2020
DOI: 10.3389/fbioe.2020.00220
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Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum

Abstract: The Epithelial-mesenchymal transition (EMT) is a cellular process implicated in embryonic development, wound healing, and pathological conditions such as cancer metastasis and fibrosis. Cancer cells undergoing EMT exhibit enhanced aggressive behavior characterized by drug resistance, tumor-initiation potential, and the ability to evade the immune system. Recent in silico, in vitro, and in vivo evidence indicates that EMT is not an all-or-none process; instead, cells can stably acquire one or more hybrid epithe… Show more

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Cited by 107 publications
(114 citation statements)
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“…We also investigated the correlation of GRHL2 levels with three transcriptomics-based EMT scoring algorithms -MLR, KS, and 76GS. While MLR and KS methods assign higher scores to mesenchymal samples, the 76GS method assigns higher scores to epithelial samples [44]. As expected, GRHL2 levels correlated positively with EMT scores calculated via the 76GS method and negatively with EMT scores calculated by MLR or KS methods across these TCGA datasets ( Fig S1).…”
Section: Resultssupporting
confidence: 70%
“…We also investigated the correlation of GRHL2 levels with three transcriptomics-based EMT scoring algorithms -MLR, KS, and 76GS. While MLR and KS methods assign higher scores to mesenchymal samples, the 76GS method assigns higher scores to epithelial samples [44]. As expected, GRHL2 levels correlated positively with EMT scores calculated via the 76GS method and negatively with EMT scores calculated by MLR or KS methods across these TCGA datasets ( Fig S1).…”
Section: Resultssupporting
confidence: 70%
“…MLR and KS score the samples on a spectrum of [0, 2] and [-1,1]; the higher the score, the more mesenchymal the sample is. On the other hand, there is no pre-defined range of scores calculated by 76GS, and the higher the 76GS score, the more epithelial the sample is [Chakraborty et al, 2020].…”
Section: Snail Is a Stronger Inducer Of Complete Emt Than Slugmentioning
confidence: 99%
“…The epithelial-mesenchymal transition (EMT) scores for each dataset was calculated using 76GS, KS and MLR methods as described earlier [Chakraborty et al, 2020] 76GS: A weighted sum of 76 gene expression levels was used to calculate the score for each sample. The mean across all tumor samples was subtracted to center the scores so that the grand mean of the score was zero.…”
Section: Emt Score Calculationmentioning
confidence: 99%
“…It has been proposed that IBC cells exhibit a partial EMT behavior, given the retention of Ecadherin levels and the trait of collective cell migration through tumor emboli [16]. Thus, following the assessment of IBC gene signatures, we quantified the EMT-ness of IBC and nIBC samples based on three different EMT scoring metrics -KS, 76GS and MLR [17]. respectively, the 76GS metric has no pre-defined scale.…”
Section: Correlation Between Ibc Gene Signature Ssgsea Scores and Emtmentioning
confidence: 99%
“…EMT scoring: Three different EMT scoring methods -KS, MLR, 76GS were used to score samples separately in the three datasets [17].…”
Section: Principle Component Analysis (Pca)mentioning
confidence: 99%