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The analysis and figure preparation codes for manuscript "Paralog Knockout Profiling Identifies DUSP4/6 as a Digenic Dependence in MAPK-Pathway Driven Cancers".

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Fig 1b Number of Paralog members with expression
Fig 1b Number of Paralog members with expression
 
 
Fig 1d Gene protein class pie chart
Fig 1d Gene protein class pie chart
 
 
Fig 1e Rug plot
Fig 1e Rug plot
 
 
Fig 1f-g HDAC1-HDAC2 expression_VS_dependency
Fig 1f-g HDAC1-HDAC2 expression_VS_dependency
 
 
Fig 2a Manhattan plot
Fig 2a Manhattan plot
 
 
Fig 2b-c CRISPR_VS_PRISM
Fig 2b-c CRISPR_VS_PRISM
 
 
Fig 3a NRAS volcano dependency
Fig 3a NRAS volcano dependency
 
 
Fig 3b DUSP heatmap
Fig 3b DUSP heatmap
 
 
Fig 3f TCGA DUSP4_6 expression
Fig 3f TCGA DUSP4_6 expression
 
 
Fig 3h ERKi resistance screen
Fig 3h ERKi resistance screen
 
 
Fig 4a DUSP CERES vs pMEK RRPA
Fig 4a DUSP CERES vs pMEK RRPA
 
 
Fig 5c-d A375 ranked depedency
Fig 5c-d A375 ranked depedency
 
 
Fig 5e DUSP4 waterfall plot
Fig 5e DUSP4 waterfall plot
 
 
Fig S1a Essentiality with paralog annotation
Fig S1a Essentiality with paralog annotation
 
 
Fig S1b MEK dependecy in NRAS
Fig S1b MEK dependecy in NRAS
 
 
Fig S1d Library distribution
Fig S1d Library distribution
 
 
Fig S1e Recombination Rate
Fig S1e Recombination Rate
 
 
Fig S2a Paralog screen replicate correlation
Fig S2a Paralog screen replicate correlation
 
 
Fig S2b Avana_correlation
Fig S2b Avana_correlation
 
 
Fig S2c Aureus-Pyogenes average pair LFC
Fig S2c Aureus-Pyogenes average pair LFC
 
 
Fig S3a Percent of synergistic hits per cell line
Fig S3a Percent of synergistic hits per cell line
 
 
Fig S3b Pie chart for synergistic hits
Fig S3b Pie chart for synergistic hits
 
 
Fig S3c Stacked bar chart of hits with groups
Fig S3c Stacked bar chart of hits with groups
 
 
Fig S3d Number of cell lines with the synergistic hits
Fig S3d Number of cell lines with the synergistic hits
 
 
Fig S3e CCLE expression versus synergy
Fig S3e CCLE expression versus synergy
 
 
Fig S3f-g PRKC Heatmap
Fig S3f-g PRKC Heatmap
 
 
Fig S4a Heatmap for MAPK pathway
Fig S4a Heatmap for MAPK pathway
 
 
Fig S4b Volcano plots for in-context synergy
Fig S4b Volcano plots for in-context synergy
 
 
Fig S5 DUSP4 AVANA correlations
Fig S5 DUSP4 AVANA correlations
 
 
Fig S6c HT144 ranked depedency
Fig S6c HT144 ranked depedency
 
 
Utility_Functions
Utility_Functions
 
 
.DS_Store
.DS_Store
 
 
.gitignore
.gitignore
 
 
ParalogV1_DUSP46.Rproj
ParalogV1_DUSP46.Rproj
 
 
PkgInfo_2021-08-12.xlsx
PkgInfo_2021-08-12.xlsx
 
 
README.md
README.md
 
 

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ParalogV1_DUSP46

The analysis and figure preparation codes for manuscript "Paralog Knockout Profiling Identifies DUSP4/6 as a Digenic Dependence in MAPK-Pathway Driven Cancers".

Please download all data for analysis at either Dropbox or Figshare.

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The analysis and figure preparation codes for manuscript "Paralog Knockout Profiling Identifies DUSP4/6 as a Digenic Dependence in MAPK-Pathway Driven Cancers".

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