keyword
MENU ▼
Read by QxMD icon Read
search

Cmap drug

keyword
https://www.readbyqxmd.com/read/28615526/identifying-prognostic-signature-in-ovarian-cancer-using-dirgenerank
#1
Jian-Yong Wang, Ling-Ling Chen, Xiong-Hui Zhou
Identifying the prognostic genes in cancer is essential not only for the treatment of cancer patients, but also for drug discovery. However, it's still a big challenge to select the prognostic genes that can distinguish the risk of cancer patients across various data sets because of tumor heterogeneity. In this situation, the selected genes whose expression levels are statistically related to prognostic risks may be passengers. In this paper, based on gene expression data and prognostic data of ovarian cancer patients, we used conditional mutual information to construct gene dependency network in which the nodes (genes) with more out-degrees have more chances to be the modulators of cancer prognosis...
July 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28599476/identification-of-gene-markers-associated-with-metastasis-in-clear-cell-renal-cell-carcinoma
#2
Hailing Yang, Pengfei Huo, Guozhang Hu, Bo Wei, Dalian Kong, Hongjun Li
The present study aimed to screen potential target genes for the early diagnosis and treatment of early metastatic clear cell renal cell carcinoma (ccRCC) using the microarray data of early metastatic and non-metastatic ccRCC samples. The DNA microarray dataset GSE47352 was downloaded from Gene Expression Omnibus and included 4 early metastatic and 5 non-metastatic ccRCC samples. Differentially expressed genes (DEGs) were screened using the limma package. Then, pheatmap package was used to conduct two-way clustering for the DEGs...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28587109/identification-of-non-electrophilic-nrf2-activators-from-approved-drugs
#3
Qing-Ye Zhang, Xin-Yi Chu, Ling-Han Jiang, Meng-Yuan Liu, Zhi-Ling Mei, Hong-Yu Zhang
Oxidative damage can lead to a wide range of diseases. Nrf2 is an important transcription factor that regulates many of the cytoprotective enzymes involved in the oxidative stress response. Therefore, targeting the regulation of Nrf2 activation is one logical and effective strategy to prevent or lower the risk of oxidative stress-related diseases. Until now, most research has focused on electrophilic indirect Nrf2 activators, but the risk of 'off-target' effects may be associated with these activators. To find novel small non-electrophilic modulators of Nrf2, we started from chemical agents derived from a connectivity map (cMap) and identified 22 non-electrophilic potential Nrf2-activating drugs through a drug repositioning tactic...
May 26, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28472897/the-anticancer-effect-of-mebendazole-may-be-due-to-m1-monocyte-macrophage-activation-via-erk1-2-and-tlr8-dependent-inflammasome-activation
#4
Kristin Blom, Wojciech Senkowski, Malin Jarvius, Malin Berglund, Jenny Rubin, Lena Lenhammar, Vendela Parrow, Claes Andersson, Angelica Loskog, Mårten Fryknäs, Peter Nygren, Rolf Larsson
Mebendazole (MBZ), a drug commonly used for helminitic infections, has recently gained substantial attention as a repositioning candidate for cancer treatment. However, the mechanism of action behind its anticancer activity remains unclear. To address this problem, we took advantage of the curated MBZ-induced gene expression signatures in the LINCS Connectivity Map (CMap) database. The analysis revealed strong negative correlation with MEK/ERK1/2 inhibitors. Moreover, several of the most upregulated genes in response to MBZ exposure were related to monocyte/macrophage activation...
