Transcription profiling of soft tissue tumors 10 cases of DTF (blue) and 13 cases of SFT (orange)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Janos Demeter
PROVIDER: E-SMDB-3271 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Determination of stromal signatures in breast carcinoma.
West Robert B RB Nuyten Dimitry S A DS Subramanian Subbaya S Nielsen Torsten O TO Corless Christopher L CL Rubin Brian P BP Montgomery Kelli K Zhu Shirley S Patel Rajiv R Hernandez-Boussard Tina T Goldblum John R JR Brown Patrick O PO van de Vijver Marc M van de Rijn Matt M
PLoS biology 20050510 6
Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patte ...[more]
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Project description:Abstract: Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells. Soft tissue tumor gene expression of 10 cases of DTF (blue), 13 cases of SFT (orange), and 35 other previously examined soft tissue tumors (black) based expression profiling on 42,000 -element cDNA microarrays. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Computed
2006-03-14 | E-GEOD-4305 | biostudies-arrayexpress
Project description:Abstract: Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells. Soft tissue tumor gene expression of 10 cases of DTF (blue), 13 cases of SFT (orange), and 35 other previously examined soft tissue tumors (black) based expression profiling on 42,000 -element cDNA microarrays. A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Keywords: clinical_history_design
2006-03-15 | GSE4305 | GEO
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2018-12-28 | GSE120025 | GEO
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits.
2012-06-22 | GSE22505 | GEO
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits. Investigate the transcriptome changes during five fruit developmental stages of two sweet orange genotypes
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