Table 1 Information of the included datasets
Category | GEO accession number | Platform | Sample type | Sample size | Experiment design | |
|---|---|---|---|---|---|---|
Gene | Tumor vs. normal | GSE11414 | GPL6244 | Cell lines | Tumor: 4; normal: 2 | genome-wide comparison of gene expression and identified genes that are differentialy expressed in osteosarcoma (U2OS, MG63) cell lines relative to normal human osteoblasts (HOB) |
GSE12865 | GPL6244 | Tumor tissues and normal cell line | Tumor: 12; normal: 2 | genome-wide comparison of gene expression and identified genes that are differentialy expressed in osteosarcoma tumour samples relative to normal human osteoblasts (HOB) | ||
GSE14359 | GPL96 | Tumor tissues and normal cell line | Tumor: 18; normal: 2 | mRNA from 5 frozen conventional osteosarcoma and 4 osteosarcoma lung metastases tumor samples and mRNA from fresh primary osteoblast cells (HOB) were extracted and hybridized to HG U133A microarrays | ||
GSE16088 | GPL96 | Tumor and normal tissues, as well as tumor cell lines | Tumor: 17; normal: 6 | Profiles of human osteosarcoma and three normal tissues, single channel design | ||
GSE19276 | GPL6848 | Tumor and normal tissues | Tumor: 44; normal: 5 | Gene expression profiling of primary osteosarcoma biopsies and compared the results to gene expression profiling of non-malignant bone to identify differentially expressed genes unique to OS in the context of the bone micorenvironment | ||
GSE28424 | GPL13376 | Tumor cell lines and normal tissues | Tumor: 19; normal: 4 | 19 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones. | ||
GSE30807 | GPL570 | Tumor cell lines and normal bone mesenchymal stem cells | Tumor: 2; normal: 1 | To analysis stem/progenitor cell-associated genes and molecules involved in regulation of self-renewal signaling pathways of cancer stem cells between UT2 cells and its parent cells: U2OS (MSC works as positive control here) | ||
GSE36001 | GPL6102 | Tumor cell lines and normal osteoblast and bone cells. | Tumor: 19; normal: 6 | Comparison of gene expression patterns in 19 osteosarcoma cell lines and 6 normal samples (osteoblasts and bones) | ||
GSE42352 | GPL10295 | Tumor cell lines, pre-chemotherapy biopsies, osteoblasts, mesenchymal stem cells | Tumor: 103; normal: 15 | Gene set analysis on previously published genome-wide gene expression data of osteosarcoma cell lines (n = 19) and osteosarcoma pre-chemotherapy biopsies (n = 84), and characterizing expression of the insulin-like growth factor receptor signaling pathways in human osteosarcoma as compared with osteoblasts and with the hypothesized progenitor cells of osteosarcoma - mesenchymal stem cells. | ||
GSE56001 | GPL10558 | Tumor cells and normal mesenchymal stem cells | Tumor: 3; normal: 9 | Analysis of gene changes in different genes modulation in mesenchymal stem cells and compared to primary human osteosarcoma cells | ||
GSE9508 | GPL6076 | Tumor and normal biopsies | Tumor: 34; normal: 5 | Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates). | ||
Metastasis vs. non-metastasis | GSE14359 | GPL96 | Conventional osteosarcoma and lung metastases tumor samples | Metastasis: 8; non-metastasis: 10 | mRNA from 5 frozen conventional osteosarcoma and 4 osteosarcoma lung metastases tumor samples and mRNA from fresh primary osteoblast cells (HOB) were extracted and hybridized to HG U133A microarrays | |
GSE18947 | GPL570 | Low and high metastatic potential cell sublines | Low metastasis: 3; high metastasis: 3 | The assay was performed among three pairs of cublines, the first two pairs of sublines comes from the different passage of sublines established with orthotopic transplantation under the established cell line named Sosp-9607, the other pair was screened by the tail-vein injection method of commercial avaliable cell line-Saos-2. | ||
GSE21257 | GPL10295 | Metastatic and non-metastatic tumor biopsies | Metastasis: 34; non-metastasis: 19 | Pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5 yrs. (n = 34) were compared with pre-chemotherapy biopsies of osteosarcoma patients who did not develop metastases within 5 yrs. (n = 19) | ||
GSE9508 | GPL6076 | Metastatic and non-metastatic tumor biopsies | Metastasis: 21; non-metastasis: 13 | Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates). | ||
Drug-treated vs. untreated | GSE16089 | GPL570 | Methotrexate-sensitive and –resistant Saos-2 cells | Methotrexate-sensitive samples: 3; methotrexate-resistant samples: 3 | Two cell lines are compared, which are Saos-2 osteosarcoma cells sensitive to methotrexate and Saos-2 cells resistant to 10e-6 M methotrexate. Six samples are provided which correspond to triplicates of each cell line. | |
GSE24401 | GPL1456 | Atorvastatin-treated and -untreated Saos-2 cells | Atorvastatin-treated samples: 3; atorvastatin-untreated samples: 3 | Dye balance-experiment comparing atorvastatin treated Saos-2 cells versus untreated cells at 6, 15 and 24 h using 2 biological replicates | ||
miRNA | GSE28423 | GPL8227 | Tumor cell lines and normal bones | Tumor cell lines: 19; normal bones: 4 | 19 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones. | |
CNV | GSE12830 | GPL4091, GPL9128 | Tumor tissues | 20 | Integrative whole-genome analysis of DNA copy number, promoter methylation and gene expression using 10 osteosarcomas with 2 biological replicates | |
GSE7077 | GPL2879 | Four osteosarcoma-derived cell lines: U-2 OS, HOS, MG-63 and SAOS-2 | 4 | To utilize oligonucleotide array CGH to identify microaberrations in osteosarcomas, likely to contain genes involved in osteosarcoma tumor oncogenesis. A better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of prognostic markers and therapeutic targets. | ||
GSE9654 | GPL2879 | 10 | To utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in osteosarcoma tumors | |||