Table 1.

Description of CellFie results included in batch-download

Results file	Description
score.csv	Matrix of task scores. Rows correspond to individual tasks and columns correspond to samples.
scoreBinary.csv	Matrix of binary task score activity (1 = active, 0 = inactive). Rows correspond to individual tasks and columns correspond to samples.
taskInfo.csv	Table linking tasks to their respective metabolic pathways systems and subsystems. This is used to map rows of the score matrices to their respective tasks.
detailScoring.csv	Detailed description of genes and reactions used to calculate task scores for every sample: •Column 1: ID of the sample •Column 2: ID of the metabolic task •Column 3: Task score for this sample •Column 4: Binary task score for this sample •Column 5: Essential reaction associated with this task •Column 6: Expression score associated with the reaction listed in column 5 (i.e., RAL -Reaction Activity Level) •Column 7: Gene used to determine the expression of the reaction in column 5 •Column 8: Original expression value of the gene listed in column 7 Information is concatenated horizontally therefore columns 9–16 will contain information for sample 2, columns 17–24 will contain information for sample 3, etc.