Zhou X, Cai S, Hong A, You Q, Yu P, Sheng N, et al
. Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res. 2004;32:5409-17 pubmed
Hinojos C, Boerwinkle E, Fornage M, Doris P. Combined genealogical, mapping, and expression approaches to identify spontaneously hypertensive rat hypertension candidate genes. Hypertension. 2005;45:698-704 pubmed
..The present approach identifies a number of genes that may influence blood pressure in SHR by virtue of allelic effects on gene expression. ..
Farrow B, Rowley D, Dang T, Berger D. Characterization of tumor-derived pancreatic stellate cells. J Surg Res. 2009;157:96-102 pubmed publisher
..Characterization of tumor-derived PSCs will facilitate further studies to determine how the tumor microenvironment promotes the aggressive behavior of pancreatic cancer. ..
Yu D, Ware C, Waterland R, Zhang J, Chen M, Gadkari M, et al
. Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation. Mol Cell Biol. 2013;33:1845-58 pubmed publisher
..These findings expand the classic view of mammalian CGI methylation as a mechanism for transcriptional silencing and indicate a functional role for 3' CGI methylation in developmental gene regulation. ..
Chen K, Deng S, Lü H, Zheng Y, Yang G, Kim D, et al
. RNA-seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. PLoS ONE. 2013;8:e72567 pubmed publisher
..In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases. ..
Kim S, Park Y, Park E, Cho J, Izzo J, Zhang D, et al
. Prognostic biomarkers for esophageal adenocarcinoma identified by analysis of tumor transcriptome. PLoS ONE. 2010;5:e15074 pubmed publisher
..This signature could provide important improvement for the management of EAC patients. ..
Greene S, Gunaratne P, Hammond S, Rosen J. A putative role for microRNA-205 in mammary epithelial cell progenitors. J Cell Sci. 2010;123:606-18 pubmed publisher
..Additionally, in normal mouse MECs, high expression of miR-205 was observed in stem-cell-enriched cell populations isolated by FACS using established cell-surface markers. ..
Huang S, Chen Y, Podsypanina K, Li Y. Comparison of expression profiles of metastatic versus primary mammary tumors in MMTV-Wnt-1 and MMTV-Neu transgenic mice. Neoplasia. 2008;10:118-24 pubmed
Hu Y, Rosen D, Zhou Y, Feng L, Yang G, Liu J, et al
. Mitochondrial manganese-superoxide dismutase expression in ovarian cancer: role in cell proliferation and response to oxidative stress. J Biol Chem. 2005;280:39485-92 pubmed
Ochoa C, Mirabolfathinejad S, Ruiz V, Evans S, Gagea M, Evans C, et al
. Interleukin 6, but not T helper 2 cytokines, promotes lung carcinogenesis. Cancer Prev Res (Phila). 2011;4:51-64 pubmed publisher
..6-fold). We conclude that there is a clear specificity for the nature of inflammation in lung cancer promotion, and IL-6 has an essential role in lung cancer promotion...
Nagaraja A, Middlebrook B, Rajanahally S, Myers M, Li Q, Matzuk M, et al
. Defective gonadotropin-dependent ovarian folliculogenesis and granulosa cell gene expression in inhibin-deficient mice. Endocrinology. 2010;151:4994-5006 pubmed publisher
..These data indicate the gonadotropins initiate an improper program of cell differentiation prior to tumor formation in the absence of inhibins. ..
Arumugam T, Brandt W, Ramachandran V, Moore T, Wang H, May F, et al
. Trefoil factor 1 stimulates both pancreatic cancer and stellate cells and increases metastasis. Pancreas. 2011;40:815-22 pubmed publisher
..The present data demonstrate that TFF1 influences both PDAC cells and stellate cells and stimulates metastasis. ..
Cao W, Zhang L, Rosen D, Bover L, Watanabe G, Bao M, et al
. BDCA2/Fc epsilon RI gamma complex signals through a novel BCR-like pathway in human plasmacytoid dendritic cells. PLoS Biol. 2007;5:e248 pubmed
..Therefore, by associating with Fc epsilon RI gamma, BDCA2 activates a novel BCR-like signaling pathway to regulate the immune functions of pDCs. ..
DeNardo D, Kim H, Hilsenbeck S, Cuba V, Tsimelzon A, Brown P. Global gene expression analysis of estrogen receptor transcription factor cross talk in breast cancer: identification of estrogen-induced/activator protein-1-dependent genes. Mol Endocrinol. 2005;19:362-78 pubmed
..These studies demonstrate that microarrays can be used in a reverse genetics approach to predict the functional promoter structure of large numbers of genes that are regulated by multiple transcription factors. ..
