Table 5.
Genes highly modulated by 3D only in B4GALNT2-expressing LS174T cells (clones S2/S11).
| Gene Symbol | Expression Neo | Expression S2/S11 | Fold Change 3D/2D Neo | Fold Change 3D/2D S2/S11 | Corrected p-Value | Gene Name | Role | Broad Functional Category | ||
|---|---|---|---|---|---|---|---|---|---|---|
| 2D | 3D | 2D | 3D | |||||||
| KIZ | 16.2 | 13.4 | 19.0 | 3.8 | −1.2 | −4.9 | 0.0086 | Kizuna centrosomal protein | Centrosomal protein necessary to endure the forces converging on the centrosomes during spindle formation. | Cytoskeleton and mitosis |
| CEP120 | 7.3 | 7.5 | 15.8 | 3.1 | 1.0 | −5.2 | 0.0086 | Centrosomal protein 120kDa | Functions in the microtubule-dependent coupling of the nucleus and the centrosome. | |
| DNAH6 | 6.3 | 5.3 | 13.1 | 2.3 | −1.2 | −5.7 | 0.0163 | Dynein, axonemal, heavy chain 6 | Member of the dynein family, which are constituents of the microtubule-associated motor protein complex. | |
| SGOL2 | 8.6 | 7.7 | 18.4 | 2.2 | −1.1 | −8.3 | 0.0086 | Shugoshin-like 2 (S. pombe) | Targets PPP2CA to centromeres, leading to cohesin dephosphorylation. | |
| STARD13 | 13.5 | 16.3 | 19.8 | 4.2 | 1.2 | −4.7 | 0.0156 | StAR-related lipid transfer (START) domain containing 13 | Involved in regulation of cytoskeletal reorganization, cell proliferation and motility. | |
| UPK1A | 4.0 | 3.7 | 1.9 | 12.0 | −1.1 | 6.3 | 0.0086 | Uroplakin 1A | Member of the tetraspanin family, mediates signaling. Decreased expression is associated with CRC progression and poor prognosis. (PMID: 25197375) | Cell signaling |
| OR52R1 | 11.2 | 10.3 | 3.3 | 15.5 | −1.1 | 4.8 | 0.0131 | Olfactory receptor, family 52, subfamily R, member 1 (gene/pseudogene) | Olfactory receptors are G-protein-coupled receptors involved in perception of smell and other functions. | |
| TAS2R45 | 42.6 | 35.9 | 68.8 | 17.2 | −1.2 | −4.0 | 0.0247 | Taste receptor, type 2, member 45 | Taste receptors play a role in the perception of bitterness and in sensing the chemical composition of the gastrointestinal content. Some taste receptors inhibit cancer growth and stemness. (PMID: 28467517) | |
| TAS2R19 | 41.9 | 31.8 | 70.3 | 17.1 | −1.3 | −4.1 | 0.0116 | Taste receptor, type 2, member 19 | ||
| TAS2R30 | 254.5 | 215.3 | 402.3 | 81.8 | −1.2 | −4.9 | 0.0168 | Taste receptor, type 2, member 30 | ||
| TNFAIP8L2 | 4.7 | 6.0 | 2.0 | 14.5 | 1.3 | 7.3 | 0.0319 | Tumor necrosis factor, alpha-induced protein 8-like 2 | Promotes Fas-induced apoptosis. (PMID: 28186089) | Apoptosis |
| MYOD1 | 3.4 | 5.7 | 2.3 | 10.4 | 1.7 | 4.4 | 0.0239 | Myogenic differentiation 1 | Mediates apoptosis through caspase 3. (PMID: 28131747) | |
| PPM1K | 16.3 | 11.7 | 25.7 | 4.0 | −1.4 | −6.5 | 0.0086 | Protein phosphatase, Mg2+/Mn2+ dependent, 1K | Regulates the mitochondrial permeability transition pore and is essential for cellular survival. | |
| SDPR (CAVIN2) | 4.3 | 1.8 | 18.3 | 2.3 | −2.4 | −8.1 | 0.0106 | Serum deprivation response | Role in caveolar biogenesis and morphology. Metastasis suppressor and activator of apoptosis. (PMID: 26739564). | |
