Table IV.
The list of 83 differentially expressed genes between AML and HV samples.
| Gene name (ID) | Gene description | Gene function | Log2FC | Adjusted p-value |
|---|---|---|---|---|
|
A, Genes overexpressed in AML | ||||
| STMN1 (3925) | Stathmin 1 | Regulation of the microtubule filament system by destabilizing microtubules | 2.91 | 1.67×10−10 |
| KITLG (4254) | KIT ligand | The ligand of the tyrosine-kinase receptor, required in hematopoiesis | 2.38 | 0.0088481 |
| CDK6 (1021) | Cyclin-dependent kinase 6 | Cell cycle regulation, G1 phase progression and G1/S transition; altered expression in multiple human cancers | 1.51 | 1.88×10−9 |
| MCM5 (4174) | Minichromosome maintenance complex component 5 | DNA replication, cell cycle regulation; upregulated in the transition from the G0 to G1/S phase | 1.42 | 0.0001986 |
| KRAS (3845) | KRAS proto-oncogene, GTPase | Oncogene, member of the small GTPase superfamily; mutated in various malignancies | 1.42 | 0.0005584 |
| CEBPA (1050) | CCAAT/enhancer binding protein α | Transcription factor, modulator of the expression of genes involved in cell cycle regulation and body weight homeostasis; mutated in AML | 1.32 | 0.0006135 |
| MYC (4609) | MYC proto-oncogene, bHLH transcription factor | Regulation of cell cycle progression, apoptosis and cellular transformation; amplified in numerous human cancers, translocated in Burkitt’s lymphoma and multiple myeloma | 1.26 | 4.32×10−7 |
| ANGPT1 (284) | Angiopoietin 1 | Role in vascular development and angiogenesis, interactions between the endothelium and surrounding matrix, blood vessel maturation and stability | 1.25 | 0.0022923 |
| SRGN (5552) | Serglycin | Hematopoietic cell granule proteoglycan, associated with complex of granzymes and perforin, and granule-mediated apoptosis | 1.17 | 0.0064793 |
| RPLP0 (6175) | Ribosomal protein lateral stalk subunit P0 | Ribosomal protein, component of the 60S subunit, protein synthesis | 1.14 | 0.0000199 |
| ENO1 (2023) | Enolase 1 | Glycolytic enzyme, structural lens protein (tau-crystallin) | 1.14 | 0.0000584 |
| SET (6418) | SET nuclear proto-oncogene | Inhibitor of histone acetylases (HAT), nucleosome acetylation and transcription | 1.07 | 0.0000584 |
| MYB (4602) | MYB proto-oncogene, transcription factor | Transcription regulator, regulation of hematopoiesis, aberrently expressed, rearranged or translocated in leukemias and lymphomas | 0.88 | 0.0058191 |
| GAL (51083) | Galanin and GMAP prepropeptide | Nociception, feeding and energy homeostasis, osmotic regulation and water balance | 0.87 | 0.0015198 |
| HSPA8 (3312) | Heat shock protein family A (Hsp70) member 8 | Chaperone, correct folding of nascent polypeptides, disassembly of clathrin-coated vesicles in transport of cell membrane components (ATPase) | 0.72 | 0.0014811 |
| ADRA2C (152) | Adrenoceptor α 2C | G protein-coupled receptor, regulation of neurotransmitter release at lower levels of nerve activity | 0.70 | 0.0017407 |
| HSPD1 (3329) | Heat shock protein family D (Hsp60) member 1 | Chaperone, folding and assembly of newly imported proteins in the mitochondria, signalling molecule in the innate immune system | 0.61 | 0.0058191 |
| IGFBP7 (3490) | Insulin like growth factor (IGF) binding protein 7 | Regulation of IGF availability in body fluids and tissues and modulation of IGF binding to its receptors, stimulation of prostacyclin production and cell adhesion | 0.59 | 0.0014913 |
| RASSF5 (83593) | Ras association domain family member 5 | Tumor suppressor, inactivated in a variety of cancers, regulation of lymphocyte adhesion, cell growth suppression | 0.58 | 0.0016728 |
| EEF1G (1937) | Eukaryotic translation elongation factor 1 g | Asubunit of the elongation factor-1 complex, enzymatic delivery of aminoacyl tRNAs to the ribosome | 0.56 | 0.0002401 |
| GSN (2934) | Gelsolin | Calcium-regulated protein, assembly and disassembly of actin filaments | 0.55 | 0.0005526 |
