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Using fuzzy association rule mining in cancer classification

Mahmoodian H, Hamiruce Marhaban M, Abdulrahim R, Rosli R, Saripan I

Australas Phys Eng Sci Med, 2011 Apr;34(1):41-54.
PMID: 21327594 DOI: 10.1007/s13246-011-0054-8

The classification of the cancer tumors based on gene expression profiles has been extensively studied in numbers of studies. A wide variety of cancer datasets have been implemented by the various methods of gene selection and classification to identify the behavior of the genes in tumors and find the relationships between them and outcome of diseases. Interpretability of the model, which is developed by fuzzy rules and linguistic variables in this study, has been rarely considered. In addition, creating a fuzzy classifier with high performance in classification that uses a subset of significant genes which have been selected by different types of gene selection methods is another goal of this study. A new algorithm has been developed to identify the fuzzy rules and significant genes based on fuzzy association rule mining. At first, different subset of genes which have been selected by different methods, were used to generate primary fuzzy classifiers separately and then proposed algorithm was implemented to mix the genes which have been associated in the primary classifiers and generate a new classifier. The results show that fuzzy classifier can classify the tumors with high performance while presenting the relationships between the genes by linguistic variables.

Matched MeSH terms: Neoplasm Proteins/analysis*
Proteomics of Grade 3 infiltrating ductal carcinoma in Malaysian Chinese breast cancer patients

Othman MI, Majid MI, Singh M, Subathra S, Seng L, Gam LH

Biotechnol Appl Biochem, 2009 Mar;52(Pt 3):209-19.
PMID: 18564057 DOI: 10.1042/BA20070271

Breast cancer is the leading cause of cancer-related mortality and morbidity among women worldwide and IDC (infiltrating ductal carcinoma) is the most common type of invasive breast cancer. The changes in the biological behaviour of cancer tissue can be predicted by measuring the differential protein expression of normal and cancerous tissues. Using a combination of SDS/PAGE and LC (liquid chromatography)-MS/MS (tandem MS), we identified 82 common and differentially expressed proteins from normal and cancerous breast tissues in 20 Malaysian Chinese patients with IDC. These proteins are extracted from the normal and cancerous tissue of patients and therefore represent the actual proteins involved in cancer development. Proteins identified possibly have significant roles in the development of breast cancer in Malaysian Chinese patients in view of their consistent expression in most of the patients, although some of the proteins had not been detected in earlier studies that were mostly carried out in Western countries. This observation suggests that molecular mechanisms leading to breast cancer development in this region may not be identical with those leading to IDC in Western regions.

Matched MeSH terms: Neoplasm Proteins/analysis*
Fulltext Survivin expression correlates with unfavourable prognoses in invasive ductal carcinoma of the breast

Al-Joudi FS, Iskandar ZA, Imran AK

Med J Malaysia, 2007 Mar;62(1):6-8.
PMID: 17682561 MyJurnal

Survivin is a 16.5-kDa intracellular protein also known as AP14 or BIRC5. It inhibits apoptosis and regulates cell division and belongs to the inhibitors of apoptosis (IAP) gene family. In the majority of neoplasms investigated for survivin expression, high levels of the IAP proteins were predictive of tumour progression, either in terms of disease-free survival or overall survival, thus providing significant prognostic information. Hence, the prognostic value of survivin expression in tumour masses of invasive ductal carcinoma has been investigated. It was found that negative and low expression of survivin correlated significantly with favourable outcomes. Conversely, high expression correlated with unfavourable outcomes. The five-year survival rate was higher among the cases with low and negative survivin expression, compared to those with higher survivin expression. However, this correlation was found to be insignificant statistically. Furthermore, a statistical model has been devised to explain the combined effects of survivin expression and its sub-cellular localisation, p-53 expression and lymph nodal involvement, on the outcomes of these patients.

Matched MeSH terms: Neoplasm Proteins/analysis*
Fulltext Chemometrics of differentially expressed proteins from colorectal cancer patients

Yeoh LC, Dharmaraj S, Gooi BH, Singh M, Gam LH

World J Gastroenterol, 2011 Apr 28;17(16):2096-103.
PMID: 21547128 DOI: 10.3748/wjg.v17.i16.2096

To evaluate the usefulness of differentially expressed proteins from colorectal cancer (CRC) tissues for differentiating cancer and normal tissues.

Matched MeSH terms: Neoplasm Proteins/analysis*
Unusual granular cell odontogenic tumor. Report of two undescribed cases with features of granular cell ameloblastoma and plexiform granular cell odontogenic tumor

Siar CH, Ng KH

J Nihon Univ Sch Dent, 1993 Jun;35(2):134-8.
PMID: 7692017

Granular cell ameloblastoma (GCA) is a well recognized variant of follicular ameloblastoma with extensive granular cell change. In contrast, plexiform granular cell odontogenic tumor (PGCOT) is a rare and recently described lesion characterized histologically by a monophasic plexiform pattern of granular cells. In this paper, two cases of an unusual granular cell odontogenic tumor exhibiting combined features of these two entities are described along with their immunohistochemical characteristics. The granular cells of both the GCA and PGCOT areas showed similar patterns of expression for keratin and S-100, which differed from those of typical ameloblastoma. No reactivity for desmin or vimentin was noted. The histomorphologic and immunohistochemical features of these hybrid tumors suggest that the granular cells present have a common origin, most probably the odontogenic epithelium.

