as chimeric clones, and naturally occuring biological phenomena such as alternative splicing.  Creation of a cluster allows one to generate a consensus sequence and then identify a long open reading frame which would suggest the possibility of that consensus representing a bona fide gene.

Tentative Human Consensus sequences (THCs)

A consensus sequence generated from human EST fragments. THCs may be validated by comparison against databases of known human gene sequences, human genomic sequences, or by identification of the ORFs or other sequence features contained within the consensus as belonging to a known human gene product.

Tertiary structure

Folding of a protein chain via interactions of its sideschain molecules including formation of disulphide bonds between cysteine residues.

Thymine

A pyrimidine base found in DNA but not in RNA.

Tissue

Section of an organ that consists of a largely homogenous population of cell types. Since many organs are multifunctional, they have developed highly specialized cell types to perform different functions. Identifying the section of an organ that is homogenous for a particular cell type ensures that the gene expression profiles extracted from those cells will accurately resemble the class of cells that make up the tissue.

Transcript

The single-stranded mRNA chain that is assembled from a gene template.

Transcription

The assembly of complementary single-stranded RNA on a DNA template.

Transcription factors

A group of regulatory proteins that are required for transcription in eukaryotes. Transcription factors bind to the promoter region of a gene and facilitate transcription by RNA polymerase.

Transfer RNA (tRNA)

A small RNA molecule that recognizes a specific amino acid, transports it to a specific codon in the mRNA, and positions it properly in the nascent polypeptide chain.

Transformation

A genetic alteration to a cell as a result of the incorporation of DNA from a genetically diferent cell or virus; can also refer to the introduction of DNA into bacterial cells for genetic manipulation.

Transgene

A foreign gene that is introduced into a cell or whole organism (eg.transgenic mice) for therapeutic or experimental purposes.

Translation

The process of converting RNA to protein by the assembly of a polypeptide chain from an mRNA molecule at the ribosome.

Transmembrane region

The region of a transmembrane protein that actually spans the membrane.  Transmembrane regions are usually hydrophobic in order to be thermodynamically compatible with the lipid bilayer portion of the membrane.  They may consist of either alpha-helical or beta-strand secondary structure elements, but in either case the external residues (the ones facing the membrane) are invariably hydrophobic while the internal residues may be hydrophilic (as in the case of a pore or channel) or polar.  One common transmembrane structural domain is the seven-helix bundle seen in numerous channel proteins.

Tissue

Transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.

Transcriptomics
Transcriptomics is the global analysis of gene expression using high-throughput technologies such as microarrays and high-throughput sequencing (HTS).

TROME database
Trome is an attempt to map transcribed RNA from different sources to the genome. It includes a filtering step that allows the removal of non-trustful data. Moreover regarding the integration process, Trome was designed such that all transcriptional data is mapped to the genome. As an example for Homo sapiens, the transcribed RNA sources are: the human EST section of EMBL, the human HTC section of EMBL, human mRNA documented in the EMBL DB, ORESTES sequences from the LICR/FAPESP Human Cancer Genome project, human mRNA documented in the NCBI curated RefSeq DB, published CHR21 gene list and SEREX sequences. For other species, similar sources are used. 

Tandem array
The same sequence, repeated multiple times, where each copy of the repeat immediately follows the previous copy. Genes encoding rRNA and the histones are usually in tandem arrays. Repetitious sequences that are NOT in a tandem array are referred to as "dispersed".

tblastn
Blast search tool in which the query is an amino acid sequence and the subjects are the six amino acid sequences translated from the six frames found in double stranded DNA. Typically used when using a protein sequence to search a nucleotide database. Go to the BLAST web page and select "tblastn."

tblastx
BLAST version in which the query is all six possible amino acid sequences derived from translation of all six frames and the subjects are the six possible amino acid sequences derived from translation of all six frames of another nucleotide sequence. Not surprisingly, this is computationally very expensive.

