看到一个预印本文章对3种EMT打分算法进行了测评，挺有意思的，标题是：《Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum》，链接在 https://www./content/10.1101/2020.01.02.892604v1.full
参考文献：An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin. Cancer Res.
two-sample Kolmogorov-Smirnov test
This score varies on a scale of −1 to 1, with the higher scores corresponding to more mesenchymal samples (Tan et al., 2014).
参考文献：Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients. EMBO Mol. Med.
multinomial logistic regression
它的值集中于0到2之间， This method particularly focuses on characterizing a hybrid E/M phenotype using the expression levels of 23 genes – 3 predictors and 20 normalizers – identified through NCI-60 gene expression data.
会把样品判断为3种状态：epithelial, mesenchymal, or hybrid E/M categories
参考文献是：2017). Survival outcomes in cancer patients predicted by a partial EMT gene expression scoring metric. Cancer Res. 77, 6415–6428. doi:10.1158/0008-5472.CAN-16-3521.
比如发表于2020年1月的文章；《Gene signatures of tumor inflammation and epithelial-to-mesenchymal transition (EMT) predict responses to immune checkpoint blockade in lung cancer with high accuracy》，链接是：https://www./science/article/pii/S0169500219306932
There is not yet a validated lung cancer EMT signature, so we prospectively generated a gene list based on previous publications describing “classic” EMT genes in cancer [23,24] with the addition of some genes specifically mentioned in studies evaluating EMT in NSCLC [27–29].
Selected genes had levels of expression that were clearly above baseline (using a cutoff of 10 reads in our data set). Supplemental Table 2 shows the list of genes included along with their average expression level.
Although the genes SNAI1, TWIST1, TWIST2, CDH2, and ZEB1 are classic mesenchymal markers, their expression levels were very low in our dataset and thus not included.
Based on these criteria, we generated the EMT signature by adding the sum of the log2 Z scores of 6 established mesenchymal genes (AGER, FN1, MMP2, SNAI2, VIM, ZEB2) and subtracting the sum of the log2 Z scores of 6 established epithelial genes (CDH1, CDH3, CLDN4, EPCAM, MAL2, and ST14) (Supplemental Table 2).
In this signature, the most mesenchymal tumors have the most positive EMT scores and the most epithelial tumors have the most negative scores.
总结起来，其实超级简单，就是选取高表达量的EMT基因，然后6个mesenchymal基因 的log2 Z scores 值的和，减去6个epithelial 基因 的log2 Z scores 值的和，所以这个EMT 打分越高就说明它是mesenchymal 的。
早在2010的PANS文章https:///10.1073/pnas.1004900107 就定义过 EMT Core Signature 基因集合We identified an EMT core signature consisting of 159 genes that were down-regulated and 87 genes that were up-regulated at least 2-fold by all of these EMT-inducing signals (Table S1). 数据在 GSE9691 和 GSE9691
然后是 2012 的 Meta-Analysis of Gene Expression https:///10.1371/journal.pone.0051136 也发布了基因集，包括 EMT-core gene list of 130 up- or downregulated genes shared between at least 10 GES datasets.和 List of 365 genes significantly regulated in at least 10 GES datasets.
也可以在 Pan‐cancer genomic datasets from The Cancer Genome Atlas (TCGA), representing over 10,000 patients and 32 distinct cancer types, provide a rich resource for examining correlative patterns involving EMT mediators in the setting of human cancers.验证：https://onlinelibrary./doi/pdf/10.1002/dvdy.24485
2015 数据库 dbEMT 但是引用率不高， - 被引用次数：28 其整理的 All the 377 human Epithelial-Mesenchymal Transition genes with cancer types 数据是可以下载的：http://dbemt./download.cgi
最后是 2020的这个最新了，The web-based EMTome portal is a resource for primary and metastatic tumour research publicly available at www.emtome.org. 文章链接是：https://www./articles/s41416-020-01178-9
