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Content-based microarray search using differential expression profiles

Jesse M Engreitz, Alexander A Morgan, Joel T Dudley, Rong Chen, Rahul Thathoo, Russ B Altman, Atul J Butte
2010 BMC Bioinformatics  
Conclusions: Content-based gene expression search generates relevant hypotheses for biological inquiry. Experiments across platforms, tissue types, and protocols inform the analysis of new datasets.  ...  Avoiding thresholds, we generate differential expression profiles that include a score for each gene measured in an experiment.  ...  Here we develop methods for content-based gene expression search using an entire experiment as a query.  ... 
doi:10.1186/1471-2105-11-603 pmid:21172034 pmcid:PMC3022631 fatcat:hfpd7t5v4zggnfgaejcgubriwq

Content-Based Search on Time-Series Microarray Databases

Ahmet Hayran, Hasan Ogul, Esma Ozkoc
2014 2014 25th International Workshop on Database and Expert Systems Applications  
We study, for the first time, the problem of content-based searching of time-series microarray experiments in large-scale gene expression databases.  ...  A comparison of different fingerprinting and distance computation schemes is presented over a retrieval framework based on the differential expression of genes in varying time points.  ...  There exist only a couple of examples using gene sets for content-based microarray experiment retrieval in the literature [20] [21] .  ... 
doi:10.1109/dexa.2014.33 dblp:conf/dexaw/HayranOO14 fatcat:656m5gydarh4zhxgysuwf752ta

Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs

Ran Elkon, Reuven Agami, Yitzhak Pilpel
2008 PLoS Computational Biology  
Applying such an integrated analysis, we uncovered a striking relationship between 39-UTR AU content and gene response in numerous microarray datasets.  ...  Our results substantiate that, after removal of AU biases, mRNA expression profiles contain ample information which allows in silico detection of miRs that are active in physiological conditions.  ...  Acknowledgments We thank the authors of the microarray datasets analyzed in this paper for making their data publicly available. Author Contributions Conceived and designed the experiments: RE RA.  ... 
doi:10.1371/journal.pcbi.1000189 pmid:18833292 pmcid:PMC2533120 fatcat:w434f2omirdrxpr4nind2riyqa

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel T. Dudley, Rohan Mallelwar, Atul J. Butte
2011 Computer applications in the biosciences : CABIOS  
Using a novel, contentbased approach, ProfileChaser retrieves expression profiles that match the differentially regulated transcriptional programs in a usersupplied experiment.  ...  We introduce ProfileChaser, a web server that allows for querying the Gene Expression Omnibus based on genomewide patterns of differential expression.  ...  Here we introduce ProfileChaser, a web server that allows for content-based gene expression search with a user-supplied experiment.  ... 
doi:10.1093/bioinformatics/btr548 pmid:21967760 pmcid:PMC3223361 fatcat:uwzt7okk3vh35h74qhbraxknum

EPITRANS: A database that integrates epigenome and transcriptome data

Soo Young Cho, Jin Choul Chai, Soo Jun Park, Hyemyung Seo, Chae-Bong Sohn, Young Seek Lee
2013 Molecules and Cells  
EPITRANS uses combined analysis of epigenetic modification and gene expression to search for cell function-related epigenetic and transcriptomic alterations (Freely available on the web at http://epitrans.org  ...  Recent initiatives to define genome-wide DNA methylation and histone modification profiles by microarray and sequencing methods have led to the construction of databases.  ...  Researchers have identified genome wide epigenetic modification profiles using microarray and sequencing methods.  ... 
doi:10.1007/s10059-013-0249-9 pmid:24213601 pmcid:PMC3887936 fatcat:svvk72s7lbchpo3pbvu6yerpw4

A Search Method to Support Temporal Transcriptome Analysis

Guenter Tusch, Shahrzad Eslamian
2019 Studies in Health Technology and Informatics  
We propose a hybrid statistical and temporal logic model to yield search pattern that can be used for pattern matching and database search to identify novel and common patterns in temporal expression experiments  ...  The method accounts for various challenges that can be found in publicly available gene expression databases.  ...  We used as an example a microarray study with differentially expressed genes grouped into three peak clusters.  ... 
doi:10.3233/shti190559 pmid:31438256 fatcat:zt2taqtf3vdr3eytvp6gk7mcqi

Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

2019 Database: The Journal of Biological Databases and Curation  
, covering 25 937 entries of differentially expressed genes.  ...  With Mr.Vc, users can easily find transcriptome data they are interested in, such as the experimental conditions in which a gene of interest was differentially expressed in, or all genes that were differentially  ...  Microarray and RNA-seq are powerful techniques to study general gene expression profiles.  ... 
doi:10.1093/database/baz069 pmid:31231774 pmcid:PMC6597751 fatcat:xx5yypglyfhytlerbbszrxgzae

Identification of sepsis subtypes in critically ill adults using gene expression profiling

