Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study

Table 2 Gene sets mapping from CP collections.

	# proteins/genes detected	exist in CP¹	# mapped gene sets	# genes in mapped gene sets
Run 1	1,170	864	225	4,231
Run 2	972	728	227	4,019
Run 3	909	677	221	4,137
*Common pathways* *for 3 runs*	682	536	192	3,828
Intersection	682	536	190	3,561
Twice	996	753	229	4,119
Union	1,373	980	244	4,273

"Gene sets" represent genes defined in CPs. The number of genes represents the sum of different genes across mapped CP.
¹ Not all proteins detected in 50-cell sample are present in the gene sets within the CP collection. The number of proteins found in the CP collections is shown here.

ISSN: 1471-2164