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DDPC: Dragon Database of Genes associated with Prostate Cancer

M. Maqungo, M. Kaur, S. K. Kwofie, A. Radovanovic, U. Schaefer, S. Schmeier, E. Oppon, A. Christoffels, V. B. Bajic
2010 Nucleic Acids Research  
We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC.  ...  Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms.  ...  In this study, we present dragon database of genes associated with prostate cancer (DDPC), an integrated knowledge database that has been developed to provide researchers with a multitude of information  ... 
doi:10.1093/nar/gkq849 pmid:20880996 pmcid:PMC3013759 fatcat:tpio2pbn7jcapkbqn52logeofm

HNF1b is involved in prostate cancer risk via modulating androgenic hormone effects and coordination with other genes

Y.L. Hu, D. Zhong, F. Pang, Q.Y. Ning, Y.Y. Zhang, G. Li, J.Z. Wu, Z.N. Mo
2013 Genetics and Molecular Research  
ACKNOWLEDGMENTS Research supported by the National Natural Science Foundation of China (#81060213 and #81272853) and the GuangXi Nature Science Foundation (#2011GXNSFB018100 and #2012GXNSFAA053152).  ...  The HNF1b-correlated genes were then compared with genes reported to be implicated in prostate cancer by Dragon Database (DDPC; http://apps.sanbi.ac.za/ddpc/) and our previous meta-analysis of 6 independent  ...  We integrated data from Gene Expression Omnibus prostate cancer genes from the Dragon Database of Genes Implicated in Prostate Cancer, and used meta-analysis data to generate a panel of HNF1b-associated  ... 
doi:10.4238/2013.april.25.4 pmid:23661456 fatcat:hyvuhovj6fhgpb76zintnpfmfy

PEpiD: A Prostate Epigenetic Database in Mammals

Jiejun Shi, Jian Hu, Qing Zhou, Yanhua Du, Cizhong Jiang, Moray Campbell
2013 PLoS ONE  
Epigenetic mechanisms play key roles in initiation and progression of prostate cancer by changing gene expression.  ...  This curated information will improve our understanding of epigenetic mechanisms of gene regulation in prostate cancer, and serve as an important resource for epigenetic research in prostate cancer.  ...  Helped with the web development: QZ YD.  ... 
doi:10.1371/journal.pone.0064289 pmid:23696878 pmcid:PMC3655999 fatcat:5gdusiwcqfekdimqcdplft36ki

Human cancer databases (Review)

ATHANASIA PAVLOPOULOU, DEMETRIOS A. SPANDIDOS, IOANNIS MICHALOPOULOS
2014 Oncology Reports  
As a result, there is an exponential growth of cancer-associated data from diverse resources, such as scientific publications, genome-wide association studies, gene expression experiments, gene-gene or  ...  cancer is one of the four major non-communicable diseases (ncD), responsible for ~14.6% of all human deaths. currently, there are >100 different known types of cancer and >500 genes involved in cancer.  ...  Database of genes associated with prostate cancer http://cbrc.kaust.edu.sa/ddpc/index.php (88) g2sBc genes-to-systems Breast cancer database http://www.itb.cnr.it/breastcancer HlungDB Human  ... 
doi:10.3892/or.2014.3579 pmid:25369839 pmcid:PMC4254674 fatcat:rqs4fdfqsze4fmypfkbqy4ibzu

Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network

Hao He, Dongdong Lin, Jigang Zhang, Yu-ping Wang, Hong-wen Deng
2017 BMC Bioinformatics  
Second, a large microarray data set of prostate cancer was used to assess the practical performance of each method.  ...  With the advancement of high-throughput technologies and enrichment of popular public databases, more and more research focuses of bioinformatics research have been on computational integration of network  ...  For the method evaluation, 703 genes related to PC from the Dragon Database of Genes associated with Prostate Cancer (DDPC) were used as reference genes [18] .  ... 
doi:10.1186/s12859-017-1567-2 pmid:28253853 pmcid:PMC5335754 fatcat:mgxsvtgaxzgldkyzqq6b3ifivy

Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

Jiajia Chen, Daqing Zhang, Wenying Yan, Dongrong Yang, Bairong Shen
2013 BioMed Research International  
The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS) technologies.  ...  Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer.  ...  Conflict of Interests The authors declare that there is no conflict of interests. Authors' Contribution Jiajia Chen, Daqing Zhang, and Wenying Yan contributed equally to this work.  ... 
doi:10.1155/2013/901578 pmid:23957008 pmcid:PMC3727129 fatcat:wmsiqvou6vbqph5wox5sapgele

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression

Yin Li, Wanwipa Vongsangnak, Luonan Chen, Bairong Shen
2014 BMC Medical Genomics  
Prostate cancer is one of the most common complex diseases with high leading cause of death in men.  ...  The identified candidate disease-associated genes showed better predictive ability of prostate cancer progression than those of published biomarkers.  ...  Subir Kumar Nandy for assisting in human prostate cancer protein interaction network reconstruction.  ... 
doi:10.1186/1755-8794-7-s1-s3 pmid:25080090 pmcid:PMC4110715 fatcat:bubwzwylvfbnper6sxvguds2ga

