Gene Set: NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP

Standard name NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP
Systematic name M17951
Brief description Top 100 probe sets contrubuting to the positive side of the 1st principal component; predominantly associated with spindle cell and pleomorphic sarcoma 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 gene sets
      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 (+)
Related gene sets (show 3 additional gene sets from the source publication)

(show 180 gene sets from the same authors)
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Organism Homo sapiens
Contributed by Nikolaos Papanikolaou (Aristoteles University of Thessaloniki)
Source platform AFFY_HG_U133
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Compendia expression profiles GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.0: First introduced

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