Template
The starting material in a PCR reaction. When referring to a DNA strand, it is also called the negative, antisense, or non-coding strand. This strand of the DNA sequence of a single gene is the complement of the 5' to 3' DNA strand known as the sense, positive, non-template, or coding strand. The term loses meaning for longer DNA sequences with genes on both strands.

Termination codon
A codon that specifies the termination of peptide synthesis; sometimes called "nonsense codons," since they do not specify any amino acid.

Tiling path
A set of overlapping clones that cover (ideally) the entire sequence being assembled.
See also: golden tiling path


Transcript
An RNA molecule (or species of RNA molecule) that is the product of transcription.

Transcription
The process of copying one strand of a DNA double helix by RNA polymerase, creating a complimentary strand of RNA called the transcript.

Transcription terminator
Also called simply a terminator, it is a section of genomic DNA that marks the end of gene or operon, where transcription should stop.

Translation
The process by which codons in an mRNA are used by the ribosome to direct protein synthesis. For more detail, please see the entry on translation at Wikipedia.

Translational start
The first codon of a coding sequence. In eukaryotes this is almost always ATG, which codes for methionine.

Translocation
Literally "a change in location." In translocations part of a chromosome is transferred to another position in the genome. In a reciprocal translocation, two nonhomologous chromosomes exchange chromosome segments ending in a telomere. In an insertional translocation, a segment of one chromosome not ending in a telomere is inserted into a location on a nonhomologous chromosome.

Transposable genetic element
A genetic element that can insert into (and exit from) a chromosome, and may therefore relocate in the genome; this class includes insertion sequences, transposons, retrotransposons, some phages, and controlling elements. Much of the middle repetitious DNA in eukaryotic genomes is made up of damaged transposable elements.

Transposons
Segments of DNA that can move around to different positions in the genome of a single cell. In the process, they may cause mutations or increase (or decrease) the amount of DNA in the genome.

tRNA
Transfer RNA, small (~75 bp) L-shaped RNA molecules that deliver specific amino acids to ribosomes according to the sequence of a bound mRNA. The proper tRNA is selected through the complementary base pairing of its three-nucleotide anticodon with the mRNA's codon, and its amino acid group is transferred to the growing polypeptide.

TwinScan
A gene prediction algorithm that uses conservation to a second "informant" genome to assist in the prediction of genes.

Tandem repeat sequences
 Multiple copies of the same base sequence on a chromosome; used as markers in physical mapping.

Targeted mutagenesis
Deliberate change in the genetic structure directed at a specific site on the chromosome. Used in research to determine the targeted region's function.

Telomere
 The end of a chromosome. This specialized structure is involved in the replication and stability of linear DNA molecules.

Teratogenic
 Substances such as chemicals or radiation that cause abnormal development of a embryo.

Thymine (T)
 A nitrogenous base, one member of the base pair AT (adenine-thymine).
 See also: base pair, nucleotide

Toxicogenomics
The study of how genomes respond to environmental stressors or toxicants. Combines genome-wide mRNA expression profiling with protein expression patterns using bioinformatics to understand the role of gene-environment interactions in disease and dysfunction.

Transcription
The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression.

Transcription factor
A protein that binds to regulatory regions and helps control gene expression.

Transcriptome
The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time

Transfection
The introduction of foreign DNA into a host cell.

Transfer RNA (tRNA)
A class of RNA having structures with triplet nucleotide sequences that are complementary to the triplet nucleotide coding sequences of mRNA. The role of tRNAs in protein synthesis is to bond with amino acids and transfer them to the  ribosomes, where proteins are assembled according to the genetic code carried by mRNA.

Transformation
A process by which the genetic material carried by an individual cell is altered by incorporation of exogenous DNA into its genome.

Transgenic
An experimentally produced organism in which DNA has been artificially
introduced and incorporated into the organism's germ line.

Translation
The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids.

Translocation
A mutation in which a large segment of one chromosome breaks off and
attaches to another chromosome.

Transposable element
A class of DNA sequences that can move from one chromosomal site to
another.

Trisomy
Possessing three copies of a particular chromosome instead of the normal two copies.