GenomeRNAi - a database for RNAi phenotypes and reagents

Download information

Download all screens

A file containing data for all screens in GenomeRNAi is available via e-mail. Please write an email to "contact at genomernai dot org" we'll send you a download link.

GenomeRNAi is licensed under a Creative Commons Attribution 3.0 Unported License.

Download frequent hitter list

Frequent hitters are gene lists sorted in descending order according to the number of times a gene has shown a phenotype. Genes showing a phenotype only once, or not at all, are not included.

Download frequent hitter list.

Download archived screens

In the process of updating pre-existing data and applying the new annotation guidelines, some screens have been removed from the GenomeRNAi database.

Typically the reason is a very low number of specific data that can be extracted from the publication, e.g. only one hit described from a genome-wide screen without providing information on the genes actually tested.

Screen data that have been removed from the database have been archived and can be downloaded here.

Download data from an individual screen

Data for individual screens can be downloaded directly from the website. For example, go to 'Browse' and click on your screen of interest. Then click on the 'Download' button to the right.

Download format

The download files consist of two sections per screen: The first section provides general information about the screen, such as authors, Pubmed ID, biomodel, assay, and the second section provides the actual gene-phenotype associations in tab delimited format. An example is given below.

NOTE: Entrez ID vs Gene ID - the Gene ID column contains the gene identifier as provided by the authors of the screen and can therefore come from various sources when comparing different screens. We have attempted to map all Gene IDs to Entrez Gene IDs in order to provide one data column with uniform identifiers.

NOTE: Stable IDs are assigned according to the following convention:
GR00123-A = core ID for a screen curated from the literature
GR00123-S = core ID for a screen submitted directly by the author
GR00123-C = core ID for a screen imported via cellHTS2
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

For more information about data fields see also our Glossary.

Download Example

#Stable ID=GR00184-A-1
#Screen Title=Self-renewal and pluripotency in human embryonic stem cells (1)
#Publication Title=A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity
#Authors=Chia et al.
#Publication Year=2010
#Pubmed ID=20953172
#Organism=Homo sapiens
#Screen Type=Cell-based
#Biosource=Cell line
#Biomodel=hESC H1
#Assay=POU5F1-GFP protein expression
#Library Manufacturer=Dharmacon
#Library=SMARTpool siRNA library
#Reagent Type=siRNA
#Score Type=Z-score
#Cutoff=< -2
#Stable ID Entrez ID Gene ID Gene Symbol Reagent ID Score Phenotype Conditions Follow Up Comment
GR00184-A-1 390992 XM_372757 HES3 M-027394-00 -0.011 none no
GR00184-A-1 3704 NM_033453 ITPA M-013681-00 -1.153 none no
GR00184-A-1 10673 NM_006573 TNFSF13B M-017586-00 -0.013 none no
GR00184-A-1 284837 NM_194310 LOC284837 M-019296-00 0.562 none no
GR00184-A-1 56999 NM_020249 ADAMTS9 M-005779-00 -0.67 none no
GR00184-A-1 1212 NM_001834 CLTB M-004003-00 -2.263 decreased POU5F1-GFP protein expression no