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Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
2009
BMC Bioinformatics
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Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. ...
Results: We propose a computationally efficient information criterion-based clustering algorithm, called ORICC, that also takes account of the ordering in time-course microarray experiments by embedding ...
Conclusion We developed a new clustering algorithm, ORICC, for short time-course microarray data, by taking a model selection approach in order-restricted statistical inference. ...
doi:10.1186/1471-2105-10-146
pmid:19445669
pmcid:PMC2696449
fatcat:hvdw4dgemzcxhi42w2lczeeqqy
A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
2009
BMC Bioinformatics
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For gene expression data obtained from a time-course microarray experiment, Liu et al. developed a new algorithm for clustering genes with similar expression profiles over time. ...
Performance of their proposal was compared with three other methods including the order-restricted inference based methodology of Peddada et al. ...
Background A short-series time-course microarray experiment induces a natural constraint on the mean expression of a gene or a probe over time. ...
doi:10.1186/1471-2105-10-438
pmid:20028515
pmcid:PMC2813245
fatcat:2nxvt6avfzag3p2i6ll3bbdhx4
Clustering of unevenly sampled gene expression time-series data
2005
Fuzzy sets and systems (Print)
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Time course measurements are becoming a common type of experiment in the use of microrarrays. ...
To address this problem, this paper proposes the Fuzzy Short Time-Series (FSTS) clustering algorithm, which clusters profiles based on the similarity of their relative change of expression level and the ...
In [3] , the proposed algorithm is based on the statistical theory of ordered-restricted inference that makes explicit use of ordering information. ...
doi:10.1016/j.fss.2004.10.014
fatcat:2ex4i3d3nbalbdefjpyfaomamy
A modified correlation coefficient based similarity measure for clustering time-course gene expression data
2008
Pattern Recognition Letters
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Gene expression levels are often measured consecutively in time through microarray experiments to detect cellular processes underlying regulatory effects observed and to assign functionality to genes whose ...
Clustering methods allow us to group genes that show similar time-course expression profiles and that are thus likely to be co-regulated. ...
for such a short series of time-ordered data. ...
doi:10.1016/j.patrec.2007.09.015
fatcat:bqiaao6jvvenxjtz5ts5mcli2y
Using hidden Markov models to analyze gene expression time course data
2003
Bioinformatics
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The experimental platform for doing the appropriate large-scale experiments to obtain time-courses of expression levels is provided by microarray technology. ...
Results: We propose to use Hidden Markov Models (HMMs) to account for the horizontal dependencies along the time axis in time course data and to cope with the prevalent errors and missing values. ...
Berhard Knab, Bernd Wichern and Barthel Steckemetz were instrumental in developing the methodology and implementing the GHMM, as were Achim Gädke, Wasinee Rungsarityotin, Thordis Linda Thorarinsdottir, ...
doi:10.1093/bioinformatics/btg1036
pmid:12855468
fatcat:ifvkbwconngqjlxpps3x2obqaq
A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation
2015
OncoTarget
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Our model thus placed known regulators in a temporal perspective, and in addition identified novel candidate regulators of thymocyte differentiation. ...
We therefore used time course expression and degradation data and a genome wide transcriptional modelling (GWTM) strategy to model the transcriptional response of genes up-regulated on pre-TCR signal transduction ...
Number of genes with fold change >2 with respect to time zero, plotted through the time course of the experiment, showing up-and down-regulated genes. ...
doi:10.18632/oncotarget.5796
pmid:26415229
pmcid:PMC4745683
fatcat:5xlr32dtwjfshpvtcdb3lyyltq
Functional bioinformatics of microarray data: from expression to regulation
2002
Proceedings of the IEEE
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Using microarrays is a powerful technique to monitor the expression of thousands of genes in a single experiment. ...
Here we integrate clustering of coexpressed genes with the discovery of binding motifs. ...
INCLUSIVE: INTEGRATED CLUSTERING, UPSTREAM SEQUENCE RETRIEVAL, AND MOTIF SAMPLING Analysis of a microarray experiment is not restricted to a single cluster experiment. ...
doi:10.1109/jproc.2002.804681
fatcat:nwo7ktqb6nam7mwgcjyaludtrm
The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics
2010
Toxicological Sciences
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Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals ...
The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to ...
