Tilescope: online analysis pipeline for high-density tiling microarray data

We developed Tilescope, a fully integrated data processing pipeline for analyzing high-density tiling-array data http://tilescope.gersteinlab.org. In a completely automated fashion, Tilescope will normalize signals between channels and across arrays, combine replicate experiments, score each array element, and identify genomic features. The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis.

[1]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[2]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[3]  G. Phillips,et al.  Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[5]  Wing Hung Wong,et al.  TileMap: create chromosomal map of tiling array hybridizations , 2005, Bioinform..

[6]  Paul P. Gardner,et al.  A hidden Markov model approach for determining expression from genomic tiling micro arrays , 2006, BMC Bioinformatics.

[7]  Clifford A. Meyer,et al.  Model-based analysis of tiling-arrays for ChIP-chip , 2006, Proceedings of the National Academy of Sciences.

[8]  Mark Gerstein,et al.  Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. , 2005, Trends in genetics : TIG.

[9]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[10]  S. Cawley,et al.  Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.

[11]  S. Dudoit,et al.  STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS , 2002 .

[12]  Franco Cerrina,et al.  Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. , 2002, Genome research.

[13]  Mark Gerstein,et al.  Bioinformatics Original Paper a Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and Chip-chip Experiments: Systematically Incorporating Validated Biological Knowledge , 2022 .

[14]  Russ B. Altman,et al.  Nonparametric methods for identifying differentially expressed genes in microarray data , 2002, Bioinform..

[15]  Wolfgang Huber,et al.  Transcript mapping with high-density oligonucleotide tiling arrays , 2006, Bioinform..

[16]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[17]  Scott A. Rifkin,et al.  A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster , 2004, Science.

[18]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[19]  Mark Gerstein,et al.  ExpressYourself: a modular platform for processing and visualizing microarray data , 2003, Nucleic Acids Res..

[20]  Deyou Zheng,et al.  Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. , 2007, Genome research.

[21]  S. Cawley,et al.  Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.

[22]  B. Matthews.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.

[23]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[24]  Alexander Eckehart Urban,et al.  High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Xiang-Jun Lu,et al.  Detecting transcriptionally active regions using genomic tiling arrays , 2006, Genome Biology.

[26]  Michael Snyder,et al.  ChIP-chip: a genomic approach for identifying transcription factor binding sites. , 2002, Methods in enzymology.

[27]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[28]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[29]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[30]  Markus Wistrand,et al.  Improving profile HMM discrimination by adapting transition probabilities. , 2004, Journal of molecular biology.

[31]  Clifford A. Meyer,et al.  A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences , 2005, ISMB.

[32]  Aled M. Edwards,et al.  Unfolding of Microarray Data , 2002, J. Comput. Biol..