library(magrittr)
library(tidyverse)
library(readxl)
library(stringr)
library(DT)
library(knitr)

Considered studies

studies <- read_excel("_data/ERKreviewTABLES.xlsx", sheet = 1, skip = 2) %>% 
  mutate(Reference = paste0("<a href='", URL, "'>", Reference, "</a>")) %>% 
  select(-`Paper Title`, -URL)
kable(studies)
StudyID Reference Method Enrichment Cell type Organism class Stimulant Stimulant time Inhibitor type Inhibitor Inhibitor time
1 Pan et al 2009 SILAC TiO2 HeLa, K562 human indirect EGF 15 min Mek, p38a/b U0126, SB202190 20 min
2 Old et al 2009 Label-free - WM115 human indirect DMSO - Mek U0126 4 hour
3 Kosako et al, 2009 FG-Ab antibody enrichment HeLa human indirect TPA - - U0126 -
4 Lewis et al, 2000 2D-GEL, MS/MS for peptide identification - K562 human indirect PMA 0, 20, 60, 120, 240 min and 24 hours Mek U0126 240 min
5 Xue et al, 2014 siKALIP (SILAC, directed-kinase) polyMAC HEK293 human direct and indirect direct-kinase assay 60 min - - -
6 Parker et al, 2014 Label-free TiO2 SW1736 human indirect - - Mek, Braf AZD6244, PLX4032 15 min and 30 min
7 Parker et al, 2015 Label-free TiO2 LM-MEL-28, LM-MEL-28R1 human indirect - - Braf PLX4032 1 month
8 Stuart et al, 2015 SILAC TiO2-ERLIC WM239A human indirect DMSO - Mek, Braf AZD6244, PLX4032 2 hours
9 Gnad et al, 2016 Label-free antibody enrichment HCT116 human indirect - - ERK, Mek G-824, cobimetinib 24 hours
10 Kubiniok et al, 2017 SILAC TiO2 HCT116, Colo205 human direct and indirect DMSO - Braf PLX4032 1 hour (every 5 minutes)
11 Carlson et al, 2011 SILAC IMAC NIH 3T3-L1 mouse direct and indirect EGF 20 min Mek U0126 10 min
12 Courcelles et al, 2013 Label-free TiO2 IEC-6 rat direct and indirect fetal bovine serum 0, 5, 15, 60 min Mek PD184352 0, 5, 15, 60 min
13 Seger et al 1995 Various Data Various Data Various Data human direct Various Data Various Data Various Data Various Data Various Data
14 PhosphoSitePlus Database (ERK1/2-substrate list) Various Data Various Data Various Data Various Data direct and indirect Various Data Various Data Various Data Various Data Various Data

ERK targets

read_excel("_data/ERKreviewTABLES.xlsx", sheet = 2, skip = 2, na = "") %>%
  replace_na(list(
    `in vitro` = "in vivo",
    `ERK Ph-motif` = "no",
    `ERK extended Ph-motif` = "no",
    `DEF-motif on all protein` = "no",
    `D-motif on all protein` = "no")
  ) %>% 
  mutate(`in vitro` = ifelse(str_detect(`in vitro`, "invitro"), 
                             "direct",
                             "indirect"),
         `Uniprot ID` = paste0('<a href ="http://www.uniprot.org/uniprot/',
                               `Uniprot ID`, '">', `Uniprot ID`, '</a>'),
         `Gene Name` = paste0('<a href ="http://www.genecards.org/cgi-bin/carddisp.pl?gene=',
                              `Gene Name`, '">', `Gene Name`, '</a>')) %>% 
  mutate(
    `Amino Acid` = as.factor(`Amino Acid`),
    `in vitro` = as.factor(`in vitro`),
    `organism` = as.factor(`organism`),
    `ERK Ph-motif` = as.factor(`ERK Ph-motif`),
    `ERK extended Ph-motif` = as.factor(`ERK extended Ph-motif`),
    `DEF-motif on all protein` = as.factor(`DEF-motif on all protein`),
    `D-motif on all protein` = as.factor(`D-motif on all protein`)
  ) %>% 
  dplyr::rename(class = `in vitro`) %>% 
  select(-`Modified Peptide`, -`Sequence`) %>% 
  datatable(filter = "top", extensions = 'Buttons', escape = F,
            options = list(
              dom = 'Bfrtip',
              scrollX = T,
              pageLength = 25,
              searchHighlight = T,
              buttons = c('copy', 'csv')
            ))