Gene expression profiles of NSCLC tumors
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Chari Raj
PROVIDER: S-ECPF-GEOD-31799 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:A custom microarray was used to measure the gene expression of NSCLC tumors. This represents a subset of samples which also have matched DNA copy number profiles from array CGH experiments
2011-09-12 | GSE31799 | GEO
Project description:A custom microarray was used to measure the gene expression of NSCLC tumors. This represents a subset of samples which also have matched DNA copy number profiles from array CGH experiments 49 microdissected NSCLC tumor samples
2011-09-11 | E-GEOD-31799 | biostudies-arrayexpress
Project description: Not available
| S-DIXA-D-1167 | biostudies-other
Project description:It has been debated for decades how cancer cells acquire metastatic capability. It is unclear whether metastases are derived from distinct subpopulations of tumor cells within the primary site with higher metastatic potential, or whether they originate from a random fraction of tumor cells. Here we show, by gene expression profiling, that human primary breast tumors are strikingly similar to the distant metastases of the same patient. Unsupervised hierarchical clustering, multidimensional scaling, and permutation testing, as well as the comparison of significantly expressed genes within a pair, reveal their genetic similarity. Our findings suggest that metastatic capability in breast cancer is an inherent feature and is not based on clonal selection.
| S-EPMC307665 | biostudies-literature
Project description:BackgroundChondrosarcomas are malignant cartilage tumors that do not respond to traditional chemotherapy or radiation. The 5-year survival rate of histologic grade III chondrosarcoma is less than 30%. An animal model of chondrosarcoma has been established--namely, the Swarm Rat Chondrosarcoma (SRC)--and shown to resemble the human disease. Previous studies with this model revealed that tumor microenvironment could significantly influence chondrosarcoma malignancy.MethodsTo examine the effect of the microenvironment, SRC tumors were initiated at different transplantation sites. Pyrosequencing assays were utilized to assess the DNA methylation of the tumors, and SAGE libraries were constructed and sequenced to determine the gene expression profiles of the tumors. Based on the gene expression analysis, subsequent functional assays were designed to determine the relevancy of the specific genes in the development and progression of the SRC.ResultsThe site of transplantation had a significant impact on the epigenetic and gene expression profiles of SRC tumors. Our analyses revealed that SRC tumors were hypomethylated compared to control tissue, and that tumors at each transplantation site had a unique expression profile. Subsequent functional analysis of differentially expressed genes, albeit preliminary, provided some insight into the role that thymosin-?4, c-fos, and CTGF may play in chondrosarcoma development and progression.ConclusionThis report describes the first global molecular characterization of the SRC model, and it demonstrates that the tumor microenvironment can induce epigenetic alterations and changes in gene expression in the SRC tumors. We documented changes in gene expression that accompany changes in tumor phenotype, and these gene expression changes provide insight into the pathways that may play a role in the development and progression of chondrosarcoma. Furthermore, specific functional analysis indicates that thymosin-?4 may have a role in chondrosarcoma metastasis.
| S-EPMC2944175 | biostudies-literature
Project description:Gene expression profiling of NSCLC tissues let to the establishment of several prognostic, predictive gene signatures with little overlap. To study factors introducing variability into gene expression microarray studies we compared interpatient (patient-to-patient) and intrapatient (tumor sub-sample) variations in gene expression profiles in stage I and II NSCLC tissues. We identified 128 probe sets which showed variable intratumoral expression Four different sites (A,B,C,D) of individual primary tumors and matched distant normal lung tissue (N) from 20 patients were used to establish gene expression patterns captured by Affymetrix HG-U133 Plus 2.0 arrays (n = 100).
| S-ECPF-GEOD-33532 | biostudies-other
Project description:The Lung3 data set consists of 89 NSCLC patients that were treated at MAASTRO Clinic, The Netherlands. For these patients pretreatment CT scans, tumour delineations and gene expression profiles were available. We used this data set to associate imaging features with gene-expression profiles. 89 samples from NSCLC patients. Samples were obtained by biopsies from cancerous tissue. Tumors were classified as Adenocarcinoma, Papillary, NOS; Squamous Cell Carcinoma, NOS; Non-Small Cell; Papillary Type; or Solid Type.
| S-ECPF-GEOD-58661 | biostudies-other
Project description:Whole genome tiling path array CGH was used to measure the copy number profiles of 271 NSCLC tumors
2011-09-12 | GSE31798 | GEO
Project description:The molecular pathology of precursor lesions leading to invasive pancreatic ductal adenocarcinomas remains relatively unknown. We have applied cDNA microarray analysis to characterize gene expression profiles in a series of intraductal papillary-mucinous tumors (IPMTs) of the pancreas, which represents one of the alternative routes of intraepithelial progression to full malignancy in the pancreatic duct system. Using a cDNA microarray containing 4992 human genes, we screened a total of 13 IPMTs including nine noninvasive and four invasive cases. Expression change in more than half of the tumors was observed for 120 genes, ie, 62 up-regulated and 58 down-regulated genes. Some of the up-regulated genes in this study have been previously described in classical pancreatic carcinomas such as lipocalin 2, galectin 3, claudin 4, and cathepsin E. The most highly up-regulated genes in IPMTs corresponded to three members of the trefoil factor family (TFF1, TFF2, and TFF3). Immunohistochemistry performed on five genes found to be differentially expressed at the RNA level (TFF1, TFF2, TFF3, lipocalin 2, and galectin 3) showed a good concordance between transcript level and protein abundance, except for TFF2. Hierarchical clustering organized the cases according to the dysplastic and invasive phenotype of theIPMTs. This analysis has permitted us to implicate several genes (caveolin 1, glypican 1, growth arrest-specific 6 protein, cysteine-rich angiogenic inducer 61) in tumor progression. The observation that several genes are differentially expressed both in IPMTs and pancreatic carcinomas suggests that they may be involved at an early stage of pancreatic carcinogenesis.
| S-EPMC1850868 | biostudies-literature
Project description:Whole genome tiling path array CGH was used to measure the copy number profiles of 271 NSCLC tumors 271 microdissected NSCLC tumors
2011-09-11 | E-GEOD-31798 | biostudies-arrayexpress