Displaying publications 1 - 20 of 44 in total

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  1. Integrating amperometric detection with electrophoresis microchip devices for biochemical assays: recent developments
    Ghanim MH, Abdullah MZ
    Talanta, 2011 Jul 15;85(1):28-34.
    PMID: 21645665 DOI: 10.1016/j.talanta.2011.04.069
    Recent advances in microfluidic systems, particularly in the Micro Total Analysis System (μTAS) or Lab On a Chip (LOC), drive the current analysis tools and equipment towards miniaturization, rapid at-line testing and mobility. The state-of-the-art microfluidic technology targets a wider range but smaller volumes of analytes, making the analytical procedure relatively easier and faster. This trend together with faster electronics and modern instrumentation systems will make real-time and in situ analysis a definite possibility. This review focuses on microchip capillary electrophoresis with amperometric detection (MCE-AD) for the detection of DNA and other electroactive analytes. The problems associated with the microchip design, in particular the choice of materials and the configuration of electrodes are discussed thoroughly and solutions are proposed. Significant developments in the related areas are also covered and reviewed critically.
    Matched MeSH terms: Microarray Analysis/instrumentation*; Microarray Analysis/trends
  2. Fulltext Transcriptome Analysis of Pseudomonas aeruginosa Biofilm Following the Exposure to Malaysian Stingless Bee Honey
    Seder N, Abu Bakar MH, Abu Rayyan WS
    Adv Appl Bioinform Chem, 2021;14:1-11.
    PMID: 33488102 DOI: 10.2147/AABC.S292143
    Introduction: Malaysian stingless bee honey (Trigona) has been aroused as a potential antimicrobial compound with antibiofilm activity. The capability of the gram-negative bacillus P. aeruginosa to sustain a fatal infection is encoded in the bacterium genome.

    Methods: In the current study, a transcriptome investigation was performed to explore the mechanism underlying the biofilm dispersal of P. aeruginosa after the exposure to Trigona honey.

    Results: Microarray analysis of the Pseudomonas biofilm treated by 20% Trigona honey has revealed a down-regulation of 3478 genes among the 6085 screened genes. Specifically, around 13.5% of the down-regulated genes were biofilm-associated genes. The mapping of the biofilm-associated pathways has shown an ultimate decrease in the expression levels of the D-GMP signaling pathway and diguanylate cyclases (DGCs) genes responsible for c-di-GMP formation.

    Conclusion: We predominantly report the lowering of c-di-GMP through the down-regulation of DGC genes as the main mechanism of biofilm inhibition by Trigona honey.

