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Cmap drug

Alvin Z Yu, Stephen A Ramsey
We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug being the difference of the two enrichment scores...
October 24, 2016: Interdisciplinary Sciences, Computational Life Sciences
Rama Raghavan, Stephen Hyter, Harsh B Pathak, Andrew K Godwin, Gottfried Konecny, Chen Wang, Ellen L Goode, Brooke L Fridley
BACKGROUND: Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer death among women in the United States (5 % of cancer deaths). The standard treatment for patients with advanced EOC is initial debulking surgery followed by carboplatin-paclitaxel combination chemotherapy. Unfortunately, with chemotherapy most patients relapse and die resulting in a five-year overall survival around 45 %. Thus, finding novel therapeutics for treating EOC is essential. Connectivity Mapping (CMAP) has been used widely in cancer drug discovery and generally has relied on cancer cell line gene expression and drug phenotype data...
October 19, 2016: BMC Genomics
Liming Wang, L Zhu, R Luan, L Wang, J Fu, X Wang, L Sui
Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language...
October 10, 2016: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C Kok, Yi Chung, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Chi-Ying F Huang, Ka-Lok Ng
BACKGROUND: Abnormal proliferation of vascular smooth muscle cells (VSMC) is a major cause of cardiovascular diseases (CVDs). Many studies suggest that vascular injury triggers VSMC dedifferentiation, which results in VSMC changes from a contractile to a synthetic phenotype; however, the underlying molecular mechanisms are still unclear. METHODS: In this study, we examined how VSMC responds under mechanical stress by using time-course microarray data. A three-phase study was proposed to investigate the stress-induced differentially expressed genes (DEGs) in VSMC...
2016: PeerJ
Lei Ren, Dafei Xie, Peng Li, Xinyan Qu, Xiujuan Zhang, Yaling Xing, Pingkun Zhou, Xiaochen Bo, Zhe Zhou, Shengqi Wang
Exposure to ionizing radiation causes damage to living tissues; however, only a small number of agents have been approved for use in radiation injuries. Radioprotector is the primary countermeasure to radiation injury and none radioprotector has indeed reached the drug development stage. Repurposing the long list of approved, non-radioprotective drugs is an attractive strategy to find new radioprotective agents. Here, we applied a computational approach to discover new radioprotectors in silico by comparing publicly available gene expression data of ionizing radiation-treated samples from the Gene Expression Omnibus (GEO) database with gene expression signatures of more than 1309 small-molecule compounds from the Connectivity Map (cmap) dataset...
September 21, 2016: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
Faycal Guedj, Jeroen LA Pennings, Lauren J Massingham, Heather C Wick, Ashley E Siegel, Umadevi Tantravahi, Diana W Bianchi
Anatomical and functional brain abnormalities begin during fetal life in Down syndrome (DS). We hypothesize that novel prenatal treatments can be identified by targeting signaling pathways that are consistently perturbed in cell types/tissues obtained from human fetuses with DS and mouse embryos. We analyzed transcriptome data from fetuses with trisomy 21, age and sex-matched euploid controls, and embryonic day 15.5 forebrains from Ts1Cje, Ts65Dn, and Dp16 mice. The new datasets were compared to other publicly available datasets from humans with DS...
2016: Scientific Reports
Lei Liu, Maria Tsompana, Yong Wang, Dingfeng Wu, Lixin Zhu, Ruixin Zhu
Drug discovery and development is a costly and time-consuming process with a high risk for failure resulting primarily from a drug's associated clinical safety and efficacy potential. Identifying and eliminating inapt candidate drugs as early as possible is an effective way for reducing unnecessary costs, but limited analytical tools are currently available for this purpose. Recent growth in the area of toxicogenomics and pharmacogenomics has provided with a vast amount of drug expression microarray data. Web servers such as CMap and LTMap have used this information to evaluate drug toxicity and mechanisms of action independently; however, their wider applicability has been limited by the lack of a combinatorial drug-safety type of analysis...
September 26, 2016: Journal of Chemical Information and Modeling
Meiyue Song, Zhenran Jiang
Emergence of compound molecular data coupled to pathway information offers the possibility of using machine learning methods for compound-pathway associations' inference. To provide insights into the global relationship between compounds and their affected pathways, a improved Rotation Forest ensemble learning method called RGRF (Relief & GBSSL - Rotation Forest) was proposed to predict their potential associations. The main characteristic of the RGRF lies in using the Relief algorithm for feature extraction and regarding the Graph-Based Semi-Supervised Learning method as classifier...