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity

Hyunjin Kim, Sang-Min Choi, Sanghyun Park
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Through the proposed method, we discovered more prostate cancer-associated genes than ten comparable methods.  ...  , we can assume that the gene is associated with the disease.  ...  ). 3 Online Mendelian Inheritance in Man (http://www.omim.org/). 4 Dragon Database of Genes Implicated in Prostate Cancer (http://www.cbrc.kaust.edu.sa/ddpc/). 5 Human Prostate Gene DataBase (http:/  ... 
doi:10.1109/tcbb.2016.2618927 pmid:27775535 fatcat:ijp4t3lygbh7vhwj74xuidfuya

Data-driven translational prostate cancer research: from biomarker discovery to clinical decision

Yuxin Lin, Xiaojun Zhao, Zhijun Miao, Zhixin Ling, Xuedong Wei, Jinxian Pu, Jianquan Hou, Bairong Shen
2020 Journal of Translational Medicine  
Prostate cancer (PCa) is a common malignant tumor with increasing incidence and high heterogeneity among males worldwide.  ...  In the era of big data and artificial intelligence, the paradigm of biomarker discovery is shifting from traditional experimental and small data-based identification toward big data-driven and systems-level  ...  expression omnibus; DDPC: The dragon database of genes associated with prostate cancer; PCP: Prostate cancer proteomics; pH: The negative of the base 10 logarithm of the molar concentration of hydrogen  ... 
doi:10.1186/s12967-020-02281-4 pmid:32143723 fatcat:gbnkp47qobbshljqtkyrjgx7da

Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil

Magbubah Essack, Aleksandar Radovanovic, Vladimir B. Bajic, Zhang Zhang
2013 PLoS ONE  
Sickle cell disease (SCD) is a fatal monogenic disorder with no effective cure and thus high rates of morbidity and sequelae.  ...  association networks and hypotheses.  ...  information on prostate cancer, etc.  ... 
doi:10.1371/journal.pone.0065190 pmid:23762313 pmcid:PMC3677893 fatcat:szlqavzcsfgfzftifx2wmd47v4

CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations

Hee-Jin Lee, Sang-Hyung Shim, Mi-Ryoung Song, Hyunju Lee, Jong C Park
2013 BMC Bioinformatics  
CoMAGC consists of 821 sentences on prostate, breast and ovarian cancers. Currently, we deal with changes in gene expression levels among other types of gene changes.  ...  We describe CoMAGC, a corpus with multi-faceted annotations of gene-cancer relations.  ...  In the pilot phase, we tested our annotation scheme on 43 annotation units extracted from MED-LINE abstracts registered to DDPC, or Dragon Database of Genes Implicated in Prostate Cancer [39] .  ... 
doi:10.1186/1471-2105-14-323 pmid:24225062 pmcid:PMC3833657 fatcat:g5xshvhgrja3fbskirviomzlty

DigSee: disease gene search engine with evidence sentences (version cancer)

Jeongkyun Kim, Seongeun So, Hee-Jin Lee, Jong C. Park, Jung-jae Kim, Hyunju Lee
2013 Nucleic Acids Research  
Understanding the association between diseases and genes can be enhanced with the identification of involved biological events in this association.  ...  For this task, we developed DigSee to search MEDLINE abstracts for evidence sentences describing that 'genes' are involved in the development of 'cancer' through 'biological events'.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt531 pmid:23761452 pmcid:PMC3692119 fatcat:x4gcjt6czzbqppfbydkt75zjjq

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

Haisu Ma, Eric E. Schadt, Lee M. Kaplan, Hongyu Zhao
2011 Computer applications in the biosciences : CABIOS  
We applied COSINE to both simulated datasets with various differential expression patterns, and three real datasets, one prostate cancer dataset, a second one from the across-tissue comparison of morbidly  ...  of gene pairs, losing potentially valuable information in the data.  ...  For method evaluation, we collected genes related to PC from the Dragon Database of Genes associated with Prostate Cancer (DDPC) (Maqungo et al., 2011) .  ... 
doi:10.1093/bioinformatics/btr136 pmid:21414987 pmcid:PMC3138081 fatcat:rutx4kuahbe3rmultpohx3omhu

Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health [chapter]

Michael Simmons, Ayush Singhal, Zhiyong Lu
2016 Advances in Experimental Medicine and Biology  
The first section addresses mining biomedical literature for the purpose of assisting database curation in personalized cancer medicine.  ...  This chapter reviews the mechanics of text mining in precision medicine and discusses several specific use cases, including database curation for personalized cancer medicine, patient outcome prediction  ...  Examples of such databases include the Osteosarcoma Database [23] and the Dragon Database of Genes associated with Prostate Cancer (DDPC) [24] .  ... 
doi:10.1007/978-981-10-1503-8_7 pmid:27807747 pmcid:PMC5931382 fatcat:z2zsqbzyyzd33ikrt5a4qavuqe

A Computational Approach to Identifying Gene-microRNA Modules in Cancer

Daeyong Jin, Hyunju Lee, Isidore Rigoutsos
2015 PLoS Computational Biology  
Then, we selected miRNAs that are closely associated with genes in the modules based on a Gaussian Bayesian network and Bayesian Information Criteria.  ...  In addition, 48.4% and 74.0% of modules from ovarian cancer and GBM, respectively, were enriched with cancer-related pathways, and 51.7% and 71.7% of miRNAs in modules were ovarian cancer-related miRNAs  ...  associated with Prostate Cancer (DDPC) [85] , and Lung Cancer Gene Database (LUGEND).  ... 
doi:10.1371/journal.pcbi.1004042 pmid:25611546 pmcid:PMC4303261 fatcat:5flyff54wvcylgxsc6asvj7qfa
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