    Matched MeSH terms: Microarray Analysis
  3. Identification of informative genes and pathways using an improved penalized support vector machine with a weighting scheme
    Chan WH, Mohamad MS, Deris S, Zaki N, Kasim S, Omatu S, et al.
    Comput Biol Med, 2016 10 01;77:102-15.
    PMID: 27522238 DOI: 10.1016/j.compbiomed.2016.08.004
    Incorporation of pathway knowledge into microarray analysis has brought better biological interpretation of the analysis outcome. However, most pathway data are manually curated without specific biological context. Non-informative genes could be included when the pathway data is used for analysis of context specific data like cancer microarray data. Therefore, efficient identification of informative genes is inevitable. Embedded methods like penalized classifiers have been used for microarray analysis due to their embedded gene selection. This paper proposes an improved penalized support vector machine with absolute t-test weighting scheme to identify informative genes and pathways. Experiments are done on four microarray data sets. The results are compared with previous methods using 10-fold cross validation in terms of accuracy, sensitivity, specificity and F-score. Our method shows consistent improvement over the previous methods and biological validation has been done to elucidate the relation of the selected genes and pathway with the phenotype under study.
    Matched MeSH terms: Microarray Analysis
  4. Fulltext G3 assisted rational design of chemical sensor array using carbonitrile neutral receptors
    Rosli AN, Bakar MA, Manan NS, Woi PM, Lee VS, Zain SM, et al.
    Sensors (Basel), 2013;13(10):13835-60.
    PMID: 24129020 DOI: 10.3390/s131013835
    Combined computational and experimental strategies for the systematic design of chemical sensor arrays using carbonitrile neutral receptors are presented. Binding energies of acetonitrile, n-pentylcarbonitrile and malononitrile with Ca(II), Mg(II), Be(II) and H⁺ have been investigated with the B3LYP, G3, CBS-QB3, G4 and MQZVP methods, showing a general trend H⁺ > Be(II) > Mg(II) > Ca(II). Hydrogen bonding, donor-acceptor and cation-lone pair electron simple models were employed in evaluating the performance of computational methods. Mg(II) is bound to acetonitrile in water by 12.5 kcal/mol, and in the gas phase the receptor is more strongly bound by 33.3 kcal/mol to Mg(II) compared to Ca(II). Interaction of bound cations with carbonitrile reduces the energies of the MOs involved in the proposed σ-p conjugated network. The planar malononitrile-Be(II) complex possibly involves a π-network with a cationic methylene carbon. Fabricated potentiometric chemical sensors show distinct signal patterns that can be exploited in sensor array applications.
    Matched MeSH terms: Microarray Analysis/instrumentation*
  5. Long term mesenchymal stem cell culture on a defined synthetic substrate with enzyme free passaging
    Duffy CR, Zhang R, How SE, Lilienkampf A, De Sousa PA, Bradley M
    Biomaterials, 2014 Jul;35(23):5998-6005.
    PMID: 24780167 DOI: 10.1016/j.biomaterials.2014.04.013
    Mesenchymal stems cells (MSCs) are currently the focus of numerous therapeutic approaches in tissue engineering/repair because of their wide multi-lineage potential and their ability to modulate the immune system response following transplantation. Culturing these cells, while maintaining their multipotency in vitro, currently relies on biological substrates such as gelatin, collagen and fibronectin. In addition, harvesting cells from these substrates requires enzymatic or chemical treatment, a process that will remove a multitude of cellular surface proteins, clearly an undesirable process if cells are to be used therapeutically. Herein, we applied a high-throughput 'hydrogel microarray' screening approach to identify thermo-modulatable substrates which can support hES-MP and ADMSC growth, permit gentle reagent free passaging, whilst maintaining multi-lineage potential. In summary, the hydrogel substrate identified, poly(AEtMA-Cl-co-DEAA) cross-linked with MBA, permitted MSCs to be maintained over 10 passages (each time via thermo-modulation), with the cells retaining expression of MSC associated markers and lineage potency. This chemically defined system allowed the passaging and maintenance of cellular phenotype of this clinically important cell type, in the absence of harsh passaging and the need for biological substrates.
    Matched MeSH terms: Microarray Analysis/instrumentation
  6. Fulltext LGR5 Activates Noncanonical Wnt Signaling and Inhibits Aldosterone Production in the Human Adrenal
    Shaikh LH, Zhou J, Teo AE, Garg S, Neogi SG, Figg N, et al.
    J Clin Endocrinol Metab, 2015 Jun;100(6):E836-44.
    PMID: 25915569 DOI: 10.1210/jc.2015-1734
    CONTEXT: Aldosterone synthesis and cellularity in the human adrenal zona glomerulosa (ZG) is sparse and patchy, presumably due to salt excess. The frequency of somatic mutations causing aldosterone-producing adenomas (APAs) may be a consequence of protection from cell loss by constitutive aldosterone production.

    OBJECTIVE: The objective of the study was to delineate a process in human ZG, which may regulate both aldosterone production and cell turnover.

    DESIGN: This study included a comparison of 20 pairs of ZG and zona fasciculata transcriptomes from adrenals adjacent to an APA (n = 13) or a pheochromocytoma (n = 7).

    INTERVENTIONS: Interventions included an overexpression of the top ZG gene (LGR5) or stimulation by its ligand (R-spondin-3).

