Proteomic Profiling of Ex Vivo Expanded CD34-Positive Haematopoetic Cells Derived from Umbilical Cord Blood

Table 2

Examples of enriched biological processes in significant regulated proteins.

Category	Number of proteins regulated (in total)	Enrichment factor	𝑃 value	Regulated proteins
	Early permanent: upregulated
Serine family amino acid metabolic process^1	4 (4)	8.04	2.3𝐸−04	PHGDH; PSPH; SHMT1; SHMT2
Translational initiation^1	28 (34)	6.62	3.7𝐸−21	EIF2B2; EIF2B4; EIF3B; EIF3E; EIF3H; EIF3K; EIF4G1; EIF4G2; EIF5B; PABPC1; RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58
Ribosome^2	27 (33)	6.58	2.9𝐸−20	PWP2; RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58
Translational elongation^1	28 (35)	6.43	1.7𝐸−20	GFM1; RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58
Cellular process involved in reproduction^1	29 (42)	5.55	3.4𝐸−18	CDK1; RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58; UBAP2L
Protein targeting to ER^1	27 (40)	5.43	1.4𝐸−16	RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58
Initiation factor^3	17 (29)	4.71	2.4𝐸−09	EIF2A; EIF2B2; EIF2B4; EIF2S1; EIF2S2; EIF3A; EIF3B; EIF3C; EIF3CL; EIF3D; EIF3E; EIF3EIP; EIF3L; EIF3H; EIF3K; EIF4A1; EIF4G1; EIF4G2; EIF5B
Protein biosynthesis^3	31 (64)	3.90	2.9𝐸−13	AARS; CARS; EEF1A1; EEF1A1P5; EEF1A2; EEF1D; EEF1G; EEF2; EIF2A; EIF2B2; EIF2B4; EIF2S1; EIF2S2; EIF3A; EIF3B; EIF3C;EIF3CL; EIF3D; EIF3E; EIF3EIP; EIF3L; EIF3H; EIF3K; EIF4A1; EIF4G1; EIF4G2; EIF5B; EPRS; ETF1; GARS; GFM1; IARS; MARS; NARS; TARS
Ribonucleoprotein^3	28 (78)	2.89	2.2𝐸−08	MRPS27; RPL12; RPL13; RPL14; RPL17; RPL18; RPL22; RPL27; RPL3; RPL38; RPL4; RPL7; RPL7A; RPL9; RPLP0; RPLP0P6; RPS10; RPS10P5; RPS13; RPS16; RPS18; RPS19; RPS2; RPS25; RPS3; RPS3A; RPS4X; RPS7; RPS8; RPSA; RPSAP58
RNA transport^2	22 (66)	2.68	3.4𝐸−06	EEF1A1; EEF1A1P5; EEF1A2; EIF2B2; EIF2B4; EIF2S1; EIF2S2; EIF3A; EIF3B; EIF3C; EIF3CL; EIF3D; EIF3E; EIF3H; EIF4A1; EIF4G1; EIF4G2; EIF5B; ELAC2; GEMIN5; NUP93; PABPC1; PABPC4; RANGAP1; XPOT
Cellular macromolecule catabolic process^1	43 (145)	2.38	2.0𝐸−09	CDK1; EIF3E; EIF4A1; EIF4G1; ETF1; FEN1; PABPC1; PABPC4; PSMC1; PSMC2; PSMD1; PSMD2; PSMD3
ncRNA metabolic process^1	21 (71)	2.38	4.3𝐸−05	AARS; CARS; ELAC2; EPRS; FTSJ3; GARS; GEMIN5; IARS; MARS; NARS; NOP2; PDCD11; RPL14
	Early permanent: downregulated
Platelet degranulation^1	13 (21)	5.43	2.8𝐸−08	ACTN1; CALM2; F13A1; FLNA; ITGA2B; ITGB3; PECAM1; PPBP; THBS1; TLN1; TUBA4A; VCL; WDR1
Focal adhesion^2	13 (22)	5.19	6.2𝐸−08	ACTN1; CRKL; FLNA; FLNB; ITGA2B; ITGB3; MYL12A; PPP1R12A; RAP1B; THBS1; TLN1; VASP; VCL
Exocytosis^1	14 (24)	5.12	2.3𝐸−08	ACTN1; CALM2;CALM1; F13A1; FLNA; ITGA2B; ITGB3; PECAM1; PLEK; PPBP; SCRN1; SNCA; THBS1; TLN1; TUBA4A; VCL; WDR1
Calmodulin binding^3	6 (11)	4.79	5.2𝐸−04	ADD3; IQGAP2; PPP3CA; SPTAN1; SPTBN1; STRN
Organic acid catabolic process^1	14 (38)	3.23	2.4𝐸−05	ACADM; ALDH6A1; BCKDHA; CPT2; DDAH2; DECR1; DLST; ECI1; DCI; ETHE1; GLUD1; GLUD2; HADHB; HIBCH; IVD; MCCC1
Cell activation^1	16 (48)	2.93	2.6𝐸−05	ACTN1; ADA; CALM2; CALM1; F13A1; FLNA; ITGA2B; PECAM1; PLEK; PPBP; PPP3CA; RAP1B; RAP1A; THBS1; TLN1; TUBA4A; VCL; WDR1; YWHAZ
	Late regulated: upregulated
Cell adhesion molecules (CAMs)^2	3 (5)	21.21	2.0𝐸−04	HLA-DRA; ITGAL; ITGB2;
Glycoprotein^3	11 (76)	5.12	2.9𝐸−06	ASAH1; CD74; GLB1; HLA-DRA; ITGAL; ITGB2; MPO; PLD3; PRTN3; RNASET2; VIM;
Signal^3	9 (67)	4.75	5.0𝐸−05	ASAH1; IL-25; CD74; GLB1; HLA-DRA; ITGAL; ITGB2; MPO; PLD3; PRTN3; RNASET2
	Late regulated: downregulated
No significant enriched GO-Terms due to protein number <30
	Long term: up- and downregulated
No significant enriched GO-Terms due to protein number <30
	Early transient: up- and downregulated
No significant enriched GO-Terms due to protein number <30

Annotations for biological processes (GOBP¹) KEGG², and Uniprot Keywords³ of regulated proteins were compared with proteins in the whole dataset. Enriched categories have at least an enrichment factor >2.3 and a P value of less than 0.001. Due to multiple functionalities of proteins, some proteins are listed in multiple categories.