Glossary of terms

Contents: #top - 0-9 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

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C

Confirmed gene

A WormBase gene prediction where every base of every exon has transcript support (EST, OST, or mRNA). These are often gene predictions whose structure has been modified to agree with the available transcript evidence. Note that the structure may still be incorrect, i.e. we may be missing an internal exon. These are usually treated as our set of highest quality gene predictions.
Source: Keith Bradnam

E

ES

Ease of Scoring
A scale used to describe the relative ease of scoring of mutant phenotypes.

• ES0 = impossible to score
• ES1 = very hard to score except by special means (such as enzyme assay or cell lineage analysis)
• ES2 = hard to score (may become easier with practice)
• ES3 = easy to score

Source: C. elegans II, 1997

Expression profile

An expression profile mountain represents a group of genes that are closely related in expression profile analysis. For more details see Kim et al. Science (2001)
Source: Eimear Kenny

I

InParanoid groups

These are derived from the April, 2005 release of InParanoid pairwise orthologies by Erik Sonnhammer and coworkers (O'Brien et al. [2005], Nucleic Acids Res. 33, D476-D480). In their original form these consist of many different species-to-species pairs. For ease of use they have been consolidated into the following levels of evolutionary relatedness: groups built solely from C. elegans-C. briggsae ortholog pairs (~13,000 "InP_Cae_*" groups); those built from metazoan ortholog pairs (~5,700 "InP_met_*" groups); and those built from non-metazoan, eukaryotic ortholog pairs (~3,500 "InP_uni_*" groups, whose last common ancestor with C. elegans was unicellular).
Source: pmid15608241

K

KOGs

KOGs are a eukaryote-specific version of the Conserved Orthologous Groups originally devised by Roman Tatusov, Eugene Koonin and others (at NCBI) for microbial genomes. KOGs are defined by a triangle of reciprocal best BlastP hits between domains of eukaryotic proteins from at least highly divergent species (i.e., species that diverged no later than the Cambrian Era) such as C. elegans, D. melanogaster, and H. sapiens. In addition, Tatusov et al. have defined TWOGs (groups defined by a pair of best BlastP hits, e.g., between C. elegans and D. melanogaster) which may represent incipient KOGs (which may become more obvious as more species have their genomes sequenced); they have also defined LSEs (lineage-specific expansions of paralogous proteins found solely in a single species such as C. elegans) and FOGs ('fuzzy' orthologous groups, such as zinc fingers, whose detailed relationships are difficult to ascertain).
Source: pmid11125040

M

ME

Male Mating Efficiency
A scale used to describe the efficiency of mutant males in genetic crosses.

• ME0 = no successful mating
• ME1 = rare successful mating
• ME2 = poor mating
• ME3 = fair-to-excellent mating
  

Source: C. elegans II, 1997

N

NA

Number of Alleles
This is the total number of alleles for each gene and is usually followed by a score, i.e. NA1 indicates that only 1 allele is known.
Source: C. elegans II, 1997

O

OA

The number of additional alleles of a gene in addition to the canonical allele. Usually followed by a score, i.e. OA > 40 = greater than 40 other alleles.
Source: C. elegans II, 1997

P

Partially confirmed gene

A WormBase gene prediction where there is some transcript support (EST, OST, or mRNA), but not for every base of every exon. These reflect genes where there may not be complete transcript data available (e.g. only 5' and 3' EST reads available) and/or where the current gene prediction needs further refinement.
Source: Keith Bradnam

Predicted gene

A WormBase gene prediction where there is no available transcript data (EST, OST, or mRNA). These may still represent perfectly valid genes and in most cases these gene predictions are supported by some other data (BLAST homology, RNAi phenotypes etc.)
Source: Keith Bradnam

Pseudogene

Most pseudogenes in WormBase represent genes that exhibit homology with other functional genes but which have become inactive through accumulation of mutations (frame shifts and internal stop codons).

Other pseudogenes in WormBase may contain valid open reading frames and additionally show evidence of transcription (EST matches), but have been classified as a pseudogene on the basis of sequence comparison to other genes. E.g. a multiple sequence alignment might reveal a high degree of sequence conservation between different genes, but one of those genes may have a premature stop codon in comparison to all other family members.

Pseudogenes are usually annotated in this way on the basis of comments from experts working on that gene family. Alternatively, some tRNA genes are classified as pseudogenes on the basis of the tRNA-scan program which automatically classifies potential pseudogenic tRNAs.

It should be noted that all of these pseudogenes in WormBase are only classified as such in relation to the sequenced Bristol N2 strain that was used for the genome project. Orthologous genes in closely related species (and possibly in other C. elegans strains) may not be pseudogenes.

R

RNAi experiments (primary targets)

These entries represent RNAi probes that have been aligned to the genome using a combination of BLAST and BLAT programs and have sequence identity to the target location of at least 95% over a stretch of at least 100 nt. Probes that satisfy these criteria are almost certain to produce RNAi effect on overlapping genes and the corresponding locations are usually the primary genomic targets of an RNAi experiment. Note that it is possible for a probe to have multiple primary targets within the genome.
Source: Igor Antoshechkin

RNAi experiments (secondary targets)

These entries represent RNAi probes that have been aligned to the genome using BLAST program and have sequence identity to the target location from 80 to 94.99% over a stretch of at least 200 nt. Probes that satisfy these criteria may or may not produce RNAi effect on overlapping genes and the corresponding locations represent possible secondary (unintended) genomic targets of an RNAi experiment.
Source: Igor Antoshechkin