    MAIN OUTCOME MEASURES: A transcriptome profile of ZG and zona fasciculata and aldosterone production, cell kinetic measurements, and Wnt signaling activity of LGR5 transfected or R-spondin-3-stimulated cells were measured.

    RESULTS: LGR5 was the top gene up-regulated in ZG (25-fold). The gene for its cognate ligand R-spondin-3, RSPO3, was 5-fold up-regulated. In total, 18 genes associated with the Wnt pathway were greater than 2-fold up-regulated. ZG selectivity of LGR5, and its absence in most APAs, were confirmed by quantitative PCR and immunohistochemistry. Both R-spondin-3 stimulation and LGR5 transfection of human adrenal cells suppressed aldosterone production. There was reduced proliferation and increased apoptosis of transfected cells, and the noncanonical activator protein-1/Jun pathway was stimulated more than the canonical Wnt pathway (3-fold vs 1.3-fold). ZG of adrenal sections stained positive for apoptosis markers.

    CONCLUSION: LGR5 is the most selectively expressed gene in human ZG and reduces aldosterone production and cell number. Such conditions may favor cells whose somatic mutation reverses aldosterone inhibition and cell loss.

    Matched MeSH terms: Microarray Analysis
  7. Fulltext Phenotype microarrays reveal metabolic dysregulations of neurospheres derived from embryonic Ts1Cje mouse model of Down syndrome
    Seth EA, Lee HC, Yusof HHBM, Nordin N, Cheah YK, Ho ETW, et al.
    PLoS One, 2020;15(7):e0236826.
    PMID: 32730314 DOI: 10.1371/journal.pone.0236826
    Down syndrome (DS), is the most common cause of intellectual disability, and is characterized by defective neurogenesis during perinatal development. To identify metabolic aberrations in early neurogenesis, we profiled neurospheres derived from the embryonic brain of Ts1Cje, a mouse model of Down syndrome. High-throughput phenotypic microarray revealed a significant decrease in utilisation of 17 out of 367 substrates and significantly higher utilisation of 6 substrates in the Ts1Cje neurospheres compared to controls. Specifically, Ts1Cje neurospheres were less efficient in the utilisation of glucose-6-phosphate suggesting a dysregulation in the energy-producing pathway. T Cje neurospheres were significantly smaller in diameter than the controls. Subsequent preliminary study on supplementation with 6-phosphogluconic acid, an intermediate of glucose-6-phosphate metabolism, was able to rescue the Ts1Cje neurosphere size. This study confirmed the perturbed pentose phosphate pathway, contributing to defects observed in Ts1Cje neurospheres. We show for the first time that this comprehensive energetic assay platform facilitates the metabolic characterisation of Ts1Cje cells and confirmed their distinguishable metabolic profiles compared to the controls.
    Matched MeSH terms: Microarray Analysis
  8. Fulltext Persistent Newcastle disease virus infection in bladder cancer cells is associated with putative pro-survival and anti-viral transcriptomic changes
    Chan LC, Kalyanasundram J, Leong SW, Masarudin MJ, Veerakumarasivam A, Yusoff K, et al.
    BMC Cancer, 2021 May 27;21(1):625.
    PMID: 34044804 DOI: 10.1186/s12885-021-08345-y
    BACKGROUND: Newcastle disease virus (NDV) is an oncolytic virus with excellent selectivity against cancer cells, both in vitro and in vivo. Unfortunately, prolonged in vitro NDV infection results in the development of persistent infection in the cancer cells which are then able to resist NDV-mediated oncolysis. However, the mechanism of persistency of infection remains poorly understood.

    METHODS: In this study, we established persistently NDV-infected EJ28 bladder cancer cells, designated as EJ28P. Global transcriptomic analysis was subsequently carried out by microarray analysis. Differentially expressed genes (DEGs) between EJ28 and EJ28P cells identified by the edgeR program were further analysed by Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) analyses. In addition, the microarray data were validated by RT-qPCR.

