Skip to main content

Table 4 Benchmarking queries

From: Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™

Capabilities

Search

criteria

Query #

Search result

# of cells returned

(# of projects with data)

Total time (sec)

Selecting a subset of cells (searching across 2.2 M cells and 32 projects)

By tags

1 tagCellType.select is any of:

[‘Enterocyte’, ‘Enterocytes’,

‘Best4+ Enterocytes’, ‘Enterocyte Progenitors’, ‘Immature Enterocytes 1’, ‘Immature Enterocytes 2’]

1

19 K cells

(5 projects)

14

 

2 tags

Above criteria on CellType.select

& Location is any of:

[‘Rectum’, ‘Decidua’, ‘Ileum’]

2

4827 cells

(2 projects)

9

Selecting cells across projects

Checking for co expression in more than 1 gene, when expression value lies in a range

• Threshold: value > = 1

• Restricting search to normalized data

‘ACE2’, ‘TMPRSS2’

3

2282 cells

(21 projects)

26

‘ACE2’, ‘TMPRSS2’, ‘DPP4’

4

561 cells

(11 projects)

32

Search expression

By gene list across all projects

‘ACE2’, ‘TMPRSS2’, ‘DPP4’

5

225 K rows

(32 projects;

download size:

8 MB)

15

By cells across multiple projects

Using the result of Query 1 to search expression on those cells

i.e. searching by ~ 19,000 cells

(in the projects with data)

6

26.7 M rows

(5 projects;

download size: 1019 MB)

27

By selected project

Project: ‘wang20_rectum’;

matrix_count: ‘normalized’

7

11.6 M rows

(1 project;

download size:

621 MB)

17

  1. Legend: Queries were organized as: searching by metadata tags (1 & 2), searching by co-expression (3, 4), searching by gene list (5), searching the results of query 1 by expression levels (6), and returning the results of a project