Additional file 22: Figure S8. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

Cluster heatmap of gene expression data for pfcrt/pfmdr1 and all other genes. The hierarchical clustering was generated using PCC values calculated using log2-transformed and normalized expression values of 2,600 genes across 110 pairwise comparisons of 11 parasite transcriptome data sets, corresponding to all possible combinations in both directions (i.e. A vs. B and B vs. A). Squares indicate areas containing genes that are all strongly correlated or strongly anti-correlated with the expression of both pfcrt and pfmdr1. (PDF 499 kb

Consensus ensemble -clustering tree reveals the recursive splitting of breast cancer subtypes

<p><b>Copyright information:</b></p><p>Taken from "Portraits of breast cancer progression"</p><p>http://www.biomedcentral.com/1471-2105/8/291</p><p>BMC Bioinformatics 2007;8():291-291.</p><p>Published online 6 Aug 2007</p><p>PMCID:PMC1978212.</p><p></p> At = 2, the ensemble clustering split the normal samples from the disease samples. At = 3, the normal cluster remained unchanged and the disease samples split into low grade (pathological grades 1 and 2) and high grade (pathological grades 2 and 3). The optimum number of clusters in the data was seven corresponding to one normal cluster, two low grade clusters and four high grade clusters. Between two values, the samples did not switch clusters, indicating that the hierarchical structure in the figure is a strong property of the data. In the final disease clusters, samples from the same patient microdissected from DCIS and IDC lesions were found in the same cluster, indicating that the disease subtypes are more heterogeneous than disease progression within a subtype

The agreement matrix for Nsamples is an N× Nmatrix whose entries are the fraction of cases across replicates for which two samples fall into the same cluster

<p><b>Copyright information:</b></p><p>Taken from "Portraits of breast cancer progression"</p><p>http://www.biomedcentral.com/1471-2105/8/291</p><p>BMC Bioinformatics 2007;8():291-291.</p><p>Published online 6 Aug 2007</p><p>PMCID:PMC1978212.</p><p></p> Red/green represent high/low fractional values across clustering methods and data perturbation replicates. The normals and the LG1 and LG2 are clearly well separated while the HG1, HG2, HG3 and HG4 separation is weaker. We find that the optimum number of clusters using gap-statistics oscillates between 6 and 7 with the HG3 and HG4 clusters merging at -6

Heatmap of expression levels of the top markers for progression from DCIS to IDC in the low grade and high grade tumor subgroups

<p><b>Copyright information:</b></p><p>Taken from "Portraits of breast cancer progression"</p><p>http://www.biomedcentral.com/1471-2105/8/291</p><p>BMC Bioinformatics 2007;8():291-291.</p><p>Published online 6 Aug 2007</p><p>PMCID:PMC1978212.</p><p></p> In each subtype, we use the upregulated genes which have good FDR under WV to stratify the samples. We show the 10 top genes for DCIS to IDC progression in LG and HG tumors. Since the sample sizes were small, the p values were computed using permutation tests and the FDR values were computed from these p values. The FDR values under WV for these genes are 0.6 for LG and 0.2 for HG

Heatmap of expression levels of the top 10 upregulated genes for progression from DCIS to IDC for each subtype

<p><b>Copyright information:</b></p><p>Taken from "Portraits of breast cancer progression"</p><p>http://www.biomedcentral.com/1471-2105/8/291</p><p>BMC Bioinformatics 2007;8():291-291.</p><p>Published online 6 Aug 2007</p><p>PMCID:PMC1978212.</p><p></p> Each subgroup is in a framed box to identify its samples and distinguish gene markers. Since the sample sizes are small, the p values were computed using permutation tests and the FDR rates inferred from these p values. The FDR rates under WV for these genes are: 0.02 for LG1, 0.2 for LG2, 0.2 for HG1, 0.5 for HG2, 0.06 for HG3 and 0.002 for HG4