Integration of Different “-omics” Technologies Identifies Inhibition of the IGF1R-Akt-mTOR Signaling Cascade Involved in the Cytotoxic Effect of Shikonin against Leukemia Cells

Table 1

Top up- and downregulated molecules in U937 cells after treatment with shikonin. Quantitative changes in the proteome were studied by stable-isotope dimethyl labeling. Microarray experiments were used to analyze changes in the mRNA and miRNA expressione.

	Proteins		mRNAs			miRNAS
	Protein names	FC	Genes	Encoded proteins	FC	ID	FC
Top upregulated molecules	Heme oxygenase 1	+14.3	MLLT11	Protein AF1q	+6.2	miR-19b-2-5p	+5.2
	WD repeat-containing protein 3	+12.1	S100A8	Protein S100-A8	+4.7	miR-20b-3p	+3.7
	Histone H4	+11.1	LY96	Lymphocyte antigen 96	+4.5	miR-155-3p	+3.4
	Cell differentiation protein RCD1 homolog	+10.0	S100A9	Protein S100-A9	+4.2	miR-181a-2-3p	+3.2
	Sorting nexin-17	+9.1	CCL2	C-C motif chemokine 2	+4.2	miR-33b-5p	+3.1
	Mannose-6-phosphate isomerase	+7.7	VIM	Vimentin	+4.2	miR-30a-3p	+2.9
	Histone H2B type 2-E	+7.1	HMOX1	Heme oxygenase 1	+4.1	miR-3907	+2.8
	Schlafen family member 11	+6.7	ANXA1	Annexin A1	+4.1	miR-223-5p	+2.7
	LIM domain and actin-binding protein 1	+6.7	MAFB	Transcription factor MafB	+3.5	miR-193b-3p	+2.7
	Neuronal-specific septin-3	+6.7	JUN	Transcription factor AP-1	+3.2	miR-92a-3p	+2.7
Top downregulated molecules	Hexokinase-1	−20.5	ALDOA	Fructose-bisphosphate aldolase A	−17.6	miR-4299	−30.6
	Vacuolar protein sorting-associated protein 11 homolog	−20.0	ACTG1	Actin, cytoplasmic 2	−11.9	miR-1915-3p	−13.8
	60S ribosomal protein L24	−7.5	CCT7	T-complex protein 1 subunit eta	−7.8	miR-2861	−9.8
	5′-Nucleotidase domain-containing protein 2	−5.4	ARPC1B	Actin-related protein 2/3 complex subunit 1B	−7.8	miR-1207-5p	−6.3
	Heterogeneous nuclear ribonucleoprotein H2	−4.5	PSMC4	26S protease regulatory subunit 6B	−7.7	miR-1290	−6.2
	ATP-dependent RNA helicase DDX3Y	−4.3	ACTB	Actin, cytoplasmic 1	−6.8	miR-638	−6.1
	Methylosome protein 50	−4.0	HSPD1	60 kDa heat shock protein, mitochondrial	−6.6	miR-1246	−6.0
	Golgi phosphoprotein 3	−3.5	SLC39A3	Zinc transporter ZIP3	−6.2	miR-1185-5p	−5.2
	Leucine-rich repeat-containing protein 58	−3.5	ERP29	Endoplasmic reticulum resident protein 29	−6.0	miR-630	−5.1
	Rho GTPase-activating protein 4	−3.1	NCF1	Neutrophil cytosol factor 1	−5.9	miR-513a-5p	−4.7