Contents

1 Introduction

1.1 About Cell-Cell Interaction (CCI)

Due to the rapid development of single-cell RNA-Seq (scRNA-Seq) technologies, wide variety of cell types such as multiple organs of a healthy person, stem cell niche and cancer stem cell have been found. Such complex systems are composed of communication between cells (cell-cell interaction or CCI).

Many CCI studies are based on the ligand-receptor (L-R)-pair list of FANTOM5 project1 Jordan A. Ramilowski, A draft network of ligand-receptor-mediated multicellular signaling in human, Nature Communications, 2015 as the evidence of CCI (http://fantom.gsc.riken.jp/5/suppl/Ramilowski_et_al_2015/data/PairsLigRec.txt). The project proposed the L-R-candidate genes by following two reasons.

  1. Subcellular Localization
    1. Known Annotation (UniProtKB and HPRD) : The term “Secreted” for candidate ligand genes and “Plasma Membrane” for candidate receptor genes
    2. Computational Prediction (LocTree3 and PolyPhobius)
  2. Physical Binding of Proteins : Experimentally validated PPI (protein-protein interaction) information of HPRD and STRING

The project also merged the data with previous L-R database such as IUPHAR/DLRP/HPMR and filter out the list without PMIDs.

Besides, the recent L-R databases such as CellPhoneDB and SingleCellSignalR manually curated L-R pairs, which are not listed in IUPHAR/DLRP/HPMR.

In Bader Laboratory, many putative L-R databases are predicted by their standards.

In our framework, we expanded such L-R databases for 134 organisms based on the ortholog relationships. We implemented such a framework as multiple R/Bioconductor annotation packages for sustainable maintenance (LRBaseDbi and LRBase.XXX.eg.db-type packages (Figure 1). XXX is the abbreviation of the scientific name of organisms such as LRBase.Hsa.eg.db for L-R database of Homo sapiens. Besides, we also developed scTensor, which is a method to detect CCI and the CCI-related L-R pairs simultaneously. This document provides the way to use LRBaseDbi, LRBase.XXX.eg.db-type packages, and scTensor package.