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89 NSCLC patients with gene expression profiles and matching CT imaging data available at TCIA.

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Patrick Grossmann

PROVIDER: E-GEOD-58661 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.

Aerts Hugo J W L HJ Velazquez Emmanuel Rios ER Leijenaar Ralph T H RT Parmar Chintan C Grossmann Patrick P Carvalho Sara S Bussink Johan J Monshouwer René R Haibe-Kains Benjamin B Rietveld Derek D Hoebers Frank F Rietbergen Michelle M MM Leemans C René CR Dekker Andre A Quackenbush John J Quackenbush John J Gillies Robert J RJ Lambin Philippe P

Nature communications 20140603

Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features ...[more]

PMID: 24892406

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89 NSCLC patients with gene expression profiles and matching CT imaging data available at TCIA.

2014-06-19 | GSE58661 | GEO

89 NSCLC patients with gene expression profiles and matching CT imaging data available at TCIA

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

Enterobacteriaceae bacterium 89 strain:89

Project description:Enterobacteriaceae bacterium 89 strain:89 Genome sequencing and assembly

| PRJNA505115 | ENA

Expression analysis of ZBP-89 deficient human primary erythroid progenitors

Project description:The molecular mechanisms underlying erythroid-specific gene regulation remain incompletely understood. Closely spaced binding sites for GATA, NF-E2/maf and CACCC interacting transcription factors play functionally important roles in globin and other erythroid-specific gene expression. We and others recently identified the CACCC-binding transcription factor ZBP-89 as a novel GATA-1 and NF-E2/mafK interacting partner. Here, we examined the role of ZBP-89 in human globin gene regulation and erythroid maturation using a primary CD34+ cell ex vivo differentiation system. We show that ZBP-89 protein levels rise dramatically during human erythroid differentiation, and that ZBP-89 occupies key cis-regulatory elements within the globin and other erythroid gene loci. ZBP-89 binding correlates strongly with RNA Pol II occupancy, active histone marks, and high-level gene expression. ZBP-89 physically associates with the histone acetyltransferases (HATs) p300 and Gcn5/Trrap, and occupies common sites with Gcn5 within the human globin loci. Lentiviral shRNA knockdown of ZBP-89 results in reduced Gcn5 occupancy, decreased acetylated histone 3 levels, lower globin and erythroid-specific gene expression, and impaired erythroid maturation. Addition of the HDAC inhibitor valproic acid partially reverses the reduced globin gene expression. These findings reveal an activating role for ZBP-89 in human globin gene regulation and erythroid differentiation. Keywords: Human primary erythroid progenitors

2011-08-02 | GSE31092 | GEO

Sinorhizobium meliloti strain:89

Project description:Sinorhizobium meliloti 89 Resequencing

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89 ccRCC UMI panel

Project description:Gene panel sequencing data of 89 clear cell renal cell carcinoma patients (ccRCC)

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Piscirickettsia salmonis LF-89 = ATCC VR-1361 isolate:Lf-89

Project description:Piscirickettsia salmonis LF-89 = ATCC VR-1361 isolate:Lf-89 Raw sequence reads

| PRJNA383157 | ENA

Expression analysis of ZBP-89 deficient human primary erythroid progenitors

2011-08-01 | E-GEOD-31092 | biostudies-arrayexpress

Molecular Classification and Prediction of Survival in Non-Small-Cell Lung Cancer

Project description:BACKGROUND: Global gene expression analysis provides a comprehensive molecular characterization of non-small cell lung cancer. The aim of this study was to evaluate the feasibility of integrating expression profiling into routine clinical work-up by including minute bronchoscopic biopsies and develop a robust prognostic gene expression signature METHODS: Tissue samples from a series of 41 chemotherapy-naïve non-small cell lung cancer patients and 15 control patients with inflammatory lung diseases were obtained during routine clinical work-up and gene expression profiles were gained using a highly sensitive oligonucleotide array platform (Novachip ; 34'207 transcripts). Gene expression signatures were analyzed by correlation with histological and clinical parameters and validated on independent published datasets and immunohistochemistry. RESULTS: Tumor tissue classification based on the gene expression results was strongly dependent on the proportion of tumor cells present in the biopsies and showed an overall sensitivity of 80% and specificity of 89%. For prognostication we developed a metagene consisting of 13 genes, which was validated on 4 independent published datasets. The robustness of this metagene has been demonstrated by a virtual independence from tumor cells present in the biopsies. Furthermore, vascular endothelial growth factor-beta, one of the key prognostic genes was validated by immunohistochemistry on 508 independent tumor samples. CONCLUSIONS: The proposed strategy of integrating functional genomics into routine clinical work-up allows molecular tumor classification and prediction of survival in patients with non-small cell lung cancer of all stages and is suitable for an integration in the daily clinical practice. Keywords: Gene expression profiling for disease state analysis in lung cancer patients 56 lung biopsies, 4 different Phenotypes: NSCLC-squa., NSCLC-NOS, NSCLC-Adeno, Ctr.-Infl.

2008-04-10 | E-GEOD-11117 | biostudies-arrayexpress

Chlamydia psittaci 89-13210

Project description:Chlamydia psittaci 89-13210 Genome sequencing

| PRJNA77041 | ENA