README.md

In lubianat/zelda: Zelda finds Links

zelda

A package to find links between two lists of genes. One of them has receptors, the other has ligands. This package makes the match.

Citation

Zelda uses datasets from two different publications. If you use it in your analysis, please cite the original publications.

For the "ramilowski_links" dataset please cite "Ramilowski, Jordan A., et al. "A draft network of ligand–receptor-mediated multicellular signalling in human." Nature communications 6 (2015): 7866."

For the "cellphone_db_links" dataset please cite "Efremova, Mirjana, et al. "CellPhoneDB v2. 0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes." bioRxiv (2019): 680926."

Dataset preparation

library(biomaRt)
library(readxl)
library(data.table)

###### Prepare table from Ramilowski et al, 2015 #####
file_url <- 'https://media.nature.com/original/nature-assets/ncomms/2015/150722/ncomms8866/extref/ncomms8866-s3.xlsx'
download.file(file_url,
              destfile = './data/bridges_from_ncomms15107.xlsx', method = 'wget')
ramilowski_links <- read_excel('./data/bridges_from_ncomms15107.xlsx', sheet = 2)
save('ramilowski_links', file = './data/ramilowski_links.RData')

####### Prepare table from CellPhoneDB ####

file_url <- "https://www.cellphonedb.org/downloads/interactions_cellphonedb.csv"
download.file(file_url,
              destfile = './data/bridges_from_cellphone_db', method = 'wget')
cellphone_db_links <- data.frame(fread('./data/bridges_from_cellphone_db'))
cellphone_db_links[] <- lapply(cellphone_db_links, function(x) gsub("simple:", "", x))
cellphone_db_links <- cellphone_db_links[grep('complex',cellphone_db_links$partner_a, invert = T), ]


listMarts()
ensembl=useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
attributes = listAttributes(ensembl)
uniprot_to_gene_symbol<- getBM(attributes = c('uniprot_gn','uniprotswissprot','hgnc_symbol'),   mart = ensembl)

cellphone_db_links$entry_name_a[!(cellphone_db_links$partner_a %in% uniprot_to_gene_symbol$uniprotswissprot)]
cellphone_db_links$ligands <- uniprot_to_gene_symbol$hgnc_symbol[match(cellphone_db_links$partner_a, uniprot_to_gene_symbol$uniprotswissprot)]
cellphone_db_links$receptors <- uniprot_to_gene_symbol$hgnc_symbol[match(cellphone_db_links$partner_b, uniprot_to_gene_symbol$uniprotswissprot)]

save('cellphone_db_links', file = './data/cellphone_db_links.RData')

List of works that use receptor-ligand databases

Applying databases

Database of Ligand-Receptor Partners (DLRP), IUPHAR and Human Plasma Membrane Receptome (HPMR) are included via Ramilowski db., but only until 2015.

• In https://www.sciencedirect.com/science/article/pii/S221112471831636X?via%3Dihub#bib33, they use the Ramilowski db with addition of known B7 family member interactions from Southan et al., 2016.

• In https://www.ncbi.nlm.nih.gov/pubmed/25704820 they claim to have established a database of 1433 interactions, but I was not able to find it anywhere.

• In https://www.nature.com/articles/nature22796 they use the database by Ramilowski et al.

• In https://www.sciencedirect.com/science/article/pii/S2211124718315043?via%3Dihub they use the database by Ramilowski et al.

• In https://www.nature.com/articles/s41592-018-0009-z#Sec8 they do not use receptor-ligand information to infer cell-cell interaction (but by its title, it could have been the case)

Describing databases

• https://doi.org/10.1093/nar/gkv1037 (Southan et al, Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016)

• https://www.nature.com/articles/ncomms8866

• https://www.biorxiv.org/content/10.1101/680926v1

• In https://www.biorxiv.org/content/biorxiv/early/2019/01/04/507871.full.pdf they build on previous databases to build a curated, R-available list of ligand-receptor interactions.

lubianat/zelda documentation built on Dec. 5, 2019, 3:26 a.m.