Zhang B, Chen H, Zhang L, Dakhova O, Zhang Y, Lewis M, et al
. A dosage-dependent pleiotropic role of Dicer in prostate cancer growth and metastasis. Oncogene. 2014;33:3099-108 pubmed publisher
..Collectively, these results highlight a pleotropic role of Dicer in tumorigenesis that is not only dosage-dependent but also tissue context-dependent. ..
Labandeira Rey M, Couzon F, Boisset S, Brown E, Bes M, Benito Y, et al
. Staphylococcus aureus Panton-Valentine leukocidin causes necrotizing pneumonia. Science. 2007;315:1130-3 pubmed
Bray M, Shaw C, Moore M, Garcia R, Zanquetta M, Durgan D, et al
. Disruption of the circadian clock within the cardiomyocyte influences myocardial contractile function, metabolism, and gene expression. Am J Physiol Heart Circ Physiol. 2008;294:H1036-47 pubmed
..These studies suggest that the cardiomyocyte circadian clock influences myocardial contractile function, metabolism, and gene expression. ..
Shchelochkov O, Patel A, Weissenberger G, Chinault A, Wiszniewska J, Fernandes P, et al
. Duplication of chromosome band 12q24.11q24.23 results in apparent Noonan syndrome. Am J Med Genet A. 2008;146A:1042-8 pubmed publisher
Daiger S, Sullivan L, Bowne S, Birch D, Heckenlively J, Pierce E, et al
. Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa. Adv Exp Med Biol. 2010;664:325-31 pubmed publisher
..After validation studies, the first DNA's tested will be from 89 unrelated adRP families in which the prevalent RP genes have been excluded. This approach should identify new RP genes and will substantially reduce the cost per patient. ..
Meadows E, Cho J, Flynn J, Klein W. Myogenin regulates a distinct genetic program in adult muscle stem cells. Dev Biol. 2008;322:406-14 pubmed publisher
..Remarkably, these changes in gene expression were distinct from those found in Myog-null embryonic skeletal muscle, indicating that myogenin has separate functions during postnatal life. ..
Dong J, Akcakanat A, Stivers D, Zhang J, Kim D, Meric Bernstam F. RNA-binding specificity of Y-box protein 1. RNA Biol. 2009;6:59-64 pubmed
..Further study is needed to determine the functional consequences of selective YB-1 mRNA binding. ..
Agbemafle B, Oesterreicher T, Shaw C, Henning S. Immediate early genes of glucocorticoid action on the developing intestine. Am J Physiol Gastrointest Liver Physiol. 2005;288:G897-906 pubmed
Duggan J, You D, Cleaver J, Larson D, Garza R, Guzmán Pruneda F, et al
. Synergistic interactions of TLR2/6 and TLR9 induce a high level of resistance to lung infection in mice. J Immunol. 2011;186:5916-26 pubmed publisher
Li L, Ren C, Yang G, Fattah E, Goltsov A, Kim S, et al
. GLIPR1 suppresses prostate cancer development through targeted oncoprotein destruction. Cancer Res. 2011;71:7694-704 pubmed publisher
..Furthermore, they reveal parallel mechanisms of c-myc downregulation by GLIPR1 that when ablated in the prostate are sufficient to drive c-Myc expression and malignant development. ..
Aravindan N, Cata J, Hoffman L, Dougherty P, Riedel B, Price K, et al
. Effects of isoflurane, pentobarbital, and urethane on apoptosis and apoptotic signal transduction in rat kidney. Acta Anaesthesiol Scand. 2006;50:1229-37 pubmed
..Anesthetic agents have been shown to modulate apoptotic signal transduction in various tissues. We examined the effects of 6 h of different general anesthetic techniques on renal cell apoptosis in rat kidneys...
Barbieri E, De Preter K, Capasso M, Johansson P, Man T, Chen Z, et al
. A p53 drug response signature identifies prognostic genes in high-risk neuroblastoma. PLoS ONE. 2013;8:e79843 pubmed publisher
..Our findings further support the concept that oncogene-driven transcriptional networks opposing p53 activation are essential for the aggressive behavior and poor response to therapy of high-risk neuroblastoma. ..
