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Determining conserved metabolic biomarkers from a million database queries

Michael E. Kurczy, Julijana Ivanisevic, Caroline H. Johnson, Winnie Uritboonthai, Linh Hoang, Mingliang Fang, Matthew Hicks, Anthony Aldebot, Duane Rinehart, Lisa J. Mellander, Ralf Tautenhahn, Gary J. Patti (+3 others)
2015 Bioinformatics  
Results: With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries.  ...  Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the  ...  Fig. 1 . 1 A cumulative mass spectrum created from a million searches of the METLIN metabolite database. (Top) representation of queries logged from across the globe.  ... 
doi:10.1093/bioinformatics/btv475 pmid:26275895 pmcid:PMC4836397 fatcat:7fck6fegnrcjhli7bjjvtzh3ty

Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani

Nithin Ravooru, Sandesh Ganji, Nitish Sathyanarayanan, Holenarsipur G. Nagendra
2014 Frontiers in Genetics  
Thus, putative functions have been defined to 105 hypothetical proteins, which exhibited a GO term correlation and PFAM domain coverage of more than 50% over the query sequence length.  ...  In addition, 7 new putative essential genes have been mined with the help of Eukaryotic Database of Essential Genes (DEG).  ...  The 105 sequences when queried against the Eukaryote Database of Essential Genes (DEG), using jackhammer with an e-value of 10 −20 , resulted in 26 sequences that had 93 hits from eukaryote DEG.  ... 
doi:10.3389/fgene.2014.00291 pmid:25206363 pmcid:PMC4144268 fatcat:pdlxpjn5ljh5pha3ojmurs734a

Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach

Dinesh Kumar Barupal, Oliver Fiehn
2019 Environmental Health Perspectives  
A vast volume of blood-related literature is available via the PubMed database for data mining.  ...  The PubMed database can be queried by use of a web interface for a limited number of queries.  ...  The Blood Exposome Database will also serve as a knowledge base to guide investigations in chronic disease risk, metabolomics, metabolic regulation, precision medicine, exposure biomarkers, and chemical  ... 
doi:10.1289/ehp4713 pmid:31557052 pmcid:PMC6794490 fatcat:52bbvoxl7vgudj4aqgfqbgdyvq

Genome-Wide Identification of Molecular Pathways and Biomarkers in Response to Arsenic Exposure in Zebrafish Liver

Hongyan Xu, Siew Hong Lam, Yuan Shen, Zhiyuan Gong, Xiaoping Pan
2013 PLoS ONE  
Based on more than 12 million SAGE tags mapped to zebrafish genes, 1,444 differentially expressed genes (750 up-regulated and 694 down-regulated) were identified from a relatively abundant transcripts  ...  (.10 TPM [transcripts per million]) based on minimal two-fold change.  ...  After mapping to the zebrafish Reference Sequence database, 5.6 million and 6.9 million uniquely mapped tags were mapped to 8,318 and 8,434 gene entries, respectively, from the arsenic-treated and untreated  ... 
doi:10.1371/journal.pone.0068737 pmid:23922661 pmcid:PMC3726666 fatcat:ch4xrxdhkbcbzbhnm66ezf3voq

Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics

Christina Ferousi, Daan R Speth, Joachim Reimann, Huub JM Op den Camp, James WA Allen, Jan TM Keltjens, Mike SM Jetten
2013 BMC Microbiology  
The molecular mechanism of anammox was recently elucidated and is suggested to proceed through a branched respiratory chain.  ...  Our results show that all available anammox genome assemblies contain a complete type II cytochrome c maturation system.  ...  A. Allen was supported by BBSRC, and Mike S. M. Jettten and Christina Ferousi were supported by ERC AG 232937 and Spinoza Premium 2012.  ... 
doi:10.1186/1471-2180-13-265 pmid:24267221 pmcid:PMC4222556 fatcat:kojo6wpuard5hae3storwvl7qm

Building the bridges to bioinformatics in nutrition research

Danielle G Lemay, Angela M Zivkovic, J Bruce German
2007 American Journal of Clinical Nutrition  
to the longer range goals of full standardization of nutrition experiments and migration of all experimental data into databases.  ...  The standardization of experimental designs and the conversion of nutrition data into a machine-readable format will bring about a renaissance in nutrition research, accelerating the ability of investigators  ...  A classification algorithm, reviewed by Kapetanovic et al (35) , would then be applied to the data from a subset of the available samples, ie, a training set, to generate a biomarker profile or bioprofile  ... 
doi:10.1093/ajcn/86.5.1261 pmid:17991634 fatcat:3vqiawqsbzcf3lkcjknsnarz4a

The NCBI BioSystems database

Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, Stephen H. Bryant
2009 Nucleic Acids Research  
This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming  ...  inference of biological relationships from the literature or multiple experimental datasets.  ...  ACKNOWLEDGEMENTS We thank the authors of the KEGG, Reactome and BioCyc databases. We also thank the NCBI Information Engineering Branch for continuing assistance with software development.  ... 
doi:10.1093/nar/gkp858 pmid:19854944 pmcid:PMC2808896 fatcat:n37jzpnjivfnjp6aiala5glyte

The Predicted Impact of Coding Single Nucleotide Polymorphisms Database

M. F. Rudd
2005 Cancer Epidemiology, Biomarkers and Prevention  
(Cancer Epidemiol Biomarkers Prev  ...  A total of 9,537 validated nsSNPs located within annotated genes were retrieved from National Center for Biotechnology Information dbSNP Build 123.  ...  The PICS Database Cancer Epidemiol Biomarkers Prev 2005;14(11).  ... 
doi:10.1158/1055-9965.epi-05-0469 pmid:16284384 fatcat:3pzfe5du5vguneshqkneac3xcm

