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Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments

Tianqing Liu, Nan Lin, Ningzhong Shi, Baoxue Zhang
2009 BMC Bioinformatics  
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

Shyamal D Peddada, David M Umbach, Shawn F Harris
2009 BMC Bioinformatics  
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

C.S. Möller-Levet, F. Klawonn, K.-H. Cho, H. Yin, O. Wolkenhauer
2005 Fuzzy sets and systems (Print)  
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

Young Sook Son, Jangsun Baek
2008 Pattern Recognition Letters  
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

A. Schliep, A. Schonhuth, C. Steinhoff
2003 Bioinformatics  
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

Hemant Sahni, Susan Ross, Alessandro Barbarulo, Anisha Solanki, Ching-In Lau, Anna Furmanski, José Ignacio Saldaña, Masahiro Ono, Mike Hubank, Martino Barenco, Tessa Cromp­ton
2015 OncoTarget  
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

Y. Moreau, F. De Smet, G. Thijs, K. Marchal, B. De Moor
2002 Proceedings of the IEEE  
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

C. A. Afshari, H. K. Hamadeh, P. R. Bushel
2010 Toxicological Sciences  
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

Numanul Subhani, Luis Rueda, Alioune Ngom, Conrad Burden
2010 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology  
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

Peili Gu, Jeffrey G. Reid, Xiaolian Gao, Chad A. Shaw, Chad Creighton, Peter L. Tran, Xiaochuan Zhou, Rafal B. Drabek, David L. Steffen, David M. Hoang, Michelle K. Weiss, Arash O. Naghavi (+9 others)
2008 PLoS ONE  
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

Jaroslav Albert, Marianne Rooman
2011 Journal of Systems and Synthetic Biology  
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]

Jaroslav Albert, Marianne Rooman
2011 arXiv   pre-print
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

Bart De Moor, Kathleen Marchal, Janick Mathys, Yves Moreau
2003 European Journal of Control  
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

R. Maitra
2009 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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  
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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