Abstract Background MicroRNAs (miRNAs) are important post-transcriptional regulators that have been demonstrated to play an role in human diseases. Elucidating the associations between miRNAs and diseases at systematic level will deepen our understanding of molecular mechanisms However, miRNA-disease identified by previous computational methods far from completeness more effort is needed. Results We developed a framework identify performing random walk analysis, focused on functional link...

Recent studies have suggested that long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) and indirectly regulate miRNA targets though competing interactions. However, the molecular mechanisms underlying these interactions are still largely unknown. In this study, lncRNA-miRNA-gene were defined as lncRNA-associated triplets (LncACTs), an integrated pipeline was developed to identify lncACTs active in cancer. Competing lncRNAs had sponge features distinct from non-competing...

Two strategies are often adopted for enrichment analysis of pathways: the all differentially expressed (DE) genes together or up- and downregulated separately. However, few studies have examined rationales these strategies. Using both microarray RNA-seq data, we show that gene pairs with functional links in pathways tended to positively correlated expression levels, which could result an imbalance between particular pathways. We then greatly reduce statistical power finding...

Abstract Motivation: The differential expression analysis focusing on inter-group comparison can capture only differentially expressed genes (DE genes) at the population level, which may mask heterogeneity of in individuals. Thus, to provide patient-specific information for personalized medicine, it is necessary conduct individual level. Results: We proposed a method detect DE disease samples by using disrupted ordering samples. In both simulated data and real paired cancer-normal sample...

Deregulations of long non-coding RNAs (lncRNAs) have been implicated in cancer initiation and progression. Current methods can only capture differential expression lncRNAs at the population level ignore heterogeneous individual patients.We propose a method (LncRIndiv) to identify differentially expressed (DE) patients by exploiting disrupted ordering levels each disease sample comparison with stable normal ordering. LncRIndiv was applied lncRNA profiles lung adenocarcinoma (LUAD). Based on...

Most of current gene expression signatures for cancer prognosis are based on risk scores, usually calculated as some summaries levels the signature genes, whose applications require presetting score thresholds and data normalization. In this study, we demonstrate critical limitations such type that scores samples will change greatly when they normalized together with different samples, which would induce spurious classification difficulty in clinical settings, independent incomparable if...

In China, there were few studies about the pathogens of acute viral encephalitis and meningitis in children recent years. The aims this study to characterize etiology prognosis Chinese children.This was a multicentre prospective study. Two hundred sixty one patients 285 enrolled. mean age 5.88 ± 3.60 years 6.39 3.57 years, respectively. Real-time reverse transcription PCR multiplex used detect human enteroviruses herpes viruses cerebrospinal fluid (CSF) with or meningitis. enzyme-linked...

Colorectal cancer (CRC) is a common worldwide, and its treatment strategies are limited. The underlying mechanism of CRC progression remains to be determined. Telomere maintenance 2 (TELO2) mTOR‑interacting protein. Both the role molecular TELO2 in remain unknown. In this study, gene expression database normal tumor tissue, addition western blot analysis, immunohistochemistry (IHC) were used determine location tissues. Clinical features tissue array collected analyzed. WST‑1, soft agar, flow...

Abstract Background Development of robust and efficient methods for analyzing interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports the assumption that genes express perform their functions modular fashions cells. Therefore, there is an open space development timely relevant algorithms use functional towards precise classification complex human diseases at level. Results Inspired by insight act as...

Current high-throughput protein-protein interaction (PPI) data do not provide information about the condition(s) under which interactions occur. Thus, identification of condition-responsive PPI sub-networks is great importance for investigating how a living cell adapts to changing environments.In this article, we propose novel edge-based scoring and searching approach extract sub-network responsive conditions related some investigated gene expression profiles. Using approach, what...

Abstract Motivation: Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is believed that current small will largely introduce false discoveries. Results: Based on statistical model, we show even it likely the selected be inconsistent presence of measurement variations. Therefore, apparently...

Abstract Motivation: According to current consistency metrics such as percentage of overlapping genes (POG), lists differentially expressed (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas proteomics and metabolism. A is characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility discovery...

