GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
Fig 2
Example use case of GeneCOCOA to predict context-specific FLT3 function using expression data from hematopoietic stem cells and acute myeloid leukemia blasts. (A) In an exemplary use case, GeneCOCOA was applied to study the co-expression patterns of FLT3 with Gene Ontology Biological Process (GO:BP) terms in bulk RNA-sequencing of CD34+ hematopoietic stem cells (HSCs) from 48 healthy subjects, and blasts from 31 patients with acute myeloid leukemia (AML) positive for FLT3-ITD mutations. Illustrations of the pelvis and cells were adapted from vector files hosted at bioicons.com under a CC BY 4.0 license. (B) The 10 highest ranked GO:BP terms with FLT3 in HSCs from healthy donors, as computed by GeneCOCOA. The corresponding significance values in AML blasts are provided for comparison. Ranks are annotated next to the bars; non-significant terms are not annotated. (C) The 10 highest-ranked GO:BP terms with FLT3 in patients with AML and FLT3-ITD mutations, as computed by GeneCOCOA. The corresponding significance values in healthy HSCs are provided for comparison. Ranks are annotated next to the bars; non-significant terms are not annotated.