Table 2 DNA motif rules extracted from the RF classified trained on the MAX dataset
From: Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest
Rule | Prediction | Reference |
|---|---|---|
IRF > =1 | GM12878 (lymphoblastoid cells) | |
JDP2 > =1 | HeLa-S3 (cervical carcinoma cells) | [54] |
AP1 > =9 & HESX1 > =2 & LMO2 > =2 | ||
EMX1 < =11 & ETS < =12 & HNF4 > =1 | HepG2 (liver cancer cells) | |
HNF4 > =1 & IRF4 < =4 & RUNX2 < =4 & TAL1 < =4 | HNF4 [50] | |
ALX3 < =26 & EVX1 > =6 & GATA > =2 & LMO2 > =2 | K562 (immortalised myelogenous leukaemia cells) | |
GATA > = 4 & HNF4 = 0 & POU4F3 < =4 | ||
No rule identified | A549 (adenocarcinomic alveolar basal epithelial cells) | Â |