Figure-3 - uploaded by Sharadindu Shil
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Aim: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early pas...
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Context 1
... monolayer culture with finite mitotic lifespan (SCC early passage cells) was established from the bullock affected with SCC of horn ( Figure-2) following the enzymatic disaggregation methods as described earlier [22]. By the first week, tumor cells were seen rounding up and growing throughout the T-25/T-75 flask (Figure-3) among the normal stromal fibroblasts that grew in parallel. ...
Context 2
... monolayer culture with finite mitotic lifespan (SCC early passage cells) was established from the bullock affected with SCC of horn ( Figure-2) following the enzymatic disaggregation methods as described earlier [22]. By the first week, tumor cells were seen rounding up and growing throughout the T-25/T-75 flask (Figure-3) among the normal stromal fibroblasts that grew in parallel. ...
Citations
... described earlier in Shil et al. (2017). Multinucleated bizarre tumour cells and spindle to polygonal shaped cells having vesicular nuclei and multiple small nucleoli were frequently seen at later passages of culture ( Fig. 3). ...
... KEGG pathway of (hsa04270) vascular smooth muscle contraction 3.03E-02 [94] NPR2 KEGG pathway of (hsa04270) vascular smooth muscle contraction 3.03E-02 [94] PIAS3 KEGG pathway of (hsa04120) ubiquitin mediated proteolysis 1.80E-02 [96][97][98] GO-BP of protein sumoylation (GO:0016925) 1.52E-02 [99][100][101] GO-MF of small conjugating protein ligase activity (GO:0019787) 1.75E-03 [102] GO-MF of SUMO ligase activity (GO:0019789) 1.54E-02 [100] PIAS3 [101,103] ...
Background
Marker detection is an important task in complex disease studies. Here we provide an association rule mining (ARM) based approach for identifying integrated markers through mutual information (MI) based statistically significant feature extraction, and apply it to acute myeloid leukemia (AML) and prostate carcinoma (PC) gene expression and methylation profiles. Methods
We first collect the genes having both expression and methylation values in AML as well as PC. Next, we run Jarque-Bera normality test on the expression/methylation data to divide the whole dataset into two parts: one that follows normal distribution and the other that does not follow normal distribution. Thus, we have now four parts of the dataset: normally distributed expression data, normally distributed methylation data, non-normally distributed expression data, and non-normally distributed methylated data. A feature-extraction technique, “mRMR” is then utilized on each part. This results in a list of top-ranked genes. Next, we apply Welch t-test (parametric test) and Shrink t-test (non-parametric test) on the expression/methylation data for the top selected normally distributed genes and non-normally distributed genes, respectively. We then use a recent weighted ARM method, “RANWAR” to combine all/specific resultant genes to generate top oncogenic rules along with respective integrated markers. Finally, we perform literature search as well as KEGG pathway and Gene-Ontology (GO) analyses using Enrichr database for in silico validation of the prioritized oncogenes as the markers and labeling the markers as existing or novel. ResultsThe novel markers of AML are {ABCB11↑∪KRT17↓} (i.e., ABCB11 as up-regulated, & KRT17 as downregulated), and {AP1S1-∪KRT17↓∪NEIL2-∪DYDC1↓}) (i.e., AP1S1 and NEIL2 both as hypo-methylated, & KRT17 and DYDC1 both as down-regulated). The novel marker of PC is {UBIAD1¶∪APBA2‡∪C4orf31‡} (i.e., UBIAD1 as up-regulated and hypo-methylated, & APBA2 and C4orf31 both as down-regulated and hypermethylated). Conclusion
The identified novel markers might have critical roles in AML as well as PC. The approach can be applied to other complex disease.Open image in new window
... KEGG pathway of (hsa04270) vascular smooth muscle contraction 3.03E-02 [94] NPR2 KEGG pathway of (hsa04270) vascular smooth muscle contraction 3.03E-02 [94] PIAS3 KEGG pathway of (hsa04120) ubiquitin mediated proteolysis 1.80E-02 [96][97][98] GO-BP of protein sumoylation (GO:0016925) 1.52E-02 [99][100][101] GO-MF of small conjugating protein ligase activity (GO:0019787) 1.75E-03 [102] GO-MF of SUMO ligase activity (GO:0019789) 1.54E-02 [100] PIAS3 [101,103] ...
