Interactions
(Package: HD2013SGI) :
The genetic interaction data.
The genetic interaction data. Pairwise interaction scores (piscore) are presented in a 6-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. BH-corrected p-values (padj) are presented in a 5-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features. An annotation of target and query genes and of phenotypes can be found in (Anno). scale is the standard deviation measure used for normalization. At first standard deviations were computed between replicates for each experiment and afterwards the median of standard deviations was computed.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: Interactions
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1 images
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QueryAnnotation
(Package: HD2013SGI) :
Annotation of all query genes in the screen
Annotation of all query genes in the screen.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: QueryAnnotation
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0 images
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TargetAnnotation
(Package: HD2013SGI) :
Annotation of all target genes in the screen
Annotation of the target genes on one target plate. It includes an ENSEMBL gene identifier, the HUGO name, the position on the plate (well), and the group of the target siRNA (sample or control).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: TargetAnnotation
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0 images
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datamatrix
(Package: HD2013SGI) :
Phenotypic data after quality control and feature selection
Phenotypic features of pairwise genetic perturbation experiments after selection of non-redundant features and quality control. D is the 6-dimensional array of experimental measurements. Its dimensions are target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. The array has a dimnames attribute, but there exists a more comprehensive annotation of target genes, query genes, and phenotypes in Anno.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: datamatrix
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1 images
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datamatrixfull
(Package: HD2013SGI) :
Phenotypic data before quality control and feature selection
Phenotypic features of pairwise genetic perturbation experiments before selection of non-redundant features and quality control. D is the 6-dimensional array of experimental measurements. Its dimensions are target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. The array has a dimnames attribute.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: datamatrixfull
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1 images
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featuresPerWell
(Package: HD2013SGI) :
Original phenotypic measurements in screen order
Original phenotypic features in screen order. Anno contains the annotation for each experiment including the plate name, row, col, and field. data is a data.frame with a column for each phenotypic feature and rows as much as there are experiments in the screen.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: featuresPerWell
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1 images
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Estimated main effects (single knock-down effects) for target and query genes. Additional overall effects for each phenotype are contained. The dataset contains an annotation of target genes, query genes, and phenotypes.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mainEffects
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1 images
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Number of genetic interactions per target gene.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: nrOfInteractionsPerTarget
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1 images
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stabilitySelection
(Package: HD2013SGI) :
Results from the feature selection method
Results from the feature selection method.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: stabilitySelection
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2 images
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