    RESULTS: Persistently NDV-infected EJ28 bladder cancer cells were successfully established and confirmed by flow cytometry. Microarray analysis identified a total of 368 genes as differentially expressed in EJ28P cells when compared to the non-infected EJ28 cells. GSEA revealed that the Wnt/β-catenin and KRAS signalling pathways were upregulated while the TGF-β signalling pathway was downregulated. Findings from this study suggest that the upregulation of genes that are associated with cell growth, pro-survival, and anti-apoptosis may explain the survivability of EJ28P cells and the development of persistent infection of NDV.

    CONCLUSIONS: This study provides insights into the transcriptomic changes that occur and the specific signalling pathways that are potentially involved in the development and maintenance of NDV persistency of infection in bladder cancer cells. These findings warrant further investigation and is crucial towards the development of effective NDV oncolytic therapy against cancer.

    Matched MeSH terms: Microarray Analysis
  9. Fulltext Microarray Profiling of Differentially Expressed Genes in Coronary Artery Bypass Grafts of High-Risk Patients with Postoperative Cognitive Dysfunctions
    Yazit NAA, Juliana N, Kadiman S, Hafidz KM, Mohd Fahmi Teng NI, Abdul Hamid N, et al.
    Int J Environ Res Public Health, 2023 Jan 13;20(2).
    PMID: 36674212 DOI: 10.3390/ijerph20021457
    Postoperative cognitive dysfunction (POCD) is cognitive decline after surgery. The authors hypothesized that gene-level changes could be involved in the pathogenesis of POCD. The present study evaluated the incidence of POCD and its associated differentially expressed genes. This was a prospective cohort study conducted on high-risk coronary artery bypass graft patients aged 40 to 75 years. POCD classification was based on a one standard deviation decline in the postoperative scores compared to the preoperative scores. The differentially expressed genes were identified using microarray analysis and validated using quantitative RT-PCR. Forty-six patients were recruited and completed the study. The incidence of POCD was identified using a set of neurocognitive assessments and found to be at 17% in these high-risk CABG patients. Six samples were selected for the gene expression analyses (3 non-POCD and 3 POCD samples). The findings showed five differentially expressed genes in the POCD group compared to the non-POCD group. The upregulated gene was ERFE, whereas the downregulated genes were KIR2DS2, KIR2DS3, KIR3DL2, and LIM2. According to the results, the gene expression profiles of POCD can be used to find potential proteins for POCD diagnostic and predictive biomarkers. Understanding the molecular mechanism of POCD development will further lead to early detection and intervention to reduce the severity of POCD, and hence, reduce the mortality and morbidity rate due to the condition.
    Matched MeSH terms: Microarray Analysis
  10. Fulltext Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
    Michailidou K, Beesley J, Lindstrom S, Canisius S, Dennis J, Lush MJ, et al.
    Nat Genet, 2015 Apr;47(4):373-80.
    PMID: 25751625 DOI: 10.1038/ng.3242
    Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.
    Matched MeSH terms: Microarray Analysis
  11. Fulltext Feature selection methods: case of filter and wrapper approaches for maximising classification accuracy
    Wah, Yap Bee, Nurain Ibrahim, Hamzah Abdul Hamid, Shuzlina Abdul-Rahman, Fong, Simon
    Pertanika Journal of Science & Technology, 2018;26(1):329-340.
    MyJurnal