| PHF20L1 | 7.4 | 7.1 | 24.2 | 2.7 | 1.0 | −8.9 | 0.0089 | PHD finger protein 20-like 1 | Predicted to be involved in regulation of transcription. Stabilizes SOX2 postranslationally. (PMID: 30089852) | Transcription regulation |
| KLF12 | 5.2 | 3.9 | 12.3 | 2.2 | −1.3 | −5.7 | 0.0235 | Kruppel-like factor 12 | Inhibitor of the AP-2 alpha transcription factor. Inhibits growth and anoikis resistance of ovarian cancer cells. (PMID: 28095864) | |
| PCF11 | 3.6 | 5.0 | 6.7 | 1.7 | 1.4 | −4.0 | 0.0086 | PCF11 cleavage and polyadenylation factor subunit | It is necessary for efficient Pol II transcription termination | |
| CTLA4 | 2.1 | 3.7 | 2.4 | 14.2 | 1.7 | 5.8 | 0.0136 | Cytotoxic T-lymphocyte-associated protein 4 | Inhibitor of T cell activation. | Immunity and inflammation |
| IL1A | 1.7 | 2.8 | 2.1 | 11.7 | 1.7 | 5.6 | 0.0259 | Interleukin 1α | Involved in immune responses and inflammatory processes. | |
| TDO2 | 3.1 | 6.5 | 7.3 | 29.0 | 2.1 | 4.0 | 0.0086 | Tryptophan 2,3-dioxygenase | In tryptophan metabolism catalyzes the first step of the kynurenine pathway. Increased kynurenine may suppress antitumor immune responses. | |
| FSIP2 | 8.3 | 5.8 | 17.0 | 2.9 | −1.4 | −5.9 | 0.0365 | Fibrous sheath interacting protein 2 | Protein associated with the sperm fibrous sheath. | Fertilization |
| SPACA1 | 5.5 | 6.4 | 4.1 | 18.2 | 1.2 | 4.5 | 0.0293 | Sperm acrosome associated 1 | Localizes to the acrosomal membrane of spermatozoa, playing a role in acrosomal morphogenesis and in sperm-egg fusion. | |
| USP11 | 6.1 | 7.0 | 3.3 | 13.3 | 1.1 | 4.0 | 0.0352 | Ubiquitin specific peptidase 11 | Encodes a cysteine protease that cleaves ubiquitin from ubiquitin-conjugated protein substrates. | Ubiquitination |
| ST13 | 6.9 | 12.8 | 2.7 | 11.0 | 1.9 | 4.1 | 0.0090 | Suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) | Mediates the association of the heat shock proteins HSP70 and HSP90. | Protein folding |
| HIST4H4 | 81.2 | 193.8 | 101.6 | 406.8 | 2.4 | 4.0 | 0.0365 | Histone cluster 4, H4 | Component of the nucleosome. | Chromatin structure |
| TRAPPC2 | 10.3 | 7.1 | 8.4 | 1.9 | −1.5 | −4.4 | 0.0086 | Trafficking protein particle complex 2 | May play a role in vesicular transport from endoplasmic reticulum to Golgi | Intracellular transport |
| C8orf74 | 6.3 | 5.3 | 10.1 | 2.3 | −1.2 | −4.4 | 0.0135 | Chromosome 8 open reading frame 74 | Little or no information | |
| NAALADL2 | 15.5 | 10.4 | 17.9 | 4.1 | −1.5 | −4.3 | 0.0196 | N-acetylated alpha-linked acidic dipeptidase-like 2 | ||
| SAMD12 | 21.1 | 17.1 | 25.8 | 6.3 | −1.2 | −4.1 | 0.0323 | Sterile alpha motif domain containing 12 | ||
| FRG2 | 40.8 | 49.1 | 40.2 | 173.8 | 1.2 | 4.3 | 0.0138 | FSHD region gene 2 | ||
| FRG2C | 3.5 | 8.4 | 7.2 | 35.0 | 2.4 | 4.9 | 0.0124 | FSHD region gene 2 family, member C | ||
Corrected p-value was calculated using the multiple test correction Benjamini–Hochberg (p < 0.05, fold change B4GALNT2 3D vs. B4GALNT2 2D). Information on the gene role were obtained from Genecards [22] and from PubMed.