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Oligonucleotide Array Sequence Analysis (0):
Recent article
Oligonucleotide Array Sequence Analysis
Developmental Cell (21)4 2011
Abstract
We show that Fgf8 and Sema3f, produced by early dental epithelium, respectively, attract and repulse mesenchymal cells, which cause them to pack tightly together during mouse tooth development. Resulting mechanical compaction-induced changes in cell shape induce odontogenic transcription factors (Pa...
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PMID: 21924961
PDF is available here.
PDF is available here.
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Developmental Cell (21)4 2011
Abstract
We generated and characterized Atxn1L(-/-) and Atxn1(-/-); Atxn1L(-/-) mice. Atxn1L(-/-) mice have hydrocephalus, omphalocele, and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1(-/-); Atxn1L(-/-) mice, suggesting that ATXN1 and ATXN1L are functionally redundan...
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PMID: 22014525
PDF is available here.
PDF is available here.
Abstract
Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopol...
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PMID: 21906101
PDF is available here.
PDF is available here.
Journal of Immunology (187)5 2011
Abstract
We demonstrated that STAT3 negatively regulates type I IFN-mediated response. STAT3 knockdown or knockout cells displayed enhanced gene expression and antiviral activity in response to IFN-α/β. Restoration of STAT3 to STAT3KO cells resulted in attenuation of the response. Upon viral infection, inc...
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PMID: 21810606
PDF is available here.
PDF is available here.
Abstract
The C57BL/6 mice were subjected to a chronic combined stress which resulted in the induction of a depressive-like state. The occurrence of a depressive-like state was defined by a decrease in sensitivity to the reward determined by the diminished preference of sweetened solutions ove...
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PMID: 21961309
PDF is available here.
PDF is available here.
EuroIntervention (7)4 2011
Abstract
We identified a set of whole blood transcripts induced at the site of coronary occlusion in the acute phase of myocardial infarction. Resolved genes indicate a predominant role for chemokines, cell-extracellular matrix, and lipoprotein alterations in the pathophysiology of acute myocardial infarctio...
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PMID: 21764664
PDF is available here.
PDF is available here.
EuroIntervention (7)4 2011
Abstract
We identified a set of whole blood transcripts induced at the site of coronary occlusion in the acute phase of myocardial infarction. Resolved genes indicate a predominant role for chemokines, cell-extracellular matrix, and lipoprotein alterations in the pathophysiology of acute myocardial infarctio...
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PMID: 21764664
PDF is available here.
PDF is available here.
Abstract
We have generated type 1 diabetic Akita mice lacking the low density lipoprotein receptor (Ins2(Akita)Ldlr(-/-)). Ins2(Akita)Ldlr(-/-) mice were severely hyperglycemic with impaired glucose tolerance. Compared with Ldlr(-/-) mice, 20-week-old Ins2(Akita)Ldlr(-/-) mice fed a 0.02% cholesterol AIN76a...
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PMID: 21606463
PDF is available here.
PDF is available here.
Abstract
We have developed a sparse Bayesian factor analysis model in which the observed expression diversity of among a large set of high-dimensional images is modeled by a small number of hidden common factors. We apply this approach on embryonic expression patterns from a Drosophila RNA in situ image data...
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PMID: 21814502
PDF is available here.
PDF is available here.
Abstract
We herein make analytical improvements by introducing a topology-preserving selection and clustering (TPSC) approach to complex large-scale microarray data. Specifically, the integration of self-organizing map (SOM) and singular value decomposition allows genome-wide selection on sound foundations o...
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PMID: 21699401
PDF is available here.
PDF is available here.
Integrative Biology (3)7 2011
Abstract
We show that, in addition to causing cell death of hormone-refractory prostate cancer cells, PJ also increases cell adhesion and decreases cell migration of the cells that do not die. We hypothesized that PJ does so by stimulating the expression and/or activation of molecules that alter the cytoskel...
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PMID: 21594291
PDF is available here.
PDF is available here.
Abstract
We analysed a set of 21 tumours (13 effusions, 8 primary carcinomas) and identified three sets of miRNAs, one that is highly expressed in both primary carcinomas and effusions, one overexpressed in primary carcinomas and one overexpressed in effusions. Levels of selected miRNAs were analysed using q...
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PMID: 20716115
PDF is available here.
PDF is available here.
PLoS Genetics (7)7 2011
Abstract
We used an integrated functional genomics strategy to robustly define Foxp2-dependent pathways, both direct and indirect targets, in the embryonic brain. Specifically, we performed genome-wide in vivo ChIP-chip screens for Foxp2-binding and thereby identified a set of 264 high-confidence neural targ...
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PMID: 21765815
PDF is available here.
PDF is available here.
