Gene expression trees in lymphoid development

doi:10.1186/1471-2172-8-25

BMC Immunology

Volume 8

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Methodology article

Gene expression trees in lymphoid development

Ivan G Costa^* , Stefan Roepcke^* and Alexander Schliep

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

author email corresponding author email* Contributed equally

BMC Immunology 2007, 8:25doi:10.1186/1471-2172-8-25


Published:	9 October 2007

Additional files

Additional data file 1:

Protocol. This file contains information on software implementations, derivations of estimation formulas and additional experiments with simulated data.

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Additional data file 2:

Supplementary Figures. Figures 1, 2 and 3 contains all clusters results from MixDTrees on BCell, TCell and LymphoidTree, and Figure 4 contains BIC results from LymphoidTree. Figures 5 and 6 contain comparisons between microRNA enrichment with MixDTrees-MAP and SOM in TCell and BCell, Figures 7 and 8 depict the empirical cumulative distribution function (cdf) of microRNA enrichment p-values from TCell and BCell, and Figures 9 and 10 contain comparisons between microRNA enrichment with MixDTrees-MAP and MixDTrees-MLE in TCell and BCell. Figure 11 describes the cluster size distribution of clustering results in TCell and BCell.

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Additional data file 3:

Supplementary Tables. Tables 1, 2 and 3 contains correlation matrices from BCell, TCell and LymphoidTree datasets; Tables 4, 5 and 6 contains enriched microRNA and gene targets from SOM results on TCell and BCell and from MixDTrees-MAP results on LymphoidTree; Tables 7, 8, 9 contains microRNA enrichment p-values for BCell, TCell and LymphoidTree on MixDTrees-MAP results; Tables 10 and 11 contains microRNA enrichment p-values for BCell and TCell on SOM results; Tables 12 and 13 contain the contingency tables comparing clusters from MixDTrees-MAP and SOM with BCell and TCell datasets; and Tables 14 and 15 contain the contingency tables comparing clusters from MixDTrees-MAP and MixDTrees-MLE with BCell and TCell datasets.

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Additional data file 4:

TCell Dataset. Data set after filtering and normalization procedures. The second column indicates the cluster assignment found by the MixDTrees.

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Additional data file 5:

BCell Dataset. Data set after filtering and normalization procedures. The second column indicates the cluster assignment found by the MixDTrees.

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Additional data file 6:

LymphoidTree Dataset. Data set after filtering and normalization procedures. The second column indicates the cluster assignment found by the MixDTrees.

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Additional data file 7:

SIM Datasets. Data sets from simulated MixDTrees. See readme.txt for file descriptions. The first column indicates the true label of the sample.

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