Figure 1

Multi-dimensional scaling of all 96 mesenchymal tumor samples. There are 19 types of tumor shown; the color coding of which is used consistently for all figures. All gene expression values were used to calculate the inter-sample Euclidean distance matrix. The distances are translated here onto a two-dimensional plane using the classical cmd-scale algorithm of R. The stress of the plot was 0.34; an index of the goodness of fit between the original distance matrix and the MDS distance (see Materials and methods). WLS, well-differentiated liposarcoma; LMA, lipoma; MLS, myxoid liposarcoma; EWS, Ewing's sarcoma; FMT, desmoid fibromatosis; CHS, chondrosarcoma; CHB, chondroblastoma; ARMS, alveolar rhabdomyosarcoma; ERMS, embryonal rhabdomyosarcoma; DCS, de-differentiated chondrosarcoma; MSS, monophasic synovial sarcoma; MPNST, malignant peripheral nerve sheath tumors; CMF, chondromyxoid fibroma; PMS, pleomorphic sarcoma; LMS, leiomyosarcoma; OS, osteosarcoma; CMA, chordoma; NFB, neurofibroma; SWN, schwannoma.