Xiao W, Liu W, Li Z, Liang D, Li L, White L, et al
. Gene expression profiling in embryonic mouse lenses. Mol Vis. 2006;12:1692-8 pubmed
..Analysis of global gene expression profiles in embryonic mouse lenses has allowed us to identify several molecular pathways that are differentially regulated during early lens development. ..
Wong K, Tsang Y, Deavers M, Mok S, Zu Z, Sun C, et al
. BRAF mutation is rare in advanced-stage low-grade ovarian serous carcinomas. Am J Pathol. 2010;177:1611-7 pubmed publisher
..In addition, advanced-stage, low-grade carcinoma patients with BRAF or KRAS mutation have a better apparent clinical outcome. However, further investigation is needed. ..
Zhang J, Coombes K. Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups. BMC Bioinformatics. 2012;13 Suppl 13:S1 pubmed publisher
..We found that the proportion of DEGs has a significant impact on FDR; this factor might have been overlooked in previous studies and deserves more thought when controlling FDR. ..
Adam L, Zhong M, Choi W, Qi W, Nicoloso M, Arora A, et al
. miR-200 expression regulates epithelial-to-mesenchymal transition in bladder cancer cells and reverses resistance to epidermal growth factor receptor therapy. Clin Cancer Res. 2009;15:5060-72 pubmed publisher
..The targets of miR-200 include ERRFI-1, which is a novel regulator of EGFR-independent growth. ..
Edvardsson K, Strom A, Jonsson P, Gustafsson J, Williams C. Estrogen receptor β induces antiinflammatory and antitumorigenic networks in colon cancer cells. Mol Endocrinol. 2011;25:969-79 pubmed publisher
..We propose that enhancing ERβ action has potential as a novel therapeutic approach for prevention and/or treatment of colon cancer. ..
Bi W, Breman A, Shaw C, Stankiewicz P, Gambin T, Lu X, et al
. Detection of ≥1Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays. Prenat Diagn. 2012;32:10-20 pubmed
..This approach has the potential to be applied for preimplantation genetic diagnosis to detect aneuploidy and common microdeletion/duplication syndromes and for noninvasive prenatal diagnosis if single fetal cells can be isolated. ..
Divakaran V, Adrogue J, Ishiyama M, Entman M, Haudek S, Sivasubramanian N, et al
. Adaptive and maladptive effects of SMAD3 signaling in the adult heart after hemodynamic pressure overloading. Circ Heart Fail. 2009;2:633-42 pubmed publisher
Amador Noguez D, Dean A, Huang W, Setchell K, Moore D, Darlington G. Alterations in xenobiotic metabolism in the long-lived Little mice. Aging Cell. 2007;6:453-70 pubmed
..The alterations in xenobiotic metabolism in Little mice constitute a form of increased stress resistance and may contribute to the extended longevity of these mice. ..
Tellez C, Davis D, Prieto V, Gershenwald J, Johnson M, McCarty M, et al
. Quantitative analysis of melanocytic tissue array reveals inverse correlation between activator protein-2alpha and protease-activated receptor-1 expression during melanoma progression. J Invest Dermatol. 2007;127:387-93 pubmed
..These findings support our hypothesis that loss of AP-2 is a crucial event in the progression of human melanoma and contributes to the acquisition of the metastatic phenotype via upregulation of PAR-1. ..
Harris D, Hazan Haley I, Coombes K, Bueso Ramos C, Liu J, Liu Z, et al
. Transformation of human mesenchymal cells and skin fibroblasts into hematopoietic cells. PLoS ONE. 2011;6:e21250 pubmed publisher
..Further studies are needed to determine whether transformed MSCs or skin fibroblasts are suitable for therapy. ..
Sun H, Chung W, Ryu S, Ju Z, Tran H, Kim E, et al
. Cyclic AMP-responsive element binding protein- and nuclear factor-kappaB-regulated CXC chemokine gene expression in lung carcinogenesis. Cancer Prev Res (Phila). 2008;1:316-28 pubmed publisher
..We propose that targeting CREB or NF-kappaB using small-molecule inhibitors, such as KG-501, holds promise as a preventive and/or therapeutic approach for NSCLC. ..
Cui X, Donehower L. Differential gene expression in mouse mammary adenocarcinomas in the presence and absence of wild type p53. Oncogene. 2000;19:5988-96 pubmed
Liang S, Zhao S, Mu X, Thomas T, Klein W. Novel retinal genes discovered by mining the mouse embryonic RetinalExpress database. Mol Vis. 2004;10:773-86 pubmed
..The gene identification approach described here demonstrates the usefulness of establishing large cDNA/EST databases from highly specialized neuronal tissues such as the retina to find novel genes. ..
