Phenovault: Database & Analysis Suite for RNAi/CRISPR Screens

Uncover New Insights into Gene Function, Reagents and Screening Data

Identifying genes responsible for imparting phenotypes is a challenge. In the past years, large RNA interference (RNAi)-based functional genomic screens were carried out to identify novel factors that impact relevant phenotypes. However, due to prevalent RNAi off-target effects and variable siRNA knock-down efficiencies, results are often dominated by false positives or previously known strong-inducing factors.

The Phenovault is a carefully curated database and analysis suite for RNAi/CRISPR screens that combines big data with dominant siRNA seed-based behaviour to help scientists uncover novel gene targets and data insights. With the largest collection of RNAi screening data and extensive data analysis algorithms, the Phenovault serves as a useful target validation and discovery tool for scientists looking to leverage past and current functional genomic screening data.

Phenovault Applications

01 Discover novel targets

Identify novel genes that impact phenotypes by seed-based analysis of RNAi screening data.

02 Assess quality of hit list

For a given screening dataset, uncover likely false positives and obtain predicted expression levels.

03 Evaluate siRNA reagents

Determine potential for siRNA off-targeting and obtain candidate off-target gene list .

04 Evaluate gene targets

Validate targets by retrospective analysis of gene disruption phenotypes produced in Phenovault screens.

05 Identify relevant gene combinations

Discover gene combinations that impart relevant phenotypes with siTOOLs' Merlin Analysis algorithm.

06 Counteract screening artefacts and siRNA off-targeting

Uncover screening artefacts (e.g. plate positional effects) and improve hit list with siRNA seed-based correction.

Supporting Information

Largest Collection of RNAi Screening Data with Phenovault

Phenovault RNAi Reagents


Screen Count per Phenovault RNAi Reagent


Amassing genome-scale screening data that often lies buried within publication supplementary materials, the Phenovault is the largest curated collection of RNAi screening data linking phenotypic read-outs to reagent sequences or ID. Inside the Phenovault: ≥ 48 publications, 374, 364 unique reagents, 20 million data points and 845 screening features.

Harnessing Dominant siRNA Seed Effects with Phenovault

Numerous publications together with our own observations indicate that seed-based siRNA off-targeting dominates most RNAi screens. The Phenovault is equipped with published and proprietary analysis algorithms that exploit this behaviour to recognise and extract genes that may impact phenotypes but are often missed by on-target analysis.


What is a seed?
The seed is a 6-base sequence at position 2 to 7 of the siRNA guide strand that dictates siRNA off-target activity based on microRNA mimicry – microRNAs use the seed to recognize and downregulate their targets via deadenylation-induced degradation or translation inhibition.

Seed effects dominate phenotypes
Correlation analysis of phenotypes produced by two siRNAs sharing the same gene target vs same seed sequence demonstrates seed-based off-targeting often dominates RNAi-based phenotypes. The figure shows ~280 million pairwise correlations based on data from a multi-parametric RNAi screen where > 100, 000 siRNAs were screened for > 15, 000 genes.

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