November 2015: Molecular Informatics
F Bonfiglio, P G Hysi, W Ek, V Karhunen, N V Rivera, M Männikkö, H Nordenstedt, M Zucchelli, F Bresso, F Williams, H Tornblom, P K Magnusson, N L Pedersen, J Ronkainen, P T Schmidt, M D'Amato
BACKGROUND: Gastroesophageal reflux disease (GERD), the regurgitation of gastric acids often accompanied by heartburn, affects up to 20% of the general population. Genetic predisposition is suspected from twin and family studies but gene-hunting efforts have so far been scarce and no conclusive genome-wide study has been reported. We exploited data available from general population samples, and studied self-reported reflux symptoms in relation to genome-wide single nucleotide polymorphism (SNP) genotypes...
August 3, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
Hsiao-Rong Chen, David H Sherr, Zhenjun Hu, Charles DeLisi
BACKGROUND: The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs-to find new uses for which they weren't intended, and to thereby reduce the overall cost of commercialization, and shorten the lag between drug discovery and availability. We report on the development, testing and application of a promising new approach to repositioning. METHODS: Our approach is based on mining a human functional linkage network for inversely correlated modules of drug and disease gene targets...
2016: BMC Medical Genomics
Said Farschtschi, Mathias Gelderblom, Sabriena Buschbaum, Hugh Bostock, Peter Grafe, Victor F Mautner
INTRODUCTION: The neuropathy in patients with neurofibromatosis type 2 (NF2) is difficult to quantify and to follow-up. This study compared 3 methods which may help to assess motor axon pathology in NF2 patients. METHODS: Nerve conduction studies in median nerves were supplemented by deriving motor unit number estimates (MUNE) from compound muscle action potential (CMAP) scans and by high resolution ultrasound (US) peripheral nerve imaging. RESULTS: CMAP amplitudes and nerve conduction velocity were normal in the vast majority of affected individuals, but CMAP scan MUNE revealed denervation and reinnervation in many peripheral nerves...
July 16, 2016: Muscle & Nerve
Qianwen Liu, Qifa Ye
BACKGROUND Our aim was to explore the mechanism of post-transplant organ function decrease induced by brain death (BD) and discover a potential candidate drug for improving the survival and organ function after BD. MATERIAL AND METHODS The microarray data developed from the liver tissues after BD were further analyzed by bioinformatics methods. The differentially expressed genes (DEGs) were computationally predicted and the DEGs that involved biological functions were explored by gene ontology (GO) analysis...
2016: Annals of Transplantation: Quarterly of the Polish Transplantation Society
Jingsong Shi, Song Jiang, Dandan Qiu, Weibo Le, Xiao Wang, Yinhui Lu, Zhihong Liu
OBJECTIVE: To investigate potential drugs for diabetic nephropathy (DN) using whole-genome expression profiles and the Connectivity Map (CMAP). METHODOLOGY: Eighteen Chinese Han DN patients and six normal controls were included in this study. Whole-genome expression profiles of microdissected glomeruli were measured using the Affymetrix human U133 plus 2.0 chip. Differentially expressed genes (DEGs) between late stage and early stage DN samples and the CMAP database were used to identify potential drugs for DN using bioinformatics methods...
2016: BioMed Research International
Jiye Wang, Mi Li, Yun Wang, Xiaoping Liu
Hepatocellular carcinoma (HCC) is the second most common cause of cancer-associated death worldwide, characterized by a high invasiveness and resistance to normal anticancer treatments. The need to develop new therapeutic agents for HCC is urgent. Here, we developed a bioinformatics method to identify potential novel drugs for HCC by integrating HCC-related and drug-affected subpathways. By using the RNA-seq data from the TCGA (The Cancer Genome Atlas) database, we first identified 1,763 differentially expressed genes between HCC and normal samples...