    Feature selection has been widely applied in many areas such as classification of spam emails, cancer cells, fraudulent claims, credit risk, text categorisation and DNA microarray analysis. Classification involves building predictive models to predict the target variable based on several input variables (features). This study compares filter and wrapper feature selection methods to maximise the classifier accuracy. The logistic regression was used as a classifier while the performance of the feature selection methods was based on the classification accuracy, Akaike information criteria (AIC), Bayesian information criteria (BIC), Area Under Receiver operator curve (AUC), as well as sensitivity and specificity of the classifier. The simulation study involves generating data for continuous features and one binary dependent variable for different sample sizes. The filter methods used are correlation based feature selection and information gain, while the wrapper methods are sequential forward and sequential backward elimination. The simulation was carried out using R, an open-source programming language. Simulation results showed that the wrapper method (sequential forward selection and sequential backward elimination) methods were better than the filter method in selecting the correct features.
    Matched MeSH terms: Microarray Analysis
  12. Gene expression in human oral squamous cell carcinoma is influenced by risk factor exposure
    Cheong SC, Chandramouli GV, Saleh A, Zain RB, Lau SH, Sivakumaren S, et al.
    Oral Oncol, 2009 Aug;45(8):712-9.
    PMID: 19147396 DOI: 10.1016/j.oraloncology.2008.11.002
    Oral squamous cell carcinoma (OSCC) is a world health problem and is associated with exposure to different risk factors. In the west, smoking and alcohol consumption are considered to be the main risk factors whilst in India and southeast Asia, betel quid (BQ) chewing is predominant. In this study, we compared the gene expression patterns of oral cancers associated with BQ chewing to those caused by smoking using Affymetrix microarrays. We found that 281 genes were differentially expressed between OSCC and normal oral mucosa regardless of aetiological factors including MMP1, PLAU, MAGE-D4, GNA12, IFITM3 and NMU. Further, we identified 168 genes that were differentially expressed between the BQ and smoking groups including CXCL-9, TMPRSS2, CA12 and RNF24. The expression of these genes was validated using qPCR using independent tissue samples. The results demonstrate that whilst common genes/pathways contribute to the development of oral cancer, there are also other gene expression changes that are specific to certain risk factors. The findings suggest that different carcinogens activate or inhibit specific pathways during cancer development and progression. These unique gene expression profiles should be taken into consideration when developing biomarkers for future use in prognostic or therapeutic applications.
    Matched MeSH terms: Microarray Analysis
  13. Fulltext Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population
    Mohamad Shah NS, Salahshourifar I, Sulong S, Wan Sulaiman WA, Halim AS
    BMC Genet, 2016 Feb 11;17:39.
    PMID: 26868259 DOI: 10.1186/s12863-016-0345-x
    BACKGROUND: Nonsyndromic orofacial clefts are one of the most common birth defects worldwide. It occurs as a result of genetic or environmental factors. This study investigates the genetic contribution to nonsyndromic cleft lip and/or palate through the analysis of family pedigrees. Candidate genes associated with the condition were identified from large extended families from the Malay population.