Basha B, Smith J, Rogers H, Cook J. What Is the Clinical Utility of Repeat SNP Array Testing in the Follow-up of Myeloid Neoplasms?: A Retrospective Analysis of 44 Patients With Serial SNP Arrays. Am J Clin Pathol. 2017;147:278-284 pubmed publisher
..Follow-up SNP array testing is not required in routine clinical use in most cases. ..
Jeong J, Kwak I, Lee K, White L, Wang X, Brunicardi F, et al
. The genomic analysis of the impact of steroid receptor coactivators ablation on hepatic metabolism. Mol Endocrinol. 2006;20:1138-52 pubmed
..This study demonstrates that the molecular targets of SRC-2 regulation in the murine liver stimulate fatty acid degradation and glycolytic pathway, whereas fatty acid, cholesterol, and steroid biosynthetic pathways are down-regulated. ..
Pichler M, Ress A, Winter E, Stiegelbauer V, Karbiener M, Schwarzenbacher D, et al
. MiR-200a regulates epithelial to mesenchymal transition-related gene expression and determines prognosis in colorectal cancer patients. Br J Cancer. 2014;110:1614-21 pubmed publisher
..05). In conclusion, our data suggest that low miR-200a expression is associated with poor prognosis in CRC patients. MiR-200a has a regulatory effect on EMT and is associated with cancer stem cell properties in CRC. ..
Dharmadhikari A, Kang S, Szafranski P, Person R, Sampath S, Prakash S, et al
. Small rare recurrent deletions and reciprocal duplications in 2q21.1, including brain-specific ARHGEF4 and GPR148. Hum Mol Genet. 2012;21:3345-55 pubmed publisher
Nacheva E, Mokretar K, Soenmez A, Pittman A, Grace C, Valli R, et al
. DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS ONE. 2017;12:e0180467 pubmed publisher
..This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance. ..
Crespo Barreto J, Fryer J, Shaw C, Orr H, Zoghbi H. Partial loss of ataxin-1 function contributes to transcriptional dysregulation in spinocerebellar ataxia type 1 pathogenesis. PLoS Genet. 2010;6:e1001021 pubmed publisher
..Altogether, these data provide evidence that partial loss of Atxn1 function contributes to SCA1 pathogenesis and raise the possibility that loss-of-function mechanisms contribute to other dominantly inherited neurodegenerative diseases. ..
Cao H, Wang J, Li X, Florez S, Huang Z, Venugopalan S, et al
. MicroRNAs play a critical role in tooth development. J Dent Res. 2010;89:779-84 pubmed publisher
..These results demonstrate that tooth development is tightly controlled by microRNAs and that specific microRNAs regulate tooth epithelial stem cell differentiation...
Hammerich Hille S, Kaipparettu B, Tsimelzon A, Creighton C, Jiang S, Polo J, et al
. SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells. J Biol Chem. 2010;285:3608-16 pubmed publisher
..Thus, this study confirms the primary role of SAFB1/SAFB2 as corepressors and also uncovers a previously unknown role for SAFB1 in the regulation of immune genes and in estrogen-mediated repression of genes. ..
Yuan X, Mitchell B, Wilhelmus K. Expression of matrix metalloproteinases during experimental Candida albicans keratitis. Invest Ophthalmol Vis Sci. 2009;50:737-42 pubmed publisher
..This study was designed to investigate the expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) during the inception and progression of experimental keratomycosis...
Yang W, Lewis M, Hess K, Wong H, Tsimelzon A, Karadag N, et al
. Decreased TGFbeta signaling and increased COX2 expression in high risk women with increased mammographic breast density. Breast Cancer Res Treat. 2010;119:305-14 pubmed publisher
..These results strongly suggest that COX2 inhibition should be investigated for breast cancer prevention despite possible increase in cardiovascular risk. ..
Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, et al
. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011;21:315-24 pubmed publisher
..melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites. ..
Cheung H, Baggerly K, Tsavachidis S, Bachinski L, Neubauer V, Nixon T, et al
. Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays. BMC Genomics. 2008;9:216 pubmed publisher
..Given the important role of alternative splicing in neural differentiation, there may be selective pressure to maintain a majority of splicing events in order to retain glial-like characteristics of the tumor cells. ..