Abstract
We hypothesized that immune gene-related signatures would predict the presence of unique histological features of lymphoid cell infiltrates in colorectal carcinoma (CRC) that correlate with clinical parameters. Metagene analysis with gene chip technology was performed on 326 CRCs, which were then sor...
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PMID: 21703392
PDF is available here.
PDF is available here.
Abstract
CD45(+) and collagen I-positive (Col(+)) fibrocytes are implicated in fibrogenesis in skin, lungs, and kidneys. Fibrocyte migration in response to liver injury was investigated using bone marrow (BM) from chimeric mice expressing luciferase (Col-Luc→wt) or green fluorescent protein (Col-GFP→wt) u...
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PMID: 21703401
PDF is available here.
PDF is available here.
Abstract
Currently, it is unknown whether defects in stem cell growth and differentiation contribute to myocardial aging and chronic heart failure (CHF), and whether a compartment of functional human cardiac stem cells (hCSCs) persists in the decompensated heart. To determine whether aging an...
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PMID: 21703415
PDF is available here.
PDF is available here.
Abstract
These results suggest a role for β-catenin in basal to ciliated and basal to Clara-like cell differentiation. Genetic stabilization of β-catenin in basal cells shortened the period of basal cell proliferation but had a minor effect on this process. Persistent β-catenin signaling regulated basal c...
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PMID: 21703416
PDF is available here.
PDF is available here.
Abstract
We established a three-dimensional (3D) human cell culture system that recapitulates the tumor heterogeneity observed in vivo. Human colon tumor cells were grown as multicellular spheroids and subsequently co-cultured with normal fibroblasts or CAFs in collagen I gels. This in vitro model system clo...
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PMID: 21703426
PDF is available here.
PDF is available here.
Abstract
We performed gene expression analysis and found that the level of P-cadherin was higher in tissue from liver metastases of colon cancer than in the corresponding primary colon cancer tissues. IHC analysis also showed that P-cadherin expression was significantly higher in liver metastases than in pai...
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PMID: 21703417
PDF is available here.
PDF is available here.
Abstract
We isolated the RNA from 70 formalin-fixed, paraffin-embedded radical prostatectomy specimens with known long-term outcomes to perform DASL expression profiling with a custom panel that we designed of 522 prostate cancer-relevant genes. We identified a panel of 10 protein-coding genes and two miRNA...
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PMID: 21703393
PDF is available here.
PDF is available here.
Abstract
We show that a clock in the Drosophila fat body drives rhythmic expression of genes involved in metabolism, detoxification, the immune response, and steroid hormone regulation. Some of these genes cycle even when the fat body clock is disrupted, indicating that they are regulated by exogenous factor...
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PMID: 21641546
PDF is available here.
PDF is available here.
Abstract
We identified 20 genes showing differential expression in UC-Ca and UC-NonCa patients, including cancer-related genes such as CYP27B1, RUNX3, SAMSN1, EDIL3, NOL3, CXCL9, ITGB2, and LYN. Using these 20 genes, we were able to build a predictive model that distinguished patients with and without UC-Ca...
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PMID: 21859567
PDF is available here.
PDF is available here.
Abstract
Abstract Shiga toxin-producing Escherichia coli O157 is a leading cause of foodborne illness worldwide. To evaluate better methods to rapidly detect and genotype E. coli O157 strains, the present study evaluated the use of ampliPHOX, a novel colorimetric detection method based on pho...
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PMID: 21288130
PDF is available here.
PDF is available here.
Abstract
We aimed to build a predictor for the response to FOLFOX using microarray gene expression profiles of primary CRC samples. Patients and methods Forty patients who underwent surgery for primary lesions were examined. All patients had metastatic or recurrent CRC and received modified FOLFOX6. Responde...
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PMID: 21680303
PDF is available here.
PDF is available here.
Abstract
We report a case of a male child referred for genetic investigation of severe language delay. Microarray analysis indicated the presence of a 220 Kb intragenic deletion at Xq21.31 involving the PCDH11X gene. Fluorescence in situ hybridization using a BAC probe mapping to intron 2 of the Protocadhe...
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PMID: 21480486
PDF is available here.
PDF is available here.
Abstract
We explored the mechanism underlying natural variation in longevity within natural populations using the model budding yeast, Saccharomyces cerevisiae. We analyzed whole-genome gene expression in four progeny of a natural S. cerevisiae strain that display differential replicative aging. Genes with d...
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PMID: 21306556
PDF is available here.
PDF is available here.
Abstract
Environmental stress results in perturbations to mitochondrial function in the preimplantation embryo and hinders subsequent embryo and possibly offspring development. Global gene expression in fetal mouse brain was investigated following targeted mitochondrial inhibition by amino-oxyacetate (AOA) fr...
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PMID: 21635818
PDF is available here.
PDF is available here.