| ZNF22 (7570) | Zinc finger protein 22 | DNA binding, transcription regulation | 0.51 | 0.0054429 |
| GAPDH (2597) | Glyceraldehyde-3-phosphate dehydrogenase | Carbohydrate metabolism, phosphorylation of glyceraldehyde-3-phosphate in the presence of inorganic phosphate and nicotinamide adenine dinucleotide (NAD) | 0.49 | 0.0015715 |
| KIT (3815) | KIT proto-oncogene receptor tyrosine kinase | Transmembrane receptor for MGF (mast cell growth factor, stem cell factor), mutated in gastrointestinal tumors, mast cell disease, AML and piebaldism | 0.46 | 0.0017591 |
| HOXA10 (3206) | Homeobox A10 | Transcription factor, regulation of gene expression, morphogenesis, differentiation, fertility, embryo viability, and hematopoietic lineage commitment | 0.43 | 0.0047731 |
| ERCC2 (2068) | ERCC excision repair 2, TFIIH core complex helicase subunit | DNA damage repair, transcription-coupled nucleotide excision repair, member of the basal transcription factor BTF2/TFIIH complex | 0.43 | 0.0005584 |
| ATP6V0C (527) | ATPase H+ transporting V0 subunit c | Component of vacuolar multisubunit enzyme ATPase (V-ATPase), acidification of eukaryotic intracellular organelles, necessary for protein sorting, zymogen activation, receptor-mediated endocytosis, synaptic vesicle proton gradient generation | 0.43 | 0.0080978 |
| HSPA9 (3313) | Heat shock protein family A (Hsp70) member 9 | Role in cell proliferation, stress response and maintenance of the mitochondria | 0.42 | 0.0026984 |
| ARHGEF12 (23365) | Rho guanine nucleotide exchange factor 12 | Numerous cellular processes initiated by extracellular stimuli through G protein-coupled receptors, fusion partner in AML | 0.42 | 0.0014811 |
| PDE3B (5140) | Phosphodiesterase 3B | Regulation of energy metabolism, energy homeostasis and energy intake | 0.42 | 0.0046975 |
| HOXB6 (3216) | Homeobox B6 | DNA binding, sequence-specific transcription factor, regulation of e.g. lung and skin development | 0.40 | 0.0000475 |
| HSP90AB1 (3326) | Heat shock protein 90α family class B member 1 | Signal transduction, protein folding and degradation, morphological evolution, role in gastric apoptosis and inflammation | 0.39 | 0.0006700 |
| ARF1 (375) | ADP ribosylation factor 1 | Phospholipase D activator, a role in vesicular trafficking, intra-Golgi transport | 0.38 | 0.0080978 |
| CTSD (1509) | Cathepsin D | Pepsin-like activity, role in protein turnover and proteolytic activation of hormones and growth factors | 0.37 | 0.0086744 |
| MAP7 (9053) | Microtubule associated protein 7 | Microtubule stabilization, essential for cell polarization, differentiation and spermatogenesis | 0.37 | 0.0058191 |
| ITGB4 (3691) | Integrin subunit β4 | Mediation in cell-matrix or cell-cell adhesion, gene expression and cell growth, receptor for the laminins, pivotal role in the biology of invasive carcinoma | 0.36 | 0.0058191 |
| MYH11 (4629) | Myosin heavy chain 11 | Major contractile protein, rearranged in AML of the M4Eo subtype | 0.35 | 0.0020442 |
| PRKAR1B (5575) | Protein kinase cAMP-dependent type I regulatory subunit β | Signaling pathway of the second messenger cAMP, regulation of ion transport, metabolism, and transcription | 0.32 | 0.0080978 |
| PKM (5315) | Pyruvate kinase M1/2 | Glycolysis, mediation of cellular metabolic effects induced by thyroid hormones, role in bacterial pathogenesis | 0.31 | 0.0006463 |
| TUBB (203068) | Tubulin β class I | Structural component of microtubules | 0.29 | 0.0081504 |
| MN1 (4330) | MN1 proto-oncogene, transcriptional regulator | Translocated in meningioma, myeloproliferation stimulation, leukemogenesis | 0.25 | 0.0070082 |
|
B, Genes underexpressed in AML | ||||
| IFITM1 (8519) | Interferon induced transmembrane protein 1 | Regulation of angiogenesis, tumorigenesis | −2.05 | 0.0000584 |
| LTB (4050) | Lymphotoxin β | Induction of the inflammatory response system, role in normal development of lymphoid tissue | −2.00 | 1.29×10−7 |