Ye L, Santarpia L, Cote G, El Naggar A, Gagel R. High resolution array-comparative genomic hybridization profiling reveals deoxyribonucleic acid copy number alterations associated with medullary thyroid carcinoma. J Clin Endocrinol Metab. 2008;93:4367-72 pubmed publisher
..Despite of RET status, all MTC might share similar oncogenetic mechanisms. Dysfunction of cell proliferation and cell death may both be involved in MTC tumorigenesis. ..
Tsao C, Teh B, Jonasch E, Shreiber Agus N, Efstathiou E, Hoang A, et al
. Inhibition of Mxi1 suppresses HIF-2alpha-dependent renal cancer tumorigenesis. Cancer Biol Ther. 2008;7:1619-27 pubmed
..Compared to Mxi1-proficient tumors, Mxi1-deficient tumors display reduced cellular proliferation. These results establish Mxi1 as an important downstream target of HIF that contributes to pVHL-deficient renal cancer tumorigenesis. ..
Cho J, Lim J, Cheong J, Park Y, Yoon S, Kim S, et al
. Gene expression signature-based prognostic risk score in gastric cancer. Clin Cancer Res. 2011;17:1850-7 pubmed publisher
..We were able to validate the robustness of the six-gene signature in an additional independent cohort. The risk score derived from the six-gene set successfully prognosticated the relapse of gastric cancer patients after gastrectomy. ..
Tsavachidou D, McDonnell T, Wen S, Wang X, Vakar Lopez F, Pisters L, et al
. Selenium and vitamin E: cell type- and intervention-specific tissue effects in prostate cancer. J Natl Cancer Inst. 2009;101:306-20 pubmed publisher
..We have also identified cell type- and zone-specific tissue effects of interventions with selenium and vitamin E that may have clinical implications. ..
Fujimoto J, Kadara H, Men T, Van Pelt C, Lotan D, Lotan R. Comparative functional genomics analysis of NNK tobacco-carcinogen induced lung adenocarcinoma development in Gprc5a-knockout mice. PLoS ONE. 2010;5:e11847 pubmed publisher
..Further experimentation to prove the reliability of the Gprc5a knockout mouse model for the study of tobacco-induced lung carcinogenesis is warranted. ..
Zhang J, Rubio V, Lieberman M, Shi Z. OLA1, an Obg-like ATPase, suppresses antioxidant response via nontranscriptional mechanisms. Proc Natl Acad Sci U S A. 2009;106:15356-61 pubmed publisher
..The beneficial effects observed upon OLA1-knockdown suggest that this regulatory ATPase is a potential novel target for antioxidative therapy. ..
Kadara H, Fujimoto J, Men T, Ye X, Lotan D, Lee J, et al
. A Gprc5a tumor suppressor loss of expression signature is conserved, prevalent, and associated with survival in human lung adenocarcinomas. Neoplasia. 2010;12:499-505 pubmed
..These results demonstrate that gene expression patterns of Gprc5a loss in nontumorigenic mouse lung epithelial cells are evolutionarily conserved and important in human lung adenocarcinomas. ..
Duz M, Karatas O, Güzel E, Turgut N, Yilmaz M, Creighton C, et al
. Identification of miR-139-5p as a saliva biomarker for tongue squamous cell carcinoma: a pilot study. Cell Oncol (Dordr). 2016;39:187-93 pubmed publisher
..713), thereby underscoring its diagnostic potential. From our results we conclude that saliva can be used as a feasible source for routine TSCC diagnostics and that miR-139-5p may serve as a potential biomarker for early TSCC detection. ..
Kondraganti S, Muthiah K, Jiang W, Barrios R, Moorthy B. Effects of 3-methylcholanthrene on gene expression profiling in the rat using cDNA microarray analyses. Chem Res Toxicol. 2005;18:1634-41 pubmed
..Elucidating the mechanisms of persistent induction of P4501A1 and other genes by MC might lead to a better understanding of the mechanisms of toxicity mediated by PAHs. ..
Wu H, Chen L, Zhang X, Zhou Q, Li J, Berger S, et al
. Aqp5 is a new transcriptional target of Dot1a and a regulator of Aqp2. PLoS ONE. 2013;8:e53342 pubmed publisher
Aravindan N, Williams M, Riedel B, Shaw A. Transcriptional responses of rat skeletal muscle following hypoxia-reoxygenation and near ischaemia-reperfusion. Acta Physiol Scand. 2005;183:367-77 pubmed
..The mechanism of skeletal muscle hypoxia has a profound effect on its subsequent transcriptional response. We identified several potential candidates as markers of skeletal muscle ischaemic damage. ..