Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge

Abstract

Prioritization or ranking of different cell types in a scRNA-Seq framework can be performed in a variety of ways, some of these include: i) obtaining an indication of the proportion of cell types between the different conditions under study, ii) counting the number of differentially expressed genes (DEGs) between cell types and conditions in the experiment or, iii) prioritizing cell types based on prior knowledge about the conditions under study (i.e., a specific disease). These methods have drawbacks and limitations thus novel methods for improving cell ranking are required. Here we present a novel methodology that exploits prior knowledge in combination with expert-user information to accentuate cell types from a scRNA-seq analysis that yield the most biologically meaningful results. Prior knowledge is incorporated in a standardized, structured manner, whereby a checklist is attained by querying MalaCards human disease database with a disease of interest. The checklist is comprised of pathways and drugs and, optionally, drug mode of actions (MOAs), associated with the disease. The user is prompted to "edit" this checklist by removing or adding terms (in the form of keywords) from the list of predefined terms. Our methodology has substantial advantages to more traditional cell ranking techniques and provides an informative complementary methodology that utilizes prior knowledge in a rapid and automated manner, that has previously not been attempted by other studies. The current methodology is also implemented as an R package entitled Single Cell Ranking Analysis Toolkit (scRANK) and is available for download and installation via GitHub (https://#hub.com/aoulas/scRANK) Author SummarySingle-cell RNA Sequencing (scRNA-Seq) provides an additive resolution down to the cellular level that was previously not available from traditional "Bulk" RNA sequencing experiments. However, it is often difficult to prioritize the specific cell-types which are primarily responsible for the cause of a disease. This work presents a novel methodology that exploits prior knowledge for a disease in combination with expert-user information to accentuate cell types from a scRNA-seq analysis that are most closely related to the molecular mechanism of a disease of interest. Prior knowledge is incorporated in a standardized, structured manner, whereby a checklist is attained by querying a human disease database called MalaCards. This checklist comes in the form of pathways and drugs and, optionally, drug mode of actions (MOAs), associated with the disease. The expert-user is prompted to "edit" the prior knowledge checklist by removing or adding terms from the list of predefined terms. This methodology has substantial advantages to more traditional cell prioritizing or ranking techniques and provides an informative complementary methodology that utilizes prior knowledge in a rapid and automated manner.