GenomeRNAi - a database for RNAi phenotypes and reagents


This glossary gives short definitions for the major terms used in this website.

Assay – Short description of the assay method from a biological point of view, e.g. ‘viability’, ‘muscle cell morphology’, ‘hTERT mRNA expression’.

Method – Short description of the assay method from a technical point of view (readout), e.g. ‘luminescence’, ‘real-time qPCR’, ‘flow cytometry’.

Biomodel – The concrete biomodel used, e.g. ‘HeLa’, ‘primary embryonic cells’.

Biosource – Type of biomodel used in RNAi screen; controlled vocabulary (‘Cell line’, ‘Primary cells’, ‘Tissue’, ‘Organism’). For in vivo screens: ‘tissue’, if tissue-specific expression of UAS-IR, ‘organism’, if ubiquitous expression of UAS-IR.

Cutoff – Score threshold or other criteria used by the authors to define hits and separate them from non-hits.

Gene ID – Gene identifiers as provided by the authors. Gene IDs separated by ‘, ’ indicate that two or more genes have been knocked down.

Mapped ID – Entrez IDs, obtained by multi-step mapping of author-provided gene identifiers, gene symbols or reagent identifiers to the Entrez database.

Phenotype – Description of the actual observation upon knockdown of a gene, rather than an interpretation of the result, e.g. ‘increased activity…’ rather than ‘suppressor…’. ‘none’ = non-hit, or not provided.

Reagent ID - Reagent IDs separated by ‘, ’ indicate that two or more reagents have been used for RNAi.

Scope – Extent of the screen, e.g. ‘genome-wide’, ‘phosphatases’, ‘selected genes’.

Score – Score as provided by author, see also score type and cutoff under screen information. Graph displays distribution of all scores provided for this screen. Red line indicates position of score in question.

Score Type – Type of score used in the screen for defining hits, e.g. ‘Z-score’, ‘percentage’, ‘frequency’.

Stable ID - Stable IDs are assigned according to the following convention:
GR00123-A= core ID for a screen curated from the literature
GR00123-C = core ID for a screen imported via cellHTS2
GR00123-S = core ID for a screen submitted directly by the author(s)
GR00123-A-0 = indicates that the data from this screen still need to be updated to the current annotation standard (pre-existing data)
GR00123-A-1, GR00123-A-2, etc = indicates that this is one screen out of several, published within the same publication

Common Abbreviations

np - (not provided) might appear in several data fields. The abbreviation means that no information for this field was available from the publication.

rp - (reference provided) might appear in several data fields. The abbreviation is used when the authors did not describe the information but provided a reference instead.

sp - (see publication) might appear in several data fields. For example, it is used in the „Conditions“ field to describe complex conditions used for the assay, e.g. summarized phenotypes from several lines in in vivo screens. If the „Score Type“ it indicates that several score types were taken for selecting hits, or when the score type was not described precisely. In the „Score“ field „sp“ is used when two or more scores were needed for defining hits.