Matched MeSH terms: Neoplasm Proteins/analysis*
Patterns of expression of intermediate filaments and S-100 protein in desmoplastic ameloblastoma

Siar CH, Ng KH

J Nihon Univ Sch Dent, 1993 Jun;35(2):104-8.
PMID: 7692015

Seventeen cases of desmoplastic ameloblastoma were examined immunohistochemically. Immunoperoxidase techniques were applied for detection of keratin, desmin, vimentin and S-100 protein expression in these tumors. The tumor epithelium of desmoplastic ameloblastoma exhibited weak, focal, inconstant keratin staining, weak, variable expression of S-100 protein, desmin immunoreactivity of mild to moderate intensity and vimentin non-reactivity. The pertinent literature on the immunohistochemistry of ameloblastomas is briefly reviewed.

Matched MeSH terms: Neoplasm Proteins/analysis*
Fulltext Expression of Ki-67, Cornulin and ISG15 in non-involved mucosal surgical margins as predictive markers for relapse in oral squamous cell carcinoma (OSCC)

Govindaraj PK, Kallarakkal TG, Mohd Zain R, Tilakaratne WM, Lew HL

PLoS One, 2021;16(12):e0261575.
PMID: 34941961 DOI: 10.1371/journal.pone.0261575

BACKGROUND: Local relapse of oral squamous cell carcinoma in non-involved mucosal surgical margins indicated possibility of field alteration in the margins, which could be predicted with certain biomarkers. The objectives were to evaluate the expression of Ki-67, Cornulin and ISG15 in non-involved mucosal surgical margins and the association of clinicopathological prognosticators with local relapse in oral squamous cell carcinoma.
METHODS: Surgical margins from the study (relapse) group (n = 23), control (non-relapse) group (n = 32) and normal oral mucosa (n = 5) were immunohistochemically stained using Ki-67, Cornulin and ISG15 antibodies. Association between expression of markers and clinicopathological prognosticators with local relapse in oral squamous cell carcinoma was analyzed statistically.
RESULTS: The study group surgical margins demonstrated significantly decreased Cornulin expression (p = 0.032). Low Cornulin expression was significantly associated with local relapse (p = 0.004) and non-tongue primary tumor (p = 0.013). Although not significantly associated with local relapse, expression of Ki-67 was significantly reduced in female patients (p = 0.041). Age above 57.5 years, Chinese & Indian ethnicity, alcohol consumption, epithelial dysplasia in surgical margins, and type III and IV patterns of invasion of tumor were also significantly related to local relapse. Regression analysis showed low expression of Cornulin (p = 0.018), and increased patient's age (p = 0.008) were predictors of local relapse in oral squamous cell carcinoma, with 34-fold risk and 18-fold risk, respectively. Expression of Ki-67 and ISG15 did not show significant association with local relapse in oral squamous cell carcinoma.
CONCLUSION: Low expression of Cornulin is an independent predictor of relapse in oral squamous cell carcinoma.

Matched MeSH terms: Neoplasm Proteins/analysis*
Fulltext Isolation, identification and quantification of differentially expressed proteins from cancerous and normal breast tissues

Othman MI, Majid MI, Singh M, Man CN, Lay-Harn G

Ann. Clin. Biochem., 2008 May;45(Pt 3):299-306.
PMID: 18482919 DOI: 10.1258/acb.2007.007104

Infiltrating ductal carcinoma (IDCA) is the most common type of breast cancer accounting for 85% of all invasive breast cancers.

Matched MeSH terms: Neoplasm Proteins/analysis
Antiatherogenic Potential of Extracts from the Gray Oyster Medicinal Mushroom, Pleurotus pulmonarius (Agaricomycetes), In Vitro

Abidin MHZ, Abdullah N, Abidin NZ

Int J Med Mushrooms, 2018;20(3):283-290.
PMID: 29717672 DOI: 10.1615/IntJMedMushrooms.2018025821

This study evaluates the in vitro inhibition of angiotensin-converting enzyme (ACE) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA) by Pleurotus pulmonarius extracts. The protective effect on the endothelial membrane against oxidative stress through the protection of nitric oxide bioavailability, as well as inhibition of endocan expression, was evaluated using human aortic endothelial cells (HAECs). Crude cold aqueous extract exhibited the most potent inhibitory activities against ACE and HMG-CoA reductase, with 61.79% and 44.30% inhibition, respectively. It also protected the bioavailability of NO released by HAECs, with 84.88% cell viability. The crude hot water extract was the most potent in inhibiting endocan expression, with 18.61% inhibition.

Matched MeSH terms: Neoplasm Proteins/analysis