Abstract
Infectious diseases are a major global public health problem. Multiple agents are now recognized to cause indistinguishable illnesses. The term 'syndrome' applies to such situations, for which early and rapid diagnosis of the infecting agent would enable prompt and appropriate therap...
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PMID: 21766906
PDF is available here.
PDF is available here.
Abstract
We make use of the random partial least squares regression technique (r-PLS) to trace connections between co-expressed genes in Mycobacterium tuberculosis using data downloaded from public microarray databases. We generated the overall topology of a microbial co-expression network with the exact com...
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PMID: 21514402
PDF is available here.
PDF is available here.
Abstract
We have validated in vivo the newly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500...
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PMID: 21593595
PDF is available here.
PDF is available here.
Abstract
We show how integrative genomics approaches can be used to characterize the role played by approximately a third of registered mouse miRNAs within the context of a liver gene regulatory network. Our analysis reveals that the transcript abundances of miRNAs are subject to regulatory control by many m...
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PMID: 21613979
PDF is available here.
PDF is available here.
Abstract
We report for the first time the use of DNA hybridization for the controllable assembly of a graphene nanosheet. Moreover, with the help of dynamic light scattering technique, we extended the above studies by exploiting the DNA-graphene dispersed sheets as highly ultrasensitive detection of oligonul...
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PMID: 21534537
PDF is available here.
PDF is available here.
Abstract
We applied either MeTA or a conventional DNA demethylating agent, 5-aza-cytidine (Aza-CR), to human embryonic kidney cell line 293T and analyzed gene expression profiles by microarray: 138 and 202 genes that are upregulated 5-fold or more were identified by MeTA and Aza-CR, respectively. The top ten...
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PMID: 21586901
PDF is available here.
PDF is available here.
Abstract
Our results demonstrated that variation in Angptl4 concentration was only modestly accounted for by genetic factors and suggest a role for Angptl4 in acquired obesity in humans....
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PMID: 21596930
PDF is available here.
PDF is available here.
Abstract
Prediction of high probability of survival from standard cancer treatments is fundamental for individualized cancer treatment strategies.
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PMID: 21558518
PDF is available here.
PDF is available here.
Xenobiotica (41)5 2011
Abstract
We use Bioconductor analysis packages on a heart development dataset to demonstrate the workflow of microarray data analysis from annotation, normalization, expression index calculation, and diagnostic plots to pathway analysis, leading to a meaningful visualization and interpretation of the data....
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PMID: 19763933
PDF is available here.
PDF is available here.
Xenobiotica (41)5 2011
Abstract
We describe the DASL (cDNA-mediated annealing, selection, extension, and ligation) Assay, a flexible, sensitive, and reproducible gene expression profiling system for parallel analysis of several hundred mRNA transcripts on the BeadArray platform. This technology is especially useful for determining...
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PMID: 18370102
PDF is available here.
PDF is available here.
Xenobiotica (41)5 2011
Abstract
We describe the laboratory implementation of Infinium whole genome genotyping (WGG) technology for whole genome association studies and copy number studies. Briefly, the Infinium WGG assay employs a single tube whole genome amplification reaction to amplify the entire genome; genomic loci of interes...
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PMID: 19381978
PDF is available here.
PDF is available here.
Abstract
Triple-negative breast cancer (TNBC) occurs in approximately 15% of all breast cancer patients, and the incidence of TNBC is greatly increased in BRCA1 mutation carriers. This study aimed to assess the impact of BRCA1 promoter methylation with respect to breast cancer subtypes in spo...
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PMID: 21593597
PDF is available here.
PDF is available here.
Abstract
We performed a comprehensive bioinformatics analysis on 1,196 mouse testis proteins screened from public protein database. Integrated function and pathway analysis were performed through Database for Annotation, Visualization and Integrated Discovery (DAVID) and ingenuity Pathway Analysis (IPA), and...
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PMID: 21615991
PDF is available here.
PDF is available here.
Abstract
We found that overexpression of SGR (Ov-SGR) resulted in the generation of singlet oxygen and other reactive oxygen species and produced a chlorophyll-dependent regional cell death phenotype on leaves of rice seedlings. Transcriptome analyses using Affymetrix Rice GeneChips revealed that Ov-SGR rice...
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PMID: 21375689
PDF is available here.
PDF is available here.
Clinical Cancer Research (17)9 2011
Abstract
Low-grade fibromyxoid sarcoma (LGFMS) is typically characterized by the specific translocation t(7;16)(q33;p11) and the corresponding fusion gene FUS-CREB3L2. The present study aimed to extract LGFMS-specific, and putatively FUS-CREB3L2-dependent, gene expression patterns to learn more about the path...
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PMID: 21536545
PDF is available here.
PDF is available here.
