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Comparing Pathway Analysis Tools

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Two different tools were used to analyze candidate genes from the methylation array to obtain associated cellular pathways for comparison. The first one is the Ingenuity Pathway Analysis (IPA) system, which automatically generates networks of gene, protein, small-molecule, and disease associations on the basis of data held in a proprietary database. Data were uploaded as an Excel file into the Ingenuity software (Ingenuity Systems, Redwood City, CA, USA) [39 (link)]. The second one is the Database for Annotation, Visualization and Integrated Discovery (DAVID) web tool, which is a high-throughput and integrated data-mining environment for analyzing the gene lists acquired from high-throughput genomic experiments [40 (link)]. Data were uploaded as a text file into the DAVID web tool. The pathway map was obtained by KEGG [41 (link)].

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Husni R.E., Shiba-Ishii A., Nakagawa T., Dai T., Kim Y., Hong J., Sakashita S., Sakamoto N., Sato Y, & Noguchi M. (2019). DNA hypomethylation-related overexpression of SFN, GORASP2 and ZYG11A is a novel prognostic biomarker for early stage lung adenocarcinoma. Oncotarget, 10(17), 1625-1636.

Publication 2019

Ingenuity software

Cellular Gene Gene networks Genomic Held Methylation Protein Redwood

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Variable analysis

independent variables

Ingenuity Pathway Analysis (IPA) system
Database for Annotation, Visualization and Integrated Discovery (DAVID) web tool

dependent variables

Associated cellular pathways for comparison

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned

Annotations

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