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: Over the past decade, there has been a steep rise in
the data-driven analysis in major areas of medicine, such as clinical
decision support system, survival analysis, patient similarity analysis,
image analytics etc. Most of the data in the field are well-structured
and available in numerical or categorical formats which can be used
for experiments directly. But on the opposite end of the spectrum,
there exists a wide expanse of data that is intractable for direct
analysis owing to its unstructured nature which can be found in the
form of discharge summaries, clinical notes, procedural notes which
are in human written narrative format and neither have any relational
model nor any standard grammatical structure. An important step
in the utilization of these texts for such studies is to transform
and process the data to retrieve structured information from the
haystack of irrelevant data using information retrieval and data mining
techniques. To address this problem, the authors present Q-Map in
this paper, which is a simple yet robust system that can sift through
massive datasets with unregulated formats to retrieve structured
information aggressively and efficiently. It is backed by an effective
mining technique which is based on a string matching algorithm
that is indexed on curated knowledge sources, that is both fast
and configurable. The authors also briefly examine its comparative
performance with MetaMap, one of the most reputed tools for medical
concepts retrieval and present the advantages the former displays over
the latter.
Abstract: Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.
Abstract: In this paper we propose a mixture of two different
distributions such as Exponential-Gamma, Exponential-Weibull and
Gamma-Weibull to model heterogeneous survival data. Various
properties of the proposed mixture of two different distributions are
discussed. Maximum likelihood estimations of the parameters are
obtained by using the EM algorithm. Illustrative example based on
real data are also given.
Abstract: Heart failure is the most common reason of death
nowadays, but if the medical help is given directly, the patient-s life
may be saved in many cases. Numerous heart diseases can be
detected by means of analyzing electrocardiograms (ECG). Artificial
Neural Networks (ANN) are computer-based expert systems that
have proved to be useful in pattern recognition tasks. ANN can be
used in different phases of the decision-making process, from
classification to diagnostic procedures. This work concentrates on a
review followed by a novel method.
The purpose of the review is to assess the evidence of healthcare
benefits involving the application of artificial neural networks to the
clinical functions of diagnosis, prognosis and survival analysis, in
ECG signals. The developed method is based on a compound neural
network (CNN), to classify ECGs as normal or carrying an
AtrioVentricular heart Block (AVB). This method uses three
different feed forward multilayer neural networks. A single output
unit encodes the probability of AVB occurrences. A value between 0
and 0.1 is the desired output for a normal ECG; a value between 0.1
and 1 would infer an occurrence of an AVB. The results show that
this compound network has a good performance in detecting AVBs,
with a sensitivity of 90.7% and a specificity of 86.05%. The accuracy
value is 87.9%.