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select_genes.Rmd
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select_genes.Rmd
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---
title: "Get Related Genes"
author: "João Cavalcante"
date: "`r Sys.setlocale('LC_TIME', 'C'); format(Sys.time(), '%d %B, %Y')`"
knit: (function(inputFile, encoding) {
rmarkdown::render(inputFile, encoding = encoding, output_dir = "../reports/") })
output:
html_document:
toc: true
toc_float: true
toc_collapsed: false
theme:
bslib: true
bootswatch: minty
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE
)
```
# Extract Autophagy and Mitophagy related genes
```{r load-libraries}
library(readr)
library(dplyr)
library(purrr)
library(biomaRt)
library(magrittr)
library(KEGGREST)
get_go_genes <- function(go_term) {
ensembl <- useEnsembl(biomart = "ensembl", dataset = 'hsapiens_gene_ensembl')
getBM(
attributes = c(
'external_gene_name',
'go_id',
'name_1006'
),
filters = 'go',
values = go_term,
mart = ensembl
)
}
```
## Get GO genes
GO terms:
* autophagy - [GO:0006914](https://amigo.geneontology.org/amigo/term/GO:0006914)
* autophagy of mitocondrion - [GO:0000422](https://amigo.geneontology.org/amigo/term/GO:0000422)
* regulation of autophagy - [GO:0010506](https://amigo.geneontology.org/amigo/term/GO:0010506)
* negative regulation of autophagy - [GO:0010507](https://amigo.geneontology.org/amigo/term/GO:0010507)
* positive regulation of autophagy - [GO:0000422](https://amigo.geneontology.org/amigo/term/GO:0000422)
* mitochondrion organization - [GO:0007005](https://amigo.geneontology.org/amigo/term/GO:0007005)
* mitochondrial fusion - [GO:0008053](https://amigo.geneontology.org/amigo/term/GO:0008053)
* mitochondrial fission - [GO:0000266](https://amigo.geneontology.org/amigo/term/GO:0000266)
* mitochondrion morphogenesis - [GO:0070584](https://amigo.geneontology.org/amigo/term/GO:0070584)
* mitochondrial inner membrane - [GO:0005743](https://amigo.geneontology.org/amigo/term/GO:0005743)
* mitochondrial outer membrane - [GO:0005741](https://amigo.geneontology.org/amigo/term/GO:0005741)
* outer mitochondrial membrane organization - [GO:0007008](https://amigo.geneontology.org/amigo/term/GO:0007008)
- Since human genes were only available for child term "protein insertion into mitochondrial outer membrane" ([GO:0045040](https://amigo.geneontology.org/amigo/term/GO:0045040)), we selected from that term instead.
* inner mitochondrial membrane organization - [GO:0007007](https://amigo.geneontology.org/amigo/term/GO:0007007)
* mitochondrial outer membrane fusion - [GO:1990626](https://amigo.geneontology.org/amigo/term/GO:1990626)
* mitochondrial inner membrane fusion - [GO:1990627](https://amigo.geneontology.org/amigo/term/GO:1990627)
```{r get-go}
go_terms <- c(
autophagy = "GO:0006914",
autophagy_of_mitocondrion = "GO:0000422",
regulation_of_autophagy = "GO:0010506",
negative_regulation_of_autophagy = "GO:0010507",
positive_regulation_of_autophagy = "GO:0000422",
mitochondrion_organization = "GO:0007005",
mitochondrial_fusion = "GO:0008053",
mitochondrial_fission = "GO:0000266",
mitochondrion_morphogenesis = "GO:0070584",
mitochondrial_inner_membrane = "GO:0005743",
mitochondrial_outer_membrane = "GO:0005741",
protein_insertion_into_mitochondrial_outer_membrane = "GO:0045040",
inner_mitochondrial_membrane_organization = "GO:0007007",
mitochondrial_outer_membrane_fusion = "GO:1990626",
mitochondrial_inner_membrane_fusion = "GO:1990627"
)
go_selected <- discard(map(go_terms, get_go_genes), ~nrow(.) == 0)
go_renamed <- go_selected %>%
bind_rows() %>%
filter(go_id %in% go_terms) %>%
filter(external_gene_name != "") %>%
mutate(database = "GO") %>%
rename(gene_symbol = external_gene_name,
annotation_id = go_id,
annotation_name = name_1006)
```
## Get KEGG genes
KEGG Pathways / BRITE:
* Mitochondrial Biogenesis - [br:hsa03029](https://www.kegg.jp/brite/hsa03029)
* Autophagy - [path:hsa04140](https://www.kegg.jp/pathway/hsa04140)
* Mitophagy - [path:hsa04137](https://www.kegg.jp/pathway/hsa04137)
We start by downloading gene to pathway mappings from the KEGG API.
```{r download, cache=TRUE}
download.file(
"https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz",
here::here("data/Homo_sapiens.gene_info.gz")
)
download.file(
"http://rest.kegg.jp/link/pathway/hsa",
here::here("data/link_pathway_entrez_hsa.tsv")
)
download.file(
"http://rest.kegg.jp/link/brite/hsa",
here::here("data/link_brite_entrez_hsa.tsv")
)
```
Then, we get the intersection between the datasets.
```{r load}
pathways <- tibble::tribble(
~pathway_id, ~pathway_name,
"br:hsa03029", "Mitochondrial Biogenesis",
"path:hsa04140", "Autophagy",
"path:hsa04137", "Mitophagy"
)
link_pathway_entrez_hsa <- read_tsv(
here::here("data/link_pathway_entrez_hsa.tsv"),
col_names = c("entrez_id", "pathway_id"),
col_types = "cc"
) %>% tidyr::separate(
entrez_id,
into = c("species", "entrez_id"),
sep = ":"
)
link_brite_entrez_hsa <- read_tsv(
here::here("data/link_brite_entrez_hsa.tsv"),
col_names = c("entrez_id", "pathway_id"),
col_types = "cc"
) %>% tidyr::separate(
entrez_id,
into = c("species", "entrez_id"),
sep = ":"
)
# Filtering for pathways/brite of interest
gene_pathways_hsa <- inner_join(link_pathway_entrez_hsa, pathways)
gene_brite_hsa <- inner_join(link_brite_entrez_hsa, pathways)
genes_kegg <- rbind(gene_pathways_hsa, gene_brite_hsa)
```
Finally, we extract the gene symbols.
```{r gene-symbols}
entrez_names_hsa <- read_tsv(
here::here("data/Homo_sapiens.gene_info.gz"),
skip = 1,
col_names = c("entrez_id", "gene_symbol"),
col_types = cols_only("-", "c", "c")
)
genes_kegg_hsa <- genes_kegg %>%
inner_join(pathways) %>%
inner_join(entrez_names_hsa) %>%
dplyr::select(-c(species, entrez_id)) %>%
rename(annotation_id = pathway_id,
annotation_name = pathway_name) %>%
mutate(database = "KEGG")
```
## Merging and writing final dataset
```{r write}
merged <- bind_rows(go_renamed, genes_kegg_hsa)
merged_collapsed <- merged %>%
group_by(gene_symbol) %>%
summarise(
annotation_ids = paste0(unique(annotation_id), collapse="|"),
annotation_names = paste0(unique(annotation_name), collapse="|"),
databases = paste0(unique(database), collapse="|"),
n_annotation = length(unique(annotation_id))
)
write_csv(merged, here::here("results/selected_genes.csv"))
write_csv(merged_collapsed, here::here("results/selected_genes_collapsed.csv"))
```