Identification of Biomarkers for Obesity associated with Diabetes using Sequence Mining Techniques

Lalitha Saroja Thota, Allam Appa Rao
2011 INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY  
The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological  ...  alignment using ClustalW tool and constructed a phylogram tree using functional protein sequences extracted from NCBI.  ...  The number of adults with diabetes in the world will rise from 135 million in 1995 to 300 million in the year 2025. The major part of this numerical increase will occur in developing countries.  ... 
doi:10.24297/ijct.v10i4.3251 fatcat:uomrfxxzzzae7lcvzusnorgrgy

Transcription-translation error: In-silico investigation of the structural and functional impact of deleterious single nucleotide polymorphisms in GULP1 gene

Opeyemi S. Soremekun, Chisom Ezenwa, Mahmoud Soliman, Tinashe Chikowore, Oyekanmi Nashiru, Segun Fatumo
2021 Informatics in Medicine Unlocked  
We, therefore, used a SNPinformatics approach to retrieve, classify, and determine the stability effect of some nsSNPs.  ...  However, being a computational study, these nsSNPs require experimental validation to explore their metabolic involvement in the pathogenesis of diseases.  ...  Single Nucleotide Polymorphism (SNP) is the most abundant form of variation in the human genome and range from 3 to 5 million in number [1] .  ... 
doi:10.1016/j.imu.2020.100503 pmid:33665355 pmcid:PMC7928429 fatcat:t6huqtdrgzfgff5baf6iufwr6q

Bioinformatics evaluation of the homologues of Schistosoma mansoni biomarker proteins of bladder cancer in other Schistosoma species [article]

Folayowon JO, Adebayo AS, Isokpehi RD, Chiaka Ijeoma Anumudu
2020 bioRxiv   pre-print
The homologues of 36 previously identified urine biomarker proteins from a Schistosoma mansoni database, were identified in other Schistosoma species using SMARTBLAST and analyzed for similarities and  ...  However, some vital biomarker proteins like venom allergen-like proteins, which had been proposed as a putative drug and vaccine target, showed more semi conserved regions in which the amino acids had  ...  MATERIALS AND METHODS Data collection Protein sequences of the 36 schistosome biomarkers were retrieved from the Uniprot database https://www.uniprot.org/ in FASTA format.  ... 
doi:10.1101/2020.09.07.285767 fatcat:ysapnfcsmbdttekp3iwuguomie

Cardiac aging: Send in the vinculin reinforcements

Kristine Y. DeLeon-Pennell, Merry L. Lindsey
2015 Science Translational Medicine  
a biomarker of either aging or heart failure.  ...  (Fig. 1) and establishing a database of results that will be useful for identifying therapeutic targets to slow or reverse cardiac aging (3).  ... 
doi:10.1126/scitranslmed.aab3391 pmid:26084802 fatcat:gdfxnh275vbhfmr7n7j527igpi

Serum proteomic analysis of Mycobacterium tuberculosis antigens for discriminating active tuberculosis from latent infection

Zhangli Peng, Ling Chen, Hong Zhang
2020 Journal of International Medical Research  
This combination of 15 TB serum biomarkers had a sensitivity of 85.4% and specificity of 90.3% in discriminating ATB from LTBI.  ...  Conclusion: Combinations of serum biomarkers can offer improved diagnostic performance in discriminating ATB from LTBI.  ...  for their assistance in collecting and processing serum samples from patients and healthy controls.  ... 
doi:10.1177/0300060520910042 pmid:32216499 pmcid:PMC7133403 fatcat:76mivk63dbgulnwjzuidzj3aae

A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma

Kai Wang, Man Zhang, Jiao Wang, Pan Sun, Jizhuang Luo, Haizhen Jin, Rong Li, Changqing Pan, Liming Lu
2021 Frontiers in Oncology  
Moreover, PLK1 could be a promising therapeutic target for LUAD.  ...  Here, by using both tissues and cells from LUAD and normal lung samples, 434 increased and 828 decreased genes of biological significance were detected, including 127 cell cycle-associated genes (95 increased  ...  The increased expression of E2F1 is conserved in almost all cancers (Figure 7) , indicating a similar role of E2F1 in these cancers from an evolutionary point of view.  ... 
doi:10.3389/fonc.2021.737152 pmid:34650921 pmcid:PMC8505978 fatcat:lzxoy6mzebgutfltw5ajynzvyu

Integrated bioinformatics analysis of aberrantly-methylated differentially-expressed genes and pathways in age-related macular degeneration

Yinchen Shen, Mo Li, Kun Liu, Xiaoyin Xu, Shaopin Zhu, Ning Wang, Wenke Guo, Qianqian Zhao, Ping Lu, Fudong Yu, Xun Xu
2020 BMC Ophthalmology  
Data from expression profile GSE29801 and methylation profile GSE102952 were obtained from the Gene Expression Omnibus database.  ...  KEGG pathway enrichment analysis indicated that Hypo-HGs were enriched in the calcium signaling pathway, whereas Hyper-LGs were enriched in sphingolipid metabolism.  ...  (GSE29801: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29801; GSE102952: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102952).  ... 
doi:10.1186/s12886-020-01392-2 pmid:32209064 fatcat:b6gtehybv5a4hbxddj6kp2ginq
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