Abstract: Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.
Abstract: Gene expression profiling is rapidly evolving into a
powerful technique for investigating tumor malignancies. The
researchers are overwhelmed with the microarray-based platforms
and methods that confer them the freedom to conduct large-scale
gene expression profiling measurements. Simultaneously,
investigations into cross-platform integration methods have started
gaining momentum due to their underlying potential to help
comprehend a myriad of broad biological issues in tumor diagnosis,
prognosis, and therapy. However, comparing results from different
platforms remains to be a challenging task as various inherent
technical differences exist between the microarray platforms. In this
paper, we explain a simple ratio-transformation method, which can
provide some common ground for cDNA and Affymetrix platform
towards cross-platform integration. The method is based on the
characteristic data attributes of Affymetrix- and cDNA- platform. In
the work, we considered seven childhood leukemia patients and their
gene expression levels in either platform. With a dataset of 822
differentially expressed genes from both these platforms, we carried
out a specific ratio-treatment to Affymetrix data, which subsequently
showed an improvement in the relationship with the cDNA data.
Abstract: Cancers could normally be marked by a number of
differentially expressed genes which show enormous potential as
biomarkers for a certain disease. Recent years, cancer classification
based on the investigation of gene expression profiles derived by
high-throughput microarrays has widely been used. The selection of
discriminative genes is, therefore, an essential preprocess step in
carcinogenesis studies. In this paper, we have proposed a novel gene
selector using information-theoretic measures for biological
discovery. This multivariate filter is a four-stage framework through
the analyses of feature relevance, feature interdependence, feature
redundancy-dependence and subset rankings, and having been
examined on the colon cancer data set. Our experimental result show
that the proposed method outperformed other information theorem
based filters in all aspect of classification errors and classification
performance.