Experts and Doctors on oligonucleotide array sequence analysis in United States

Summary

Locale: United States
Topic: oligonucleotide array sequence analysis

Top Publications

  1. Xiao J, Huang Y, Dai Z, Sadee W, Chen J, Liu S, et al. Chemoresistance to depsipeptide FK228 [(E)-(1S,4S,10S,21R)-7-[(Z)-ethylidene]-4,21-diisopropyl-2-oxa-12,13-dithia-5,8,20,23-tetraazabicyclo[8,7,6]-tricos-16-ene-3,6,9,22-pentanone] is mediated by reversible MDR1 induction in human cancer cell lines. J Pharmacol Exp Ther. 2005;314:467-75 pubmed
    ..This study reveals a significant role of histone acetylation in MDR1 transcription, which seems to mediate FK228 resistance. ..
  2. Ye P, Mariniello B, Mantero F, Shibata H, Rainey W. G-protein-coupled receptors in aldosterone-producing adenomas: a potential cause of hyperaldosteronism. J Endocrinol. 2007;195:39-48 pubmed
    ..There are also sporadic increased expressions of these genes in the CPAs. Together, these findings suggest a potential role of altered GPCR expression in many cases of PA and provide candidate GPCR for further study...
  3. Liang J, Parchaliuk D, Medina S, Sorensen G, Landry L, Huang S, et al. Activation of p53-regulated pro-apoptotic signaling pathways in PrP-mediated myopathy. BMC Genomics. 2009;10:201 pubmed publisher
    ..It is evident that several mechanistic features contribute to the myopathy observed in PrP over-expressing mice and that p53-related apoptotic pathways appear to play a major role. ..
  4. Romano R, Smalley K, Liu S, Sinha S. Abnormal hair follicle development and altered cell fate of follicular keratinocytes in transgenic mice expressing DeltaNp63alpha. Development. 2010;137:1431-9 pubmed publisher
    ..Our data provide evidence supporting a role for DeltaNp63alpha in actively suppressing hair follicle differentiation and directing IFE cell lineage commitment. ..
  5. Chen S, Claus R, Lucas D, Yu L, Qian J, Ruppert A, et al. Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. Blood. 2011;117:862-71 pubmed publisher
    ..Collectively, this study confirms the importance of the silencing of ID4 in murine and human CLL pathogenesis. ..
  6. Boyd N, Nunes S, Jokinen J, Krishnan L, Chen Y, Smith K, et al. Microvascular mural cell functionality of human embryonic stem cell-derived mesenchymal cells. Tissue Eng Part A. 2011;17:1537-48 pubmed publisher
    ..This demonstrates that hESC-derived mesenchymal cells possess the molecular machinery expected in a perivascular progenitor cells and can play a functional role in stabilizing EC networks in in vitro three-dimensional culture. ..
  7. Mödder U, Oursler M, Khosla S, Monroe D. Wnt10b activates the Wnt, notch, and NF?B pathways in U2OS osteosarcoma cells. J Cell Biochem. 2011;112:1392-402 pubmed publisher
    ..Interestingly, Wnt3a failed to induce the Notch and NF?B pathways, demonstrating Wnt-specificity. In conclusion, our data demonstrate that Wnt10b, but not Wnt3a, stimulates the NF?B and Notch pathways in U2OS osteosarcoma cells. ..
  8. Zhu L, Liu X, Wang H, Khajuria C, Reese J, Whitworth R, et al. Rapid mobilization of membrane lipids in wheat leaf sheaths during incompatible interactions with Hessian fly. Mol Plant Microbe Interact. 2012;25:920-30 pubmed publisher
    ..Our results suggest that rapid mobilization of membrane lipids constitutes an important step for wheat to defend against HF attack. ..
  9. Hasegawa Y, Mans J, Mao S, Lopez M, Baker H, Handfield M, et al. Gingival epithelial cell transcriptional responses to commensal and opportunistic oral microbial species. Infect Immun. 2007;75:2540-7 pubmed
    ..Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of F. nucleatum and contribute to the greater pathogenic potential of F. nucleatum than of S. gordonii...

More Information

Publications411 found, 100 shown here

  1. Cambon A, Khalyfa A, Cooper N, Thompson C. Analysis of probe level patterns in Affymetrix microarray data. BMC Bioinformatics. 2007;8:146 pubmed
    ..We discuss implications for probe sequence selection for confirmatory analysis using real time PCR. ..
  2. Campbell M, Segear E, Beers L, Knauber D, Suttle J. Dormancy in potato tuber meristems: chemically induced cessation in dormancy matches the natural process based on transcript profiles. Funct Integr Genomics. 2008;8:317-28 pubmed publisher
    ..We conclude that BE-induced cessation of dormancy initiates transcript profiles similar to the natural processes that control dormancy...
  3. Barger J, Kayo T, Pugh T, Prolla T, Weindruch R. Short-term consumption of a resveratrol-containing nutraceutical mixture mimics gene expression of long-term caloric restriction in mouse heart. Exp Gerontol. 2008;43:859-66 pubmed publisher
    ..Examination of key genes and pathways affected by NCM suggests that Foxo1 is a critical upstream mediator of its actions. ..
  4. Yadav R, Girke T, Pasala S, Xie M, Reddy G. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc Natl Acad Sci U S A. 2009;106:4941-6 pubmed publisher
    ..The gene expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. ..
  5. Barton V, Donson A, Kleinschmidt DeMasters B, Gore L, Liu A, Foreman N. PARP1 expression in pediatric central nervous system tumors. Pediatr Blood Cancer. 2009;53:1227-30 pubmed publisher
    ..0053). PARP1 protein was also prominent in high-grade tumors (P = 0.022). These findings indicate that PARP1 is expressed in high-grade pediatric CNS tumors, implicating PARP1 inhibition as a potential therapeutic target. ..
  6. Marsh B, Stevens S, Packard A, Gopalan B, Hunter B, Leung P, et al. Systemic lipopolysaccharide protects the brain from ischemic injury by reprogramming the response of the brain to stroke: a critical role for IRF3. J Neurosci. 2009;29:9839-49 pubmed publisher
  7. Saul K, Koke J, Garcia D. Activating transcription factor 3 (ATF3) expression in the neural retina and optic nerve of zebrafish during optic nerve regeneration. Comp Biochem Physiol A Mol Integr Physiol. 2010;155:172-82 pubmed publisher
    