Human Gene Set: NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN


Standard name NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN
Systematic name M17937
Brief description Top 100 probe sets contrubuting to the negative side of the 1st principal component; predominantly associated with synovial sarcoma and myxoid/round cell liposarcoma samples.
Full description or abstract In soft tissue sarcomas, the diagnosis of malignant fibrous histiocytoma (MFH) has been a very controversial issue, and MFH is now considered to be reclassified into pleomorphic subtypes of other sarcomas. To characterize MFH genetically, we used an oligonucleotide microarray to analyze gene expression in 105 samples from 10 types of soft tissue tumors. Spindle cell and pleomorphic sarcomas, such as dedifferentiated liposarcoma, myxofibrosarcoma, leiomyosarcoma, malignant peripheral nerve sheath tumor (MPNST), fibrosarcoma and MFH, showed similar gene expression patterns compared to other tumors. Samples from those five sarcoma types could be classified into respective clusters based on gene expression by excluding MFH samples. We calculated distances between MFH samples and other five sarcoma types (dedifferentiated liposarcoma, myxofibrosarcoma, leiomyosarcoma, MPNST and fibrosarcoma) based on differentially expressed genes and evaluated similarities. Three of the 21 MFH samples showed marked similarities to one of the five sarcoma types, which were supported by histological findings. Although most of the remaining 18 MFH samples showed little or no histological resemblance to one of the five sarcoma types, 12 of them showed moderate similarities in terms of gene expression. These results explain the heterogeneity of MFH and show that the majority of MFHs could be reclassified into pleomorphic subtypes of other sarcomas. Taken together, gene expression profiling could be a useful tool to unveil the difference in the underlying molecular backgrounds, which leads to a rational taxonomy and diagnosis of a diverse group of soft tissue sarcomas.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 17464315   Authors: Nakayama R,Nemoto T,Takahashi H,Ohta T,Kawai A,Seki K,Yoshida T,Toyama Y,Ichikawa H,Hasegawa T
Exact source Table 3S: 1st PCA genes (-)
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Source species Homo sapiens
Contributed by Nikolaos Papanikolaou (Aristoteles University of Thessaloniki)
Source platform or
identifier namespace		 AFFY_HG_U133
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NCI-60 cell lines (National Cancer Institute)
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Version history 3.0: First introduced

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