Computational protocol: Pulmonary adenocarcinoma with mucin production modulates phenotype according to common genetic traits: a reappraisal of mucinous adenocarcinoma and colloid adenocarcinoma

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Protocol publication

[…] Statistical analyses were performed using JMP IN software (SAS Institute, Inc., Cary, NC) and VassarStats for Statistical Computation at website. Qualitative or quantitative data were compared by Fisher exact t test, chi‐squared test, Mann–Whitney test and Kruskal–Wallis test as appropriate. Unsupervised and supervised hierarchical clustering analyses were performed using Cluster 3.0 software ( /) and visualized using Java TreeView ( The defining features of the diverse clusters corresponded to the different IHC percentages used for the relevant markers. Similarity was measured using Spearman rank correlation metric and clustering was performed by centroid linkage. Contingency analysis and relative mosaic plots were performed by means of JMP IN software and calculating P values through the likelihood ratio test. Mosaic plots indicated graphically the fraction (expressed from 0.0 to 1.0) of patients belonging to the different clusters after stratifying for the different tumour subtypes. For all tests, two‐sided P values were taken into account, with a threshold < 0.05 as being statistically significant. […]

Pipeline specifications

Software tools VassarStats, TreeView, JTreeView
Applications Miscellaneous, Phylogenetics
Organisms Hemisus marmoratus
Diseases Adenocarcinoma, Breast Neoplasms, Adenocarcinoma, Mucinous, Neoplasms, Retinoblastoma, Tuberculosis, Meningeal
Chemicals Progesterone, Steroids