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:Soft Tissue Tumor Gene Expression of Ten Cases of DTF (blue) and Thirteen Cases of SFT (orange), Based on Expression Profiling on 42,000 Element cDNA Microarrays.
| S-ECPF-SMDB-3271 | biostudies-other
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
Project description:In 1976, a spontaneous mutant derived from Poncirus trifoliata (L.) Raf with short juvenile phase, namely, precocious trifoliate orange, was found in Yichang, Hubei province, China. Compared with 6 to 8 years of the wild-type trifoliate orange, almost all of the seedlings germinated from precocious trifoliate orange only have 1 to 2 years’ juvenile period, and 20% seedlings even flowered in the year after germination. Therefore, precocious trifoliate orange is an ideal material for studying the role of miRNAs involved in citrus juvenile and adult developmental stages. To characterize these miRNAs expressed at the juvenile and adult development stages of citrus, Affymetrix miRNA arrays were used to generate miRNA profiles of shoot meristems of trifoliate orange, the results revealed that some miRNAs were down-regulated expressed at adult stage compared with juvenile stage. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated.
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Project description:Background/purpose:Oral metastatic carcinomas are rarely found in oral soft tissues. This study reported the clinicopathological features of 13 intraoral soft tissue metastatic carcinomas. Materials and methods:A total of 13 intraoral soft tissue metastatic carcinomas were included in this study. The clinicopathological features of the 13 cases including the primary cancer site, metastatic intraoral soft tissue region, clinical presentation, and histopathological diagnoses were examined and reported. Results:The 13 intraoral soft tissue metastatic carcinomas occurred in 13 patients (11 males and 2 females) with a mean age of 59.4 (range, 39-78) years. Nine cases originated from the liver (69.2%), and one each from the colon (7.7%), pancreas (7.7%), thyroid (7.7%), and kidney (7.7%). The histopathological diagnoses of the metastatic lesions were hepatocellular carcinoma in 9 cases, adenocarcinomas in 2 cases (one each from the colon and pancreas), clear cell carcinoma of the kidney in one case, and follicular thyroid carcinoma in one case. The gingiva and alveolar mucosa were the major metastatic sites (10 cases, 76.9%), followed by the buccal mucosa (two cases, 15.4%), and soft palate (one case, 7.7%). Twelve metastatic lesions manifested as ulcerated, easy-bleeding, and pyogenic granuloma-like lesions. Conclusion:The results of our series of 13 cases indicate that intraoral soft tissue metastatic carcinomas have a male predilection with a male to female ratio of 11:2, are commonly found in the gingiva and alveolar mucosa (76.9%), present frequently as an easy-bleeding pyogenic granuloma-like lesion (92.3%). In addition, the most common primary cancer site is the liver.
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Project description:Gene expression profiling reveals a potential role of Orange cells (BT-OC) in stimulating hair growth in dermal papilla cells. HFDPCs were human primary cells line, treated with 1:2000 Orange cells (BT-OC) for 48 h. Microarray gene expression profiling was conducted for three biological replicates
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Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.
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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.
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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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