Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform
Fig 2
Case studies demonstrating knowledge-guided analysis.
(A) Each of the KnowEnG analysis pipelines is shown as a box with corresponding colored arrows connecting to their general inputs and outputs. Because the outputs of a pipeline are often valid inputs for another pipeline, a convenient “handover” mechanism in the KnowEnG web portal enables chaining together multiple pipelines, facilitating deeper and multifaceted analysis of the user’s data. (B) The analysis workflow for Case Study 1 with unused pipelines shaded gray. Simple descriptions of the case study–specific inputs and outputs are provided, along with notes on where to find the detailed methods or figures of the results. The pipeline step of the workflow that incorporates knowledge-guided analysis is indicated with the blue network icon. (C) Analysis workflow for Case Study 2. (D) Analysis workflow for Case Study 3. ESCC, esophageal squamous cell carcinoma; GO, Gene Ontology; KnowEnG, Knowledge Engine for Genomics; LUSC, lung squamous cell carcinoma; TCGA, the Cancer Genome Atlas.