data-raw/stk_annotation.R

In AliSajid/KINNET: Kinase INteraction NETwork Generation

## code to prepare `stk_annotation` dataset goes here

library(tidyverse)
library(devtools)

# Loading Annotation ------------------------------------------------------

annotation <-
  read_csv(
    "data-raw/data/RegPhos_Annotation_human.csv",
    col_types = cols(.default = col_character())
  ) |>
  mutate(
    Kinase = str_to_upper(Kinase),
    Group = str_to_upper(Group),
    Family = str_to_upper(Family),
    Subfamily = str_to_upper(Subfamily),
    Gene_Symbol = str_to_upper(Gene_Symbol)
  )

non_human <- c("CK2A1-RS", "SGK424", "STLK6-RS")

annotation_clean <- annotation |>
  select(Kinase, Group, Family, Subfamily, Gene_Symbol) |>
  filter(!Kinase %in% non_human) |>
  mutate(Gene_Symbol = if_else(is.na(Gene_Symbol), Kinase, Gene_Symbol))


# Processing UKA Mapping --------------------------------------------------

uka_map <-
  read_csv("data-raw/data/uka_pep2kinase_STK.csv",
           col_types = cols(.default = col_character())) |>
  select(ID, Kinase_UniprotName) |>
  rename(Kinase = Kinase_UniprotName) |>
  filter(!is.na(Kinase)) |>
  unique()

uka_matched_by_kinase <- uka_map |>
  left_join(annotation_clean, by = "Kinase") |>
  filter(!is.na(Family), !is.na(Group))

uka_matched_by_family <- uka_map |>
  rename(Family = Kinase) |>
  left_join(annotation_clean, by = "Family") |>
  filter(!is.na(Kinase), !is.na(Group))

uka_matched_by_subfamily <- uka_map |>
  rename(Subfamily = Kinase) |>
  left_join(annotation_clean, by = "Subfamily") |>
  filter(!is.na(Kinase), !is.na(Group), !is.na(Family))

uka_matched_by_gene <- uka_map |>
  rename(Gene_Symbol = Kinase) |>
  left_join(annotation_clean, by = "Gene_Symbol") |>
  filter(!is.na(Kinase), !is.na(Group), !is.na(Family))




# Processing KRSA Mapping -------------------------------------------------

krsa_map <-
  read_csv(
    "data-raw/data/KRSA_Mapping_STK_Separated.csv",
    col_types = cols(.default = col_character())
  )

krsa_matched_by_family <- krsa_map |>
  left_join(annotation_clean, by = "Family") |>
  filter(!is.na(Kinase), !is.na(Group))

krsa_matched_by_kinase <- krsa_map |>
  rename(Kinase = Family) |>
  left_join(annotation_clean, by = "Kinase") |>
  filter(!is.na(Family), !is.na(Group))

krsa_matched_by_subfamily <- krsa_map |>
  rename(Subfamily = Family) |>
  left_join(annotation_clean, by = "Subfamily") |>
  filter(!is.na(Kinase), !is.na(Group), !is.na(Family))

krsa_matched_by_gene <- krsa_map |>
  rename(Gene_Symbol = Family) |>
  left_join(annotation_clean, by = "Gene_Symbol") |>
  filter(!is.na(Kinase), !is.na(Group), !is.na(Family))


# Processing Special Cases -----------------------------------------------


# ERK, PAKA, MTOR, PAKB are special cases from KRSA

krsa_mtor <- annotation |>
  filter(str_detect(UniProt_ID, "MTOR")) |>
  select(Kinase, Group, Family, Subfamily, Gene_Symbol) |>
  mutate(Match = "MTOR") |>
  left_join(krsa_map, by = c(Match = "Family")) |>
  select(-Match)

krsa_paka <- annotation |>
  filter(str_detect(Subfamily, "PAKA")) |>
  select(Kinase, Group, Family, Subfamily, Gene_Symbol) |>
  mutate(Match = "PAKA") |>
  left_join(krsa_map, by = c(Match = "Family")) |>
  select(-Match)

krsa_pakb <- annotation |>
  filter(str_detect(Subfamily, "PAKB")) |>
  select(Kinase, Group, Family, Subfamily, Gene_Symbol) |>
  mutate(Match = "PAKB") |>
  left_join(krsa_map, by = c(Match = "Family")) |>
  select(-Match)

krsa_erks <- map_dfr(c(1:5, 7),
                     function(x) {
                       annotation |>
                         filter(Kinase == str_c("ERK", 1, sep = "")) |>
                         select(Kinase, Group, Family, Subfamily, Gene_Symbol) |>
                         mutate(Match = "ERK") |>
                         left_join(krsa_map, by = c(Match = "Family")) |>
                         select(-Match)
                     })


# Putting it all together -------------------------------------------------

stk_annotation <- bind_rows(
  krsa_matched_by_family,
  krsa_matched_by_kinase,
  krsa_matched_by_subfamily,
  krsa_matched_by_gene,
  krsa_erks,
  krsa_mtor,
  krsa_paka,
  krsa_pakb,
  uka_matched_by_family,
  uka_matched_by_gene,
  uka_matched_by_kinase,
  uka_matched_by_subfamily
) |>
  select(ID, Group, Family, Subfamily, Kinase, Gene_Symbol) |>
  unique() |>
  write_csv("data-raw/data/STK_Annotation.csv")