Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CaArray_merco-00121: In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

ABSTRACT: Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determined by microarray analysis, revealing unique cell-specific profiles. Gene expression differences for malignant and nonmalignant epithelial cells (tumor versus benign hyperplastic epithelium) could be identified without being confounded by contributions from stroma that dominate many samples or sacrificing possible paracrine influences. Cell-specific expression of selected genes was validated by immunohistochemistry and quantitative PCR. The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations. merco-00121 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG_U95Av2 Organism: Homo sapiens (ncbitax) Material Types: whole_orrganism, synthetic_RNA, organism_part, total_RNA Disease States: Normal, Prostate Cancer

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Mervi Heiskanen

PROVIDER: E-GEOD-82132 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.

Stuart Robert O RO Wachsman William W Berry Charles C CC Wang-Rodriguez Jessica J Wasserman Linda L Klacansky Igor I Masys Dan D Arden Karen K Goodison Steven S McClelland Michael M Wang Yipeng Y Sawyers Anne A Kalcheva Iveta I Tarin David D Mercola Dan D

Proceedings of the National Academy of Sciences of the United States of America 20040101 2

Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determi ...[more]

PMID: 14722351

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Project description:The microarray gene expression pattern was studied using 798 different cancer cell lines. The cancer cell lines are obtained from different centers. Annotation information were provided in the supplementary file. golub-00327 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HT_HG-U133A Organism: Homo sapiens (ncbitax) Tissue Sites: leukemia, Urinary tract, Lung, BiliaryTract, Autonomic Ganglion, Thyroid gland, Stomach, Breast, Pancreas, Head and Neck, Lymphoma, Colorectal, Placenta, Liver, Brain, Bone, pleura, Skin, endometrium, Ovary, cervix, Oesophagus, Connective and Soft Tissue, Muscle, Kidney, Prostate, Adrenal Gland, Eye, Testis, Smooth Muscle Tissue, Vulva, Unknow Material Types: cell, synthetic_RNA, whole_organism, total_RNA, BVG Disease States: M3 acute myeloid leukemia, hairy cell leukemia, transitional cell carcinoma, Adenocarcinoma, B cell lymphoma unspecified, Acute Lymphoblastic Leukemia, blast phase chronic myeloid leukemia, Carcinoma, M6 acute myeloid leukemia, Neuroblastoma, follicular carcinoma, ductal carcinoma, Burkitt Lymphoma, Squamous Cell Carcinoma, M5 acute myeloid leukemia, Mycosis Fungoides and Sezary Syndrome, Acute T-Cell Lymphoblastic Leukemia, Adult T-Cell Leukemia/Lymphoma, M2 Therapy-Related Myeloid Neoplasm, Choriocarcinoma, Plasma Cell Myeloma, Hepatocellular Carcinoma, anaplastic large cell lymphoma, primitive neuroectodermal tumor-medulloblastoma, M4 acute myeloid leukemia, B Acute Lymphoblastic Leukemia, Acute Leukemia of Ambiguous Lineage, Osteosarcoma, Hodgkin Lymphoma, Mesothelioma, chondrosarcoma, Glioblastoma Multiforme, Malignant Melanoma, carcinosarcoma-malignant mesodermal mixed tumor, bronchioloalveolar adenocarcinoma, chronic lymphocytic leukemia-small lymphocytic lymphoma, micropapillary carcinoma, diffuse large B cell lymphoma, myelodysplastic syndrome, giant cell carcinoma, teratoma, multipotential sarcoma, Small Cell Carcinoma, ASTROCYTOMA, Fibrosarcoma, mucoepidermoid carcinoma, Rhabdomyosarcoma, L1 Acute T-Cell Lymphoblastic Leukemia, Glioma, Anaplastic Astrocytoma, Non-small cell carcinoma, Large Cell Carcinoma, mucinous carcinoma, Acute Myeloid Leukemia, malignant fibrous histiocytoma-pleomorphic sarcoma, clear cell carcinoma, B cell lymphoma unspecified, Anaplastic Carcinoma, Ewings sarcoma-peripheral primitive neuroectodermal tumor, undifferentiated carcinoma, Sarcoma, Embryonal Rhabdomyosarcoma, epithelioid sarcoma, renal cell carcinoma, carcinoid-endocrine tumor, Synovial Sarcoma, lymphoid neoplasm, rhabdoid tumor, Refractory Anemia with Excess Blasts, Liposarcoma, biphasic mesothelioma, adrenal cortical carcinoma, adenosquamous carcinoma, L2 Acute T-Cell Lymphoblastic Leukemia, chronic myeloid leukemia, Micropapillary Serous Carcinoma, desmoplastic, acute leukemia, Retinoblastoma, teratocarcinoma, clear cell renal cell carcinoma, Follicular Lymphoma, Wilms Tumor, M7 acute myeloid leukemia, gliosarcoma, embryonal carcinoma, Leiomyosarcoma, medullary carcinoma, granulosa cell tumor, papillary carcinoma, NS Acute Lymphoblastic Leukemia, papillary transitional cell carcinoma, small cell adenocarcinoma, epithelial dysplasia, hyperplasia, tubular adenocarcinoma, metaplasia, papillary ductal carcinoma, chronic eosinophilic leukemia-hypereosinophilic syndrome, #N/A, malignant trichilemmal cyst, Medullary Breast Carcinoma, L2 Acute Lymphoblastic Leukemia, Osteoblastic Osteosarcoma

Dataset Information

CaArray_merco-00121: In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

Publications

In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.

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