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Content-based microarray search using differential expression profiles
2010
BMC Bioinformatics
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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
2014
2014 25th International Workshop on Database and Expert Systems Applications
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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
2008
PLoS Computational Biology
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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
2011
Computer applications in the biosciences : CABIOS
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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
2013
Molecules and Cells
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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
2019
Studies in Health Technology and Informatics
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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
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, 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
2012
Critical Care
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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
2007
BMC Developmental Biology
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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
2009
PLoS ONE
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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
2008
Briefings in Functional Genomics & Proteomics
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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
2009
BMC Genomics
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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
2008
Nucleic Acids Research
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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
2007
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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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