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TileMap
What’s New (Oct 1, 2007): (1) TileMap is upgraded to TileMap Version 2 (tilemapv2). (2) The new version is supported as part of CisGenome Project. This page will continue to be active to support TileMap version 1, but TileMap v2 will be supported through CisGenome website instead of here. !! (3) We have now developed a Graphic User Interface and a CisGenome Browser which allow you to visualize your data in the context of gene structures. Please go to CisGenome website for more information. The newly released CisGenome is a more powerful tool that supports not only tiling array analysis, but also various types of downstream analysis, including retrieving gene annotation, retrieving DNA sequences, motif discovery and motif mapping, key motif determination, etc.
What’s New (Mar 15, 2006): (1) A bug in tilemap_importaffy was reported and fixed. The bug was relevant to loading *.bpmap file (version 2 and above). What’s New (Nov 10, 2005): (1) TileMap source code is released together with the unix version. Users can use the enclosed makefile to compile the *.c files. (1) tilemap_importaffy is updated. The updated version can now handle the new affymetrix *.bpmap file format (version 1 to version 3). (2) Links to supplementary data are now posted on this website.
TileMap is a tool designed for tiling array data analysis. It can be used to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest. Basic algorithm and main features: (1) Tiling array is a new type of microarray that interrogates genomes with high density probes. TileMap is a two step procedure to create chromosomal map of tiling array hybridizations. In the first step, a test-statistic is computed for each probe based on a hierarchical empirical Bayes model. In the second step, the test-statistics of probes within a genomic region are used to infer whether the region is of interest or not (i.e. whether it shows transcriptional activities or protein binding patterns of interest). (2) TileMap can be used to search for complex transcriptional or protein binding patterns such as "(mutant 1 < wild type < mutant 2) and [tumor > wild type) or (tumor <mutant 5)]". (3) TileMap uses a hierarchical empirical Bayes model to pool information from all probes across the array. The model significantly increases the sensitivity of the analysis when there are only 2~3 replicates within each condition. (4) Users can choose to combine neighboring probes either by using a Hidden Markov Model (HMM) or a Moving Average method (MA). (5) TileMap uses Unbalanced Mixture Subtraction (UMS) to provide approximate local false discovery rate (lfdr) estimates for MA and provide model parameters for HMM. Compared with permutation test, UMS performs better in providing lfdr for complex multiple sample comparisons such as "mt1<wt<mt2". While UMS intends to estimate lfdr for a null hypothesis H0: "not {mt1<wt<mt2}", permutation test usually can only provide lfdr for a null H0': "mt1=wt=mt2". The algorithm used by TileMap is described in: Ji, H. and Wong, W.H. (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21(18):3629-3636. [PDF] [Supplemetary Data] Data to support the paper can be downloaded here: The executable version of TileMap can be downloaded here: (a) Readme (b) Executables: Windows, Unix After you downloaded and unzipped TileMap (Windows users can use WinZip, RAR, etc. to unzip the package; Mac OS X users can use "gzip -d tilemap_macosx.tar.gz" and then "tar xvf tilemap_macosx.tar"; users of other unix platforms can request source code from the address below and run "makefile"), you should find the following test data files in the directory where TileMap is installed. If not, you can download them here: (c) Sample Data: testdata.txt (d) Sample Parameter Files: testarg.txt, test.cmpinfo Then you can enter the directory where TileMap is installed and try to run it as follows: > tilemap testarg.txt Note: Windows users can choose Windows "Start" menu, click "Run", type "cmd", press Enter. A window will be opened for you to input commands. Enter the directory where TileMap is installed using "cd [path]" command, and run TileMap as above. If TileMap is installed correctly, it should start to analyze the test data. If you encountered problems or bugs when using TileMap, please email hji@jhsph.edu. Academic users who wish to run TileMap on other platforms can email hji@jhsph.edu to get source code in ANSI C. Detailed instructions on how to use TileMap and a few examples can be found here:
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