| FCN1 (2219) | Ficolin 1 | Plasma protein with elastin-binding activity, expressed in the peripheral blood leukocytes | −1.93 | 0.0000173 |
| BIRC3 (330) | BIculoviral IAP repeat containing 3 | Inhibition of apoptosis by binding to tumor TRAF1 and TRAF2 necrosis factor receptor-associated factors | −1.90 | 0.0014913 |
| LYZ (4069) | Lysozyme | Antimicrobial agent, cleavage of bacterial cell wall peptidoglycan | −1.85 | 0.0005526 |
| ADD3 (120) | Adducin 3 | Membrane skeletal protein, assembly of spectrin-actin network; expression restricted to brain and hematopoietic tissues | −1.60 | 0.0014913 |
| S100A9 (6280) | S100 calcium binding protein A9 | Regulation of cell cycle progression and differentiation, inhibition of casein kinase, antifungal and antibacterial activity | −1.59 | 0.0014811 |
| FCER1G (2207) | Fc fragment of IgE receptor Ig | Key molecule involved in allergic reactions | −1.39 | 0.0006135 |
| PTPRE (5791) | Protein tyrosine phosphatase, receptor type E | Signaling molecule, regulation of cell growth, differentiation, mitotic cycle and oncogenic transformation | −1.39 | 0.0024662 |
| CD74 (972) | CD74 molecule | Associates with class II major histocompatibility complex (MHC), chaperone regulating antigen presentation for immune response, mediation in survival pathways and cell proliferation | −1.23 | 0.0058191 |
| TMSB4X (7114) | Thymosin β4, X-linked | Actin sequestering protein, regulation of actin polymerization, cell proliferation, migration, and differentiation | −1.05 | 1.32×10−8 |
| PF4 (5196) | Platelet factor 4 | Member of the CXC chemokine family, involved in platelet aggregation, inhibitor of hematopoiesis, angiogenesis and T-cell function | −0.97 | 0.0002201 |
| B2M (567) | β-2-microglobulin | Serum protein associating with the MHC class I heavy chain on the surface of nucleated cells, antibacterial activity | −0.95 | 0.0006700 |
| HLA-DPB1 (3115) | Major histocompatibility complex, class II, DP β1 | Central role in the immune system by presenting peptides derived from extracellular proteins, expressed in B lymphocytes, dendritic cells and macrophages | −0.77 | 0.0025915 |
| CSF3R (1441) | Colony stimulating factor 3 receptor | Cytokine controlling production, differentiation, and function of granulocytes, involvement in cell surface adhesion and recognition processes | −0.71 | 0.0025443 |
| HOXA9 (3205) | Homeobox A9 | DNA-binding transcription factor, regulation of gene expression, morphogenesis, and differentiation, translocated in myeloid leukemias | −0.70 | 0.0006135 |
| CCL5 (6352) | C-C motif chemokine ligand 5 | Chemokine involved in immunoregulatory and inflammatory processes, chemoattractant for blood monocytes, memory T helper cells and eosinophils | −0.53 | 0.0033854 |
| CCL3 (6348) | C-C motif chemokine ligand 3 | Small inducible cytokine, macrophage inflammatory protein 1 α, role in inflammatory responses | −0.51 | 0.0034134 |
| RARA (5914) | Retinoic acid receptor α | Nuclear retinoic acid receptor, transcription regulation in a ligand-dependent manner, regulation of development, differentiation, apoptosis, granulopoeisis, and clock genes, translocated in acute promyelocytic leukemia | −0.49 | 0.0053657 |
| CCL19 (6363) | C-C motif Chemokine ligand 19 | Cytokine involved in immunoregulatory and inflammatory processes, antimicrobial, role in normal lymphocyte recirculation and homing | −0.46 | 0.0000612 |
| NFKBIA (4792) | NFKB inhibitor α | Interactions with REL dimers to inhibit NF-κB/REL complexes involved in inflammatory responses | −0.46 | 0.0054429 |
| TNFSF10 (8743) | TNF superfamily member 10 | Cytokine from the tumor necrosis factor (TNF) ligand family, preferential induction of apoptosis in transformed and tumor cells | −0.46 | 0.0033432 |
| CD52 (1043) | CD52 molecule | Lymphocyte surface antigene, involved in fertilisation and response to therapy in large granular lymphocytic leukemia, AML and MDS | −0.45 | 0.0095319 |
