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Reporter assay results compared with eVIP Pathways and GSEA.

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posted on 2021-07-02, 17:35 authored by Alexis M. Thornton, Lishan Fang, April Lo, Maria McSharry, David Haan, Casey O’Brien, Alice H. Berger, Marios Giannakis, Angela N. Brooks

Pathway reporter assay results are more consistent with eVIP Pathway prediction than with GSEA. Results from a pathway reporter array using different sample group comparisons (first 3 columns). Pathways were considered significant with p-value under .05, then the direction of difference is reported as inhibited or activated. The last two columns are eVIP Pathway and GSEA Investigate Gene Sets results (GOF = Gain of Function, COF = Change of function). GSEA Investigate Gene Sets was run on RNF43 G659fs mutation-specific genes. Only significant pathways (FDR q-value < .05) that contain at least 10 genes in the overlap are shown.

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    PLOS Computational Biology

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    RASRNF 43 R 117fs RNF 43 G 659fsKRASeVIP 2 softwareAdditional eVIP Pathways analysisexpression-based variant impact phe...Western blot analysischange-of-function mutationG 659fs variantsRNF 43 WTGOFeVIP 2 methodGFP control cDNAgene variantsRNF 43 WT functiongene variant functiondecision tree-based algorithmeVIP 2RNF 43 G 659fsHEK 293T cellsuse gene expression datapathwaycolon adenocarcinoma patient samplesTNFBRAF missense mutationsgene expression signatures

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