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Table 3 Gene Selection (IG) based on Consensus p-Median on the Sherf dataset

From: A p-Median approach for predicting drug response in tumour cells

Gene name

Biological process

Role (referred literature)

SPARC

Regulation of cell proliferation; signal transduction

SPARC is a secreted protein, acidic and rich in cysteines. It is a matrix associated protein that elicits changes in cell shape, inhibits cell cycle progression, and influences the synthesis of extracellular matrix. Clinical evidence indicates that SPARC expression correlates with tumor progression [42]. The gene product has been associated with tumor suppression but has also been correlated with metastasis based on changes to cell shape which can promote tumor cell invasion [43].

MAP1B

Microtubule bundle formation; negative regulation of intracellular transport

MAP1B interacts with a wide variety of proteins, there is growing consideration that MAP1B plays a crucial role in cytoskeleton stability and may also have a role in other cellular functions as well [44]. DAPK-1 promotes autophagy by binding to the microtubule-associated protein MAP1B, which is an LC3 interactor with anti-autophagic functions [45].

DNAJA3

Apoptosis; cell death; negative regulation of cell proliferation

It is an important cell death regulator and could exert tumor suppressor activity [46]. The results establish DNAJA3 as a novel regulator of p53-mediated apoptosis, and suggest that therapies designed to enhance DNAJA3’s function in promoting mitochondrial localization of p53 and apoptosis could be an effective therapy in many cancers [47].

SGK1

Apoptosis

SGK1 is a downstream target of cell survival and that it is primarily regulated at the level of transcription [48],[49].

ELF3

Inflammatory response;

Transcriptional inhibition of ELF3 could be a one of the mechanisms of colonic carcinogenesis [50].

CDKN2A

Cell cycle arrest; cell cycle checkpoint; negative regulation of cell growth; negative regulation of cell proliferation

CDKN2A is an important tumor suppressor gene and is specifically required for p53 activation under oncogenic stress [51]. Suppression of CDKN2A, a cell-cycle regulator, occurs in essentially all common human cancers [52]. Inactivating these tumor suppressors directly promotes tumorigenesis due to lack of control over cellular processes [53].

SPINT2

Cellular component movement

SPINT2 play important roles in controlling the aggressive nature and spread of cancer, displaying a unique therapeutic potential [54].

GJA1

Apoptosis

GJA1 is involved in several kinds of tumor, as breast, lung, prostate and ovarian [55],[56] and [57].

AKT3

Signal transduction

AKT signaling pathway is activated in human cancers and consequences for molecularly targeted therapies. AKT isoform may play a positive or negative role in cell migration and invasion. AKT is also involved in regulation of tumor angiogenesis [58].

EpCAM

Positive regulation of cell proliferation

EpCAM has oncogenic potential and is activated by release of its intracellular domain, which can signal into the cell nucleus by engagement of elements of the wnt pathway [59]. Regulated intramembrane proteolysis activates EpCAM as a mitogenic signal transducer in vitro and in vivo [60].

  1. The reported genes refer to the outperforming BN (85.63% of accuracy) trained according to the solution generated by the Consensus p-Median (d-g) with μ=1.6.