Table IV.
Most upregulated molecules of nilotinib treated cells in ingenuity pathway analysis.
| Gene symbol | Gene name | logFC | Regulates | General function | Function related to bone biology |
|---|---|---|---|---|---|
| RPS23 | Ribosomal protein S23 | 3.45 | rnr | Encodes a ribosomal protein which is a component of the 40S subunit. | N/A |
| ZFP184 | Zinc finger protein 184 | 3.43 | N/A | Takes part in sequence-specific DNA binding and in the regulation of transcription. | N/A |
| EDNRB | Endothelin receptor type B | 3.04 | Cyclooxygenase, SLC9A3, nitric oxide, VEGFA, EDN1, Nos, HIF1A, TYR, DNS promoter, Adcy, Ca2+, GNAI1, GNAO1, RNA polymerase II | Non-specific, G protein-coupled receptor for endothelin 1, 2, and 3. Located primarily in the vascular endothelial cells. Involved in vasoconstriction, vasodilation, bronchoconstriction and cell proliferation. | N/A |
| DKK4 | Dickkopf homolog 4 | 2.99 | N/A | A member of the dickkopf family. The secreted protein involved in embryonic development through interactions with the Wingless (WNT) signaling pathway. DKKs are important in vertebrate development. They locally inhibit Wnt regulated processes, such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. DKKs are implicated in bone formation and bone disease. | Positively regulates osteoblast apoptosis, and negatively regulates osteoblast proliferation, differentiation and the Wnt/β catenin signaling pathway (29). |
| GABRB1 | γ-aminobutyric acid (GABA) A receptor, subunit β1 | 2.83 | Ion, chloride | A multisubunit chloride channel that mediates inhibitory synaptic transmission in the central nervous system. | N/A |
| RPL17 | Ribosomal protein L17 | 2.41 | N/A | Encodes a ribosomal protein that is a component of the 60S subunit. There are multiple processed pseudogenes of this gene dispersed through the genome, which is typical for genes encoding ribosomal proteins. Alternative splicing results in multiple transcript variants. | N/A |
| KLHL41 | Kelch-like 41 | 2.37 | N/A | Member of the kelch-like family. Thought to function in skeletal muscle development and differentiation. Regulates proliferation and differentiation of myoblasts and is involved in myofibril assembly. Required for pseudopod elongation in transformed cells. | N/A |
| NANOG | Nanog homeobox | 2.06 | GATA4, FAK, NANOG, FOXD3, POU5F1, PDCD4, CDK6, AHR, GATA6, ZFP42, DNA promoter, DNA endogenous promoter, RNA polymerase II, SEC22B, PCDHA2 | Transcription regulator involved in inner cell mass and ES cells proliferation and self-renewal. Prevents ES cell differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. | Involved in bone healing (30), negatively regulates bone morphogenetic cascade and Wingless signaling pathway. |
| RPL39 | Ribosomal protein L39 | 1.99 | N/A | Encodes a ribosomal protein that is a component of the 60S subunit. | N/A |
Gene symbols, names were listed to standard GeneCards (http://www.genecards.org). Functions were listed to GeneCards (http://www.genecards.org), NCBI (http://www.ncbi.nlm.nih.gov/gene) and IPA (https://reports.ingenuity.com). Data on the function of the most upregulated molecules in bone biology were collected from literature. ES, embryonic stem.