    RESULTS: A significant nonparametric linkage (NPL) score was detected in family 100. Other suggestive NPL and logarithm of the odds (LOD) scores were attained from families 50, 58, 99 and 100 under autosomal recessive mode. Heterogeneity LOD (HLOD) score ≥ 1 was determined for all families, confirming genetic heterogeneity of the population and indicating that a proportion of families might be linked to each other. Several candidate genes in linkage intervals were determined; LPHN2 at 1p31, SATB2 at 2q33.1-q35, PVRL3 at 3q13.3, COL21A1 at 6p12.1, FOXP2 at 7q22.3-q33, FOXG1 and HECTD1 at 14q12 and TOX3 at 16q12.1.

    CONCLUSIONS: We have identified several novel and known candidate genes for nonsyndromic cleft lip and/or palate through genome-wide linkage analysis. Further analysis of the involvement of these genes in the condition will shed light on the disease mechanism. Comprehensive genetic testing of the candidate genes is warranted.

    Matched MeSH terms: Microarray Analysis
  14. Fulltext NFIX as a Master Regulator for Lung Cancer Progression
    Rahman NIA, Abdul Murad NA, Mollah MM, Jamal R, Harun R
    Front Pharmacol, 2017;8:540.
    PMID: 28871224 DOI: 10.3389/fphar.2017.00540
    About 40% of lung cancer cases globally are diagnosed at the advanced stage. Lung cancer has a high mortality and overall survival in stage I disease is only 70%. This study was aimed at finding a candidate of transcription regulator that initiates the mechanism for metastasis by integrating computational and functional studies. The genes involved in lung cancer were retrieved using in silico software. 10 kb promoter sequences upstream were scanned for the master regulator. Transient transfection of shRNA NFIXs were conducted against A549 and NCI-H1299 cell lines. qRT-PCR and functional assays for cell proliferation, migration and invasion were carried out to validate the involvement of NFIX in metastasis. Genome-wide gene expression microarray using a HumanHT-12v4.0 Expression BeadChip Kit was performed to identify differentially expressed genes and construct a new regulatory network. The in silico analysis identified NFIX as a master regulator and is strongly associated with 17 genes involved in the migration and invasion pathways including IL6ST, TIMP1 and ITGB1. Silencing of NFIX showed reduced expression of IL6ST, TIMP1 and ITGB1 as well as the cellular proliferation, migration and invasion processes. The data was integrated with the in silico analyses to find the differentially expressed genes. Microarray analysis showed that 18 genes were expressed differentially in both cell lines after statistical analyses integration between t-test, LIMMA and ANOVA with Benjamini-Hochberg adjustment at p-value < 0.05. A transcriptional regulatory network was created using all 18 genes, the existing regulated genes including the new genes PTCH1, NFAT5 and GGCX that were found highly associated with NFIX, the master regulator of metastasis. This study suggests that NFIX is a promising target for therapeutic intervention that is expected to inhibit metastatic recurrence and improve survival rate.
    Matched MeSH terms: Microarray Analysis
  15. MicroRNAs associated with tumour migration, invasion and angiogenic properties in A549 and SK-Lu1 human lung adenocarcinoma cells
    Ho CS, Yap SH, Phuah NH, In LL, Hasima N
    Lung Cancer, 2014 Feb;83(2):154-62.
    PMID: 24360396 DOI: 10.1016/j.lungcan.2013.11.024
    Dysregulation in miRNA expression contributes towards the initiation and progression of metastasis by regulating multiple target genes. In this study, variations in miRNA expression profiles were investigated between high and low invasive NSCLC cell lines followed by identification of miRNAs with targets governing NSCLC's metastatic potential.
    Matched MeSH terms: Microarray Analysis
  16. Fulltext Unsupervised Network Analysis of the Plastic Supraoptic Nucleus Transcriptome Predicts Caprin2 Regulatory Interactions
    Loh SY, Jahans-Price T, Greenwood MP, Greenwood M, Hoe SZ, Konopacka A, et al.
    eNeuro, 2017 12 21;4(6).
    PMID: 29279858 DOI: 10.1523/ENEURO.0243-17.2017
    The supraoptic nucleus (SON) is a group of neurons in the hypothalamus responsible for the synthesis and secretion of the peptide hormones vasopressin and oxytocin. Following physiological cues, such as dehydration, salt-loading and lactation, the SON undergoes a function related plasticity that we have previously described in the rat at the transcriptome level. Using the unsupervised graphical lasso (Glasso) algorithm, we reconstructed a putative network from 500 plastic SON genes in which genes are the nodes and the edges are the inferred interactions. The most active nodal gene identified within the network was Caprin2. Caprin2 encodes an RNA-binding protein that we have previously shown to be vital for the functioning of osmoregulatory neuroendocrine neurons in the SON of the rat hypothalamus. To test the validity of the Glasso network, we either overexpressed or knocked down Caprin2 transcripts in differentiated rat pheochromocytoma PC12 cells and showed that these manipulations had significant opposite effects on the levels of putative target mRNAs. These studies suggest that the predicative power of the Glasso algorithm within an in vivo system is accurate, and identifies biological targets that may be important to the functional plasticity of the SON.