Abstract
We report a whole-genome analysis of DNA methylation profiles in fresh-frozen oropharyngeal squamous cell carcinoma (OPSCC) tissues and normal mucosa samples using microarray technology with patient genomic DNA. We initially compared whole-genome patterns of DNA methylation among 24 OPSCC primary tu...
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PMID: 21514414
PDF is available here.
PDF is available here.
Abstract
We show herein that transforming growth factor (TGF)-β induced a Smad3-dependent sustained stimulation of Egr2 gene expression in normal fibroblasts. Overexpression of Egr-2 was sufficient to stimulate collagen gene expression and myofibroblast differentiation, whereas these profibrotic TGF-β resp...
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PMID: 21514423
PDF is available here.
PDF is available here.
Abstract
Estrogen receptor (ER) remains one of the most important biomarkers for breast cancer subtyping and prognosis, and comparative genome hybridization has greatly contributed to the understanding of global genetic imbalance. The authors used single-nucleotide polymorphism (SNP) arrays to compare overall...
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PMID: 21523713
PDF is available here.
PDF is available here.
Transplantation (91)8 2011
Abstract
We studied early transcriptional changes of inflammatory mediators in the grafts during combined auxiliary liver-kidney transplantation using microarrays and real-time polymerase chain reaction. The results were correlated to clinical data.
Liver and kidney grafts both exhibited an u...
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PMID: 21494202
PDF is available here.
PDF is available here.
Abstract
We have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequ...
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PMID: 21473983
PDF is available here.
PDF is available here.
Clinical Cancer Research (17)8 2011
Abstract
To determine the differential gene expression between oral squamous cell carcinoma (OSCC) with and without metastasis to cervical lymph nodes and to assess prediction of nodal metastasis by using molecular features.
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PMID: 21300763
PDF is available here.
PDF is available here.
Abstract
Our aim was to define the effect of DNA variants at 16 drug metabolising enzymes on Tac dose in patients with kidney transplants....
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PMID: 21480817
PDF is available here.
PDF is available here.
Acta Medica Okayama (65)2 2011
Abstract
We analyzed the gene expression profile in the remnant kidney tissues of 5/6 nephrectomized mice using a DNA microarray system and compared it with that of sham-operated control mice. The 5/6 nephrectomized mice showed glomerular hypertrophy and an increase in the extracellular matrix in the glomeru...
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PMID: 21519365
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)4 2011
Abstract
Many aspects of plant metabolism that are involved in plant growth and development are influenced by light-regulated diurnal rhythms as well as endogenous clock-regulated circadian rhythms. To identify the rhythmic proteins in rice, periodically grown (12h light/12h dark cycle) seedlings were harvest...
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PMID: 21300183
PDF is available here.
PDF is available here.
Abstract
We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices o...
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PMID: 21524350
PDF is available here.
PDF is available here.
Abstract
We hypothesize that dysregulation of immune-related genes modifies synaptic functions and stability in this region....
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PMID: 21091092
PDF is available here.
PDF is available here.
Abstract
Abstract
We hypothesized that spatial distribution may be partially driven by genetic predisposition, and we aimed to explore relations among candidate genes and the spatial distribution of white matter brain lesions in MS....
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PMID: 21436341
PDF is available here.
PDF is available here.
Integrative Biology (3)4 2011
Abstract
We have performed gene co-expression network analysis in three independent microarray datasets and identified two microenvironment networks in human breast cancer tissues. Network I represents crosstalk and cooperation of ECM microenvironment and soluble factors during breast malignancy. The correla...
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PMID: 21165486
PDF is available here.
PDF is available here.
Abstract
We show that in the human, although there are no differences in expression of NF-κB p65, or IκB-α between upper- or lower-segment myometrium or before or after labour, there is nuclear localization of serine-256-phospho-p65 and serine-536-phospho-p65 in both upper- and lower-segment myometrium bo...
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PMID: 20406326
PDF is available here.
PDF is available here.
Nature Immunology (12)4 2011
Abstract
We report an unbiased analysis of the cytotoxic T lymphocyte (CTL) serine-threonine phosphoproteome by high-resolution mass spectrometry. We identified approximately 2,000 phosphorylations in CTLs, of which approximately 450 were controlled by T cell antigen receptor (TCR) signaling. A significantly...
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PMID: 21399638
PDF is available here.
PDF is available here.
Abstract
Our results, which were based on a rigorous replication approach, show that the gene coding for a potential drug target of cardiovascular importance features altered methylation patterns in smokers. To date, this gene had not attracted attention in the literature on smoking....
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PMID: 21457905
PDF is available here.
PDF is available here.
Abstract
We determined TOP2A status in 61 breast tumor samples by real-time PCR, DNA microarrays, immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH), and then evaluated these results with clinical-pathological features and breast cancer intrinsic subtypes. First, we observed a statisti...
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PMID: 21435434
PDF is available here.
PDF is available here.