May 4, 2017: Immunopharmacology and Immunotoxicology
https://www.readbyqxmd.com/read/28256512/transcriptome-based-repurposing-of-apigenin-as-a-potential-anti-fibrotic-agent-targeting-hepatic-stellate-cells
#5
Daniel F Hicks, Nicolas Goossens, Ana Blas-García, Takuma Tsuchida, Benjamin Wooden, Michael C Wallace, Natalia Nieto, Abigale Lade, Benjamin Redhead, Arthur I Cederbaum, Joel T Dudley, Bryan C Fuchs, Youngmin A Lee, Yujin Hoshida, Scott L Friedman
We have used a computational approach to identify anti-fibrotic therapies by querying a transcriptome. A transcriptome signature of activated hepatic stellate cells (HSCs), the primary collagen-secreting cell in liver, and queried against a transcriptomic database that quantifies changes in gene expression in response to 1,309 FDA-approved drugs and bioactives (CMap). The flavonoid apigenin was among 9 top-ranked compounds predicted to have anti-fibrotic activity; indeed, apigenin dose-dependently reduced collagen I in the human HSC line, TWNT-4...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28150521/drug-repurposing-and-therapeutic-anti-microrna-predictions-for-inhibition-of-oxidized-low-density-lipoprotein-induced-vascular-smooth-muscle-cell-associated-diseases
#6
Shun-Tsung Chen, Chien-Hung Huang, Victor C Kok, Chi-Ying F Huang, Jin-Shuei Ciou, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng
Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28139721/therapeutic-properties-of-scutellaria-baicalensis-in-db-db-mice-evaluated-using-connectivity-map-and-network-pharmacology
#7
Bu-Yeo Kim, Kwang Hoon Song, Chi-Yeon Lim, Su-In Cho
We have reported that an extract of Scutellaria baicalensis (ESB) has effects against obesity and hypertriglyceridemia in type 2 diabetic animal model (db/db mouse). In the present study, we tried to explain the pharmacological effects of ESB by integrating gene expression information from db/db mouse liver with that of ESB-treated HepG2 hepatocellular carcinoma cells. Using Connectivity Map (cmap) analysis, we found an inverse relationship in the pharmaceutical profiles based on gene expression between db/db mouse liver and ESB-treated HepG2 cells...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069634/a-review-of-connectivity-map-and-computational-approaches-in-pharmacogenomics
#8
Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina Galzko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28058586/key-genes-in-stomach-adenocarcinoma-identified-via-network-analysis-of-rna-seq-data
#9
Li Shen, Lizhi Zhao, Jiquan Tang, Zhiwei Wang, Weisong Bai, Feng Zhang, Shouli Wang, Weihua Li
RNA-seq data of stomach adenocarcinoma (STAD) were analyzed to identify critical genes in STAD. Meanwhile, relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. Gene expression data of STAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. Relationships with correlation coefficient > 0.6 were retained in the gene co-expression network. Functional enrichment analysis was performed for the genes in the network with DAVID and KOBASS 2...
January 5, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/27778232/a-computational-systems-biology-approach-for-identifying-candidate-drugs-for-repositioning-for-cardiovascular-disease
#10
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
https://www.readbyqxmd.com/read/27756228/drug-discovery-using-clinical-outcome-based-connectivity-mapping-application-to-ovarian-cancer
#11
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
https://www.readbyqxmd.com/read/27737314/analyzing-gene-expression-profiles-in-dilated-cardiomyopathy-via-bioinformatics-methods
#12
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
https://www.readbyqxmd.com/read/27703845/identify-potential-drugs-for-cardiovascular-diseases-caused-by-stress-induced-genes-in-vascular-smooth-muscle-cells
#13
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
https://www.readbyqxmd.com/read/27664700/radiation-protective-effects-of-baclofen-predicted-by-a-computational-drug-repurposing-strategy
#14
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...
November 2016: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/27586445/an-integrated-human-murine-transcriptome-and-pathway-approach-to-identify-prenatal-treatments-for-down-syndrome
#15
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...
September 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27508329/connection-map-for-compounds-cmc-a-server-for-combinatorial-drug-toxicity-and-efficacy-analysis
#16
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
https://www.readbyqxmd.com/read/27491036/inferring-association-between-compound-and-pathway-with-an-improved-ensemble-learning-method
#17
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
https://www.readbyqxmd.com/read/27485664/a-meta-analysis-of-reflux-genome-wide-association-studies-in-6750-northern-europeans-from-the-general-population
#18
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...
February 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27475327/a-network-based-approach-to-drug-repositioning-identifies-plausible-candidates-for-breast-cancer-and-prostate-cancer
#19
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
https://www.readbyqxmd.com/read/27422240/muscle-action-potential-scans-and-ultrasound-imaging-in-neurofibromatosis-type-2
#20
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 follow up. In this study we compared 3 methods that may help assess motor axon pathology in NF2 patients. METHODS: Nerve conduction studies in median nerves were supplemented by deriving motor unit number estimates (MUNEs) 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...
March 2017: Muscle & Nerve
keyword
keyword
46355
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"