Using a class of statistics called order-restricted inference, candidate temporal gene profiles are defined in terms of inequalities among mean expression levels at time or dose points. ...
doi:10.1093/toxsci/kfq373
pmid:21177775
pmcid:PMC3145387
fatcat:pf2gz6c6frccfhtdr4yb2wdfny
New approaches to clustering microarray time-series data using multiple expression profile alignment
2010
2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
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An important process in functional genomic studies is clustering microarray time-series data, where genes with similar expression profiles are expected to be functionally related. ...
Clustering microarray time-series data via pairwise alignment of piecewise linear profiles has been recently introduced. ...
A regression-based method was proposed in [8] to address the challenges in clustering short time-series expression data. ...
doi:10.1109/cibcb.2010.5510385
dblp:conf/cibcb/SubhaniRNB10
fatcat:6abu5frm2fdkhb2cp4wmabecqa
Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells
2008
PLoS ONE
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Conclusion/Significance: Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. ...
Methodology/Principal Findings: In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript ...
Fountain, Alejandro Garbino, Ana Islam, Terry Huynh, Lauren McFarlane, Khoi Pham, Tracey Robinson, Deborah Forst, Olivia Dziadek, Anne Katchy, Benjamin Lukose, Pathik Desai, and Rachel Atkins for assistance with ...
doi:10.1371/journal.pone.0002548
pmid:18648548
pmcid:PMC2481296
fatcat:sa4yyl5wjbc6vnmcghiqh7ubfu
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli
2011
Journal of Systems and Synthetic Biology
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Clustering of genes with similar expression profiles allows for a course-grained view of the GRN and a probabilistic determination of the connectivity among the clusters. ...
Coexpression of genes or, more generally, similarity in the expression profiles poses an unsurmountable obstacle to inferring the gene regulatory network (GRN) based solely on data from DNA microarray ...
Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided ...
doi:10.1007/s11693-011-9079-2
pmid:21949674
pmcid:PMC3159693
fatcat:4nimgs5ywrhdbdzgnjm4hxegqa
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli
[article]
2011
arXiv
pre-print
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Clustering of genes with similar expression profiles allows for a course-grained view of the GRN and a probabilistic determination of the connectivity among the clusters. ...
Coexpression of genes or, more generally, similarity in the expression profiles poses an unsurmountable obstacle to inferring the gene regulatory network (GRN) based solely on data from DNA microarray ...
Results and Discussion The abundance of the information obtained from DNA microarrays scales with the number of time points. ...
arXiv:1106.0143v1
fatcat:nhqvl22embcglp4ao4iw2xfjvu
Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars
2003
European Journal of Control
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Algorithms we discuss are Principal Component Analysis, clustering techniques such as hierarchical clustering and Adaptive Quality Based Clustering and statistical sampling methods, such as Monte Carlo ...
In this paper, we discuss datasets that are being generated by microarray technology, which makes it possible to measure in parallel the activity or expression of thousands of genes simultaneously. ...
Analysis of microarray experiment is not restricted to a single cluster experiment. ...
doi:10.3166/ejc.9.237-278
fatcat:w26h4jvugjg35abzgqctb2yubi
Initializing Partition-Optimization Algorithms
2009
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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Results on test experiments are excellent. We also provide a detailed comparative assessment of the suggested algorithm with many commonly used initialization approaches in the literature. ...
Results on test experiments are excellent. We also provide a detailed comparative assessment of the suggested algorithm with many commonly-used initialization approaches in the literature. ...
In order to portray variability in measurement, the observed replicated data at each time-point are displayed along with the mean. ...
doi:10.1109/tcbb.2007.70244
pmid:19179708
fatcat:l7ukzei6wnayflsbrjcmr7ovky
Letters to the Editor
2001
The journals of gerontology. Series A, Biological sciences and medical sciences
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B328
LETTERS TO THE EDITOR The Validity of Prior Microarray Studies When considering the likely validity of our published conclusions regarding gene expression profile changes with aging in mice (2, ...
In some cases it may, as Prolla and colleagues suggest, be simpler to examine the best candidate genes one at a time, in new sets of animals, using alternative methods (like RT-PCR or Northern blotting ...
doi:10.1093/gerona/56.8.b327
pmid:11487590
fatcat:2a24zfpzfba6tmxytnctpb75xy
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