2016: OncoTargets and Therapy
J C Lu, Y P Zhang
In this study, we examined the molecular mechanism of thyroid carcinoma (THCA) using bioinformatics. RNA-sequencing data of THCA (N = 498) and normal thyroid tissue (N = 59) were downloaded from The Cancer Genome Atlas. Next, gene expression levels were calculated using the TCC package and differentially expressed genes (DEGs) were identified using the edgeR package. A co-expression network was constructed using the EBcoexpress package and visualized by Cytoscape, and functional and pathway enrichment of DEGs in the co-expression network was analyzed with DAVID and KOBAS 2...
2016: Genetics and Molecular Research: GMR
Wei Zhou, Xiang-gang Song, Chao Chen, Shu-mei Wang, Sheng-wang Liang
Action mechanism and material base of compound Danshen dripping pills in treatment of carotid atherosclerosis were discussed based on gene expression profile and molecular fingerprint in this paper. First, gene expression profiles of atherosclerotic carotid artery tissues and histologically normal tissues in human body were collected, and were screened using significance analysis of microarray (SAM) to screen out differential gene expressions; then differential genes were analyzed by Gene Ontology (GO) analysis and KEGG pathway analysis; to avoid some genes with non-outstanding differential expression but biologically importance, Gene Set Enrichment Analysis (GSEA) were performed, and 7 chemical ingredients with higher negative enrichment score were obtained by Cmap method, implying that they could reversely regulate the gene expression profiles of pathological tissues; and last, based on the hypotheses that similar structures have similar activities, 336 ingredients of compound Danshen dripping pills were compared with 7 drug molecules in 2D molecular fingerprints method...
August 2015: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Hyun-Mi Oh, Joo Hyun Park, Dae Heon Song, Myung Eun Chung
MT10107 is botulinum neurotoxin type A derived drug which utilizes the 150 kDa portion without complexing proteins and human serum albumin contents. To evaluate the efficacy and the safety of MT10107, it was compared with onabotulinumtoxinA in this double-blind, randomized controlled trial. Twenty-five healthy males received a randomly selected dose of MT10107 into the extensor digitorum brevis (EDB) muscle of one foot, and an equivalent dose of onabotulinumtoxinA (BOTOX) was injected into the contralateral EDB muscle...
January 2016: Toxins
Bina Eftekharsadat, Arash Babaei-Ghazani, Afshin Habibzadeh
Carpal tunnel syndrome (CTS) is a neuropathy due to the compression of the median nerve. It is shown that gabapentin in high doses is effective in treatment of CTS patients. In this study we evaluated the efficacy of low doses of gabapentin in treatment of CTS patients. Ninety patients with CTS were randomly assigned to groups A, B and C. Gabapentin was administered to group A with dose of 100 mg/day and to group B with dose of 300 mg/day for 2 months. Group C received no treatment. Before and after treatment, patients were evaluated using Visual analogue scale (VAS) for pain and parasthesia, Boston carpal tunnel questionnaire (BCTQ) including Symptom Severity Scale (SSS) and Functional Status Scale (FSS) to evaluate the efficacy of the treatment...
2015: Iranian Journal of Pharmaceutical Research: IJPR
Xinyan Liu, Xiaoqin Yang, Xinmei Chen, Yantao Zhang, Xuebin Pan, Guiping Wang, Yun Ye
Drug-induced gene expression patterns that invert disease profiles have recently been illustrated to be a new strategy for drug-repositioning. In the present study, we validated this approach and focused on prediction of novel drugs for lung adenocarcinoma (AC), for which there is a pressing need to find novel therapeutic compounds. Firstly, connectivity map (CMap) analysis computationally predicted bezafibrate as a putative compound against lung AC. Then this hypothesis was verified by in vitro assays of anti-proliferation and cell cycle arrest...
2015: Journal of Cancer
Feng-Hsiang Chung, Zhen-Hua Jin, Tzu-Ting Hsu, Chueh-Lin Hsu, Hsueh-Chuan Liu, Hoong-Chien Lee
Gene-set-based analysis (GSA), which uses the relative importance of functional gene-sets, or molecular signatures, as units for analysis of genome-wide gene expression data, has exhibited major advantages with respect to greater accuracy, robustness, and biological relevance, over individual gene analysis (IGA), which uses log-ratios of individual genes for analysis. Yet IGA remains the dominant mode of analysis of gene expression data. The Connectivity Map (CMap), an extensive database on genomic profiles of effects of drugs and small molecules and widely used for studies related to repurposed drug discovery, has been mostly employed in IGA mode...
2015: PloS One
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