David M Maslove, Benjamin M Tang, Anthony S McLean
2012 Critical Care  
We used microarray-based gene expression data from adult patients with sepsis in order to identify molecularly distinct sepsis subtypes.  ...  Methods: We used partitioning around medoids (PAM) and hierarchical clustering of gene expression profiles from neutrophils taken from a cohort of septic patients in order to identify distinct subtypes  ...  Gene expression microarray data may be useful in identifying sepsis subtypes based on differential expression of key genes [4] .  ... 
doi:10.1186/cc11667 pmid:23036193 pmcid:PMC3682285 fatcat:lfzpqh3vvfd5dpkcw32i5hucly

Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs

Marinus FW te Pas, Ina Hulsegge, Albart Coster, Marco H Pool, Henri H Heuven, Luc LG Janss
2007 BMC Developmental Biology  
Results indicated regulation of the expression of genes involved in proliferation and differentiation of myoblasts, and energy metabolism.  ...  Results: PERL scripts were developed that used the names of the genes on the microarray to search databases. Synonyms of gene names were added to the list by searching the Gene Ontology database.  ...  Previously we reported myogenesis differentiation phasespecific regulation of the gene expression using microarrays.  ... 
doi:10.1186/1471-213x-7-66 pmid:17567520 pmcid:PMC1919358 fatcat:odw4g657xzf7bkoshwupms7azu

The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

Herbert Schulz, Raivo Kolde, Priit Adler, Irène Aksoy, Konstantinos Anastassiadis, Michael Bader, Nathalie Billon, Hélène Boeuf, Pierre-Yves Bourillot, Frank Buchholz, Christian Dani, Michael Xavier Doss (+24 others)
2009 PLoS ONE  
been arranged in "Expression Waves" and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during  ...  during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have  ...  The validation rate of the microarray expression profiling data was 90.7%, based on results obtained independently in eleven consortium laboratories.  ... 
doi:10.1371/journal.pone.0006804 pmid:19727443 pmcid:PMC2731164 fatcat:y27smlptr5ei5ofcanlfowmtke

Microarray data analysis and mining approaches

F. Cordero, M. Botta, R. A. Calogero
2008 Briefings in Functional Genomics & Proteomics  
Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification.  ...  In this article, we will review approaches used to detect differentially expressed genes and to link differential expression to specific biological functions.  ...  INTRODUCTION Microarray-based transcription profiling is now a consolidated methodology and large-scale microarray studies are becoming a crucial aspect of a new way of conceiving experimental biology.  ... 
doi:10.1093/bfgp/elm034 pmid:18216026 fatcat:kytju66zsjfgjc64myixoeac7y

An expression database for roots of the model legume Medicago truncatula under salt stress

Daofeng Li, Zhen Su, Jiangli Dong, Tao Wang
2009 BMC Genomics  
Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago  ...  showing metabolic maps, and comparing and visualizing expression profiles.  ...  The home page briefly introduces MtED's content and our microarray experiments.  ... 
doi:10.1186/1471-2164-10-517 pmid:19906315 pmcid:PMC2779821 fatcat:wk2rdhefc5cfnjcbbm425uzucu

NRED: a database of long noncoding RNA expression

Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, Mark L. Crowe, Sean M. Grimmond, John S. Mattick
2008 Nucleic Acids Research  
We have constructed a public repository, the Noncoding RNA Expression Database (NRED), which provides gene expression information for thousands of long ncRNAs in human and mouse.  ...  The database contains both microarray and in situ hybridization data, much of which is described here for the first time.  ...  ACKNOWLEDGEMENTS We thank Stephen Bruce, Evgeny Glazov, David Hume, Andrew Jackson, Peter Koopmam, Guangyu Li, Mark Mehler, George Muscat, Andrew Perkins and Kate Schroder for providing RNA samples for microarray  ... 
doi:10.1093/nar/gkn617 pmid:18829717 pmcid:PMC2686506 fatcat:mqvvzipkovgu5mm2dbmompeije

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes

J. M. Mazzarelli, J. Brestelli, R. K. Gorski, J. Liu, E. Manduchi, D. F. Pinney, J. Schug, P. White, K. H. Kaestner, C. J. Stoeckert
2007 Nucleic Acids Research  
The expression datasets are derived using different microarray platforms, including the BCBC Panc-Chips and Affymetrix gene expression arrays.  ...  For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site.  ...  Expression profiles are accessed using the Expression Profile link and are displayed as graphs ( Figure 2C ).  ... 
doi:10.1093/nar/gkl748 pmid:17071715 pmcid:PMC1781120 fatcat:va3unfr4ofakxngy7jlecu5dcu

dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers

Zhen Yang, Liangcai Wu, Anqiang Wang, Wei Tang, Yi Zhao, Haitao Zhao, Andrew E. Teschendorff
2016 Nucleic Acids Research  
An easy-to-use web interface was constructed that allows users to make a quick search of the differentially expressed miRNAs in certain cancer types.  ...  Large amount of differentially expressed miRNAs have been identified in various cancers by using high-throughput methods.  ...  NEW FEATURES AND DATABASE UTILITY Improved experimental description For each of the microarray data sets presented, we reviewed the samples profiled and classified the experiments for differential expression  ... 
doi:10.1093/nar/gkw1079 pmid:27899556 pmcid:PMC5210560 fatcat:sodcz4jiercifgshum2y43zpx4
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