| PLBD1 (79887) | Phospholipase B domain containing 1 | Role in the defence against microorganisms, generation of lipid mediators of inflammation | −0.43 | 0.0058191 |
| CAPN10 (11132) | Calpain 10 | Calcium-dependent cysteine protease, associated with type 2 or non-insulin-dependent diabetes | −0.38 | 0.0005178 |
| STAT5B (6777) | Signal transducer and activator of transcription 5B | Transcription factor, signal transduction triggered by IL2, IL4, CSF1, and growth hormones, involved in apoptosis, adult mammary gland development, and sexual dimorphism of liver gene expression | −0.36 | 0.0026984 |
| PGK1 (5230) | Phosphoglycerate kinase 1 | Glycolytic enzyme, conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate, involved in angiogenesis of tumor cells | −0.35 | 0.0064868 |
| RALGDS (5900) | Ral guanine nucleotide dissociation stimulator | Effector of Ras-related GTPase, signaling for a variety of cellular processes | −0.35 | 0.0070755 |
| SPTBN1 (6711) | Spectrin β, non-erythrocytic 1 | Actin crosslinking and molecular scaffold protein, cytoskeleton functioning, determination of cell shape, arrangement of transmembrane proteins, and organization of organelles | −0.35 | 0.0056936 |
| BTG1 (694) | BTG anti-proliferation factor 1 | Anti-proliferative activity, co-activator of cell differentiation, regulation of cell growth | −0.34 | 0.0079167 |
| TRADD (8717) | TNFRSF1A associated via death domain | Programmed cell death signaling and NF-κB activation, suppression of TRAF2-mediated apoptosis | −0.34 | 0.0005526 |
| CYP2E1 (1571) | Cytochrome P450 family 2 subfamily E member 1 | Involved in drug metabolism, synthesis of cholesterol, steroids and other lipids, induced by ethanol, the diabetic state, and starvation | −0.33 | 0.0052990 |
| MAP4K2 (5871) | Mitogen-activated protein kinase kinase kinase kinase 2 | Involved in B-cell differentiation, activated by TNF-α, interacting with TNF receptor-associated factor 2 (TRAF2) | −0.32 | 0.0001674 |
| IGF1 (3479) | Insulin like growth factor 1 | Involved in mediating growth and development | −0.32 | 0.0032632 |
| STK4 (6789) | Serine/threonine kinase 4 | Acting upstream of the stress-induced mitogen-activated protein kinase cascade, involved in apoptosis and chromatin condensation induction | −0.31 | 0.0022923 |
| HCK (3055) | HCK proto-oncogene, Src family tyrosine kinase | Hemopoietic protein, present myeloid and B-lymphoid cell lineages, role in activation of the respiratory burst, neutrophil migration and degranulation of neutrophils | −0.29 | 0.0059276 |
| PDGFRB (5159) | Platelet-derived growth factor receptor β | Cell surface tyrosine kinase receptor for growth factors, development of the cardiovascular system, rearrangement of the actin cytoskeleton | −0.28 | 0.0001623 |
| RHOB (388) | Ras homolog family member B | Tumor suppressor, regulation of cytoskeletal dynamics and vesicle trafficking, control of endothelial barrier function | −0.28 | 0.0048010 |
| XBP1 (7494) | X-box binding protein 1 | Transcription factor regulating MHC class II genes, increase of viral protein expression | −0.27 | 0.0014913 |
| IFNA1 (3439) | Interferon α1 | Antiviral activity, pathogen clearance and tissue inflammation | −0.26 | 0.0024163 |
| PIM1 (5292) | Pim-1 proto-oncogene, serine/threonine kinase | Signal transduction in blood cells, propagation of cell proliferation and survival, tumorigenesis, overexpressed in hematopoietic malignancies and prostate cancer | −0.24 | 0.0013396 |
| PXN (5829) | Paxillin | Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion) | −0.24 | 0.0086744 |
The genes were identified with a significance level of α 0.01 and ranked according to the normalized expression fold change (Log2FC). p-values were corrected for multiple testing. Gene descriptions and functions come from the NCBI gene database.