Autophagy is a process that degrades intracellular constituents, such as long‐lived or damaged proteins and organelles, to buffer metabolic stress under starvation conditions. Deregulation of autophagy involved in the progression cancer. However, predictive value for breast cancer prognosis remains unclear. First, based on gene expression profiling, we found genes were implicated Then, using Cox proportional hazard regression model, detected prognostic signature training dataset. We...

In high-throughput studies of diseases, terms enriched with disease-related genes based on Gene Ontology (GO) are routinely found. However, most current algorithms used to find significant GO cannot handle the redundancy that results from dependencies terms. Simply some numerical considerations, developed for reducing this may produce do not account biologically interesting cases. article, we present several rules design a tool called GO-function extracting relevant statistically disease....

Background and Aims : Cancer invasion metastasis may associate with the phenotype transition called epithelial-mesenchymal (EMT). We aim to evaluate impact of four-and-a-half LIM protein 2 (FHL2) on EMT colon cancer. Methods: The functional role FHL2 in was determined by overexpression or small interfering RNA-mediated depletion FHL2. Mechanisms expression activity E-cadherin β-catenin were assessed. Results: highly expressed primary metastatic cancer but not normal tissues. critical for...

Advanced gastric cancer (GC) has a poor prognosis and its treatment strategies are not very efficient. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) emerged as plausible GC marker, however the role molecular mechanism of hnRNPA1 in cell invasion migration remains unknown. In present study, gene expression across normal tumor tissue (GENT) database was used to evaluate mRNA various types cancer. Western blot analysis (WB) immunohistochemistry (IHC) were performed detect protein tissues...

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches.However, FFPE are usually considered an unreliable source gene expression analysis due to the partial RNA degradation.In this study, through comparing profiles between and paired fresh-frozen (FF) three cancer types, we firstly showed that measurements of thousands genes had at least two-fold change in compared with FF samples.Therefore, transcriptional signature based on risk scores...

It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals. We compared the measurements mRNA samples, 25 pg 1000 mRNA, which were amplified and profiled by Smart-seq, DP-seq CEL-seq techniques using Illumina HiSeq 2000 platform, with those paired high-input (50 ng) samples. Even input, we found that thousands genes had at least 2 folds-change levels in...

// Qingzhou Guan 1 , Rou Chen Haidan Yan Hao Cai You Guo 1, 2 Mengyao Li Xiangyu Mengsha Tong Lu Ao Hongdong Guini Hong Zheng Key Laboratory of Ministry Education for Gastrointestinal Cancer, Department Bioinformatics, Fujian Medical University, Fuzhou, 350001, China Preventive Medicine, School Basic Medicine Sciences, Gannan Ganzhou, 341000, Correspondence to: Guo, email: guoz@ems.hrbmu.edu.cn Hong, hongguini08@gmail.com Keywords: gene expression profiling, multiple platforms,...

Abstract Background It is one of the ultimate goals for modern biological research to fully elucidate intricate interplays and regulations molecular determinants that propel characterize progression versatile life phenomena, name a few, cell cycling, developmental biology, aging, progressive recurrent pathogenesis complex diseases. The vast amount large-scale genome-wide time-resolved data becoming increasing available, which provides golden opportunity unravel challenging...

// Jun Cheng 1 , You Guo 1, 2 Qiao Gao 3 Hongdong Li Haidan Yan Mengyao Hao Cai Weicheng Zheng Xiangyu Weizhong Jiang Department of Bioinformatics, Key Laboratory Ministry Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350001, China Preventive Medicine, School Basic Medicine Sciences, Gannan Ganzhou, 341000, Colorectal Surgery, University Union Hospital, Correspondence to: Guo, email: guoz@ems.hrbmu.edu.cn Jiang, jiangwz362100@163.com Keywords: the proportions...

5-Fluorouracil (5-FU)-based chemotherapy is currently the first-line treatment for gastric cancer. In this study, using gene expression profiles a panel of cell lines with drug sensitivity data and two cohorts patients, we extracted signature consisting pairs (KCNE2 API5, KCNE2 PRPF3) whose within-sample relative orderings (REOs) could robustly predict prognoses cancer patients treated 5-FU-based chemotherapy. This REOs-based was insensitive to experimental batch effects be directly applied...