    Matched MeSH terms: Microarray Analysis
  17. Fulltext Dielectrophoretic manipulation and separation of microparticles using microarray dot electrodes
    Yafouz B, Kadri NA, Ibrahim F
    Sensors (Basel), 2014;14(4):6356-69.
    PMID: 24705632 DOI: 10.3390/s140406356
    This paper introduces a dielectrophoretic system for the manipulation and separation of microparticles. The system is composed of five layers and utilizes microarray dot electrodes. We validated our system by conducting size-dependent manipulation and separation experiments on 1, 5 and 15 μm polystyrene particles. Our findings confirm the capability of the proposed device to rapidly and efficiently manipulate and separate microparticles of various dimensions, utilizing positive and negative dielectrophoresis (DEP) effects. Larger size particles were repelled and concentrated in the center of the dot by negative DEP, while the smaller sizes were attracted and collected by the edge of the dot by positive DEP.
    Matched MeSH terms: Microarray Analysis/instrumentation; Microarray Analysis/methods*
  18. Topologically significant directed random walk with applied walker network in cancer environment
    Seah CS, Kasim S, Saedudin RR, Md Fudzee MF, Mohamad MS, Hassan R, et al.
    Pak J Pharm Sci, 2019 May;32(3 Special):1395-1408.
    PMID: 31551221
    Numerous cancer studies have combined different datasets for the prognosis of patients. This study incorporated four networks for significant directed random walk (sDRW) to predict cancerous genes and risk pathways. The study investigated the feasibility of cancer prediction via different networks. In this study, multiple micro array data were analysed and used in the experiment. Six gene expression datasets were applied in four networks to study the effectiveness of the networks in sDRW in terms of cancer prediction. The experimental results showed that one of the proposed networks is outstanding compared to other networks. The network is then proposed to be implemented in sDRW as a walker network. This study provides a foundation for further studies and research on other networks. We hope these finding will improve the prognostic methods of cancer patients.
    Matched MeSH terms: Microarray Analysis
  19. Fulltext An enhanced topologically significant directed random walk in cancer classification using gene expression datasets
    Seah CS, Kasim S, Fudzee MFM, Law Tze Ping JM, Mohamad MS, Saedudin RR, et al.
    Saudi J Biol Sci, 2017 Dec;24(8):1828-1841.
    PMID: 29551932 DOI: 10.1016/j.sjbs.2017.11.024
    Microarray technology has become one of the elementary tools for researchers to study the genome of organisms. As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analysis, cancerous classification is an emerging important trend. Significant directed random walk is proposed as one of the cancerous classification approach which have higher sensitivity of risk gene prediction and higher accuracy of cancer classification. In this paper, the methodology and material used for the experiment are presented. Tuning parameter selection method and weight as parameter are applied in proposed approach. Gene expression dataset is used as the input datasets while pathway dataset is used to build a directed graph, as reference datasets, to complete the bias process in random walk approach. In addition, we demonstrate that our approach can improve sensitive predictions with higher accuracy and biological meaningful classification result. Comparison result takes place between significant directed random walk and directed random walk to show the improvement in term of sensitivity of prediction and accuracy of cancer classification.
    Matched MeSH terms: Microarray Analysis
  20. Fulltext Gene expression profiles in human HepG2 cells treated with extracts of the Tamarindus indica fruit pulp
    Razali N, Aziz AA, Junit SM
    Genes Nutr, 2010 Dec;5(4):331-41.
    PMID: 21189869 DOI: 10.1007/s12263-010-0187-5
    Tamarindus indicaL. (T. indica) or locally known as asam jawa belongs to the family of Leguminosae. The fruit pulp had been reported to have antioxidant activities and possess hypolipidaemic effects. In this study, we attempted to investigate the gene expression patterns in human hepatoma HepG2 cell line in response to treatment with low concentration of the fruit pulp extracts. Microarray analysis using Affymetrix Human Genome 1.0 S.T arrays was used in the study. Microarray data were validated using semi-quantitative RT-PCR and real-time RT-PCR. Amongst the significantly up-regulated genes were those that code for the metallothioneins (MT1M, MT1F, MT1X) and glutathione S-transferases (GSTA1, GSTA2, GST02) that are involved in stress response. APOA4, APOA5, ABCG5 and MTTP genes were also significantly regulated that could be linked to hypolipidaemic activities of the T. indica fruit pulp.
    Matched MeSH terms: Microarray Analysis
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