Additional file 6 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

Table S5. Classification results. The results of classification of the BCCA and the MILE cases using our decision tree are available as part of the online supplementary materials. The first sheet reports classification results of 176 BCCA patients. For each case sample ID, age, gender and the corresponding cohort are reported. The other columns of the table include: • Sequenced Tissue: Bone marrow (BM) or peripheral blood (PB). • RIN: The RNA Integrity Number, a value in the range of 1–10 measuring the quality of the RNA samples [84]. A higher value corresponds to less degradation of RNA. • Subtype: The AML subtypes were diagnosed based on chromosomal abnormalities and other factors. AML-NK stands for AML with normal karyotype. tAML and tMDS are therapy related. • Type: All AML subtypes were labeled as AML. MDS and tMDS were labeled as MDS, and 21 gray-highlighted cases that had clinical and pathological characteristics of both diseases were labeled as AML-MDS. • Prediction (Full Tree) The label predicted by the decision tree using the inferred extracellular matrix and HOXA&B eigengenes. relevant misclassified. • Prediction (Shrunk Tree) The label predicted by the shrunk decision tree using expression of only 14 genes from the extracellular matrix and HOXA&B modules. • Signature The leaf of the full decision tree determined based on the expression of the extracellular matrix (ECM) and HOXA&B eigengenes. Similarly, the second sheet reports classification results of 366 patients from the MILE dataset. Additional information such as IPSS, blast, and karyotype categories are included from MILE study [16]. The misclassified cases by either the full or the shrunk tree are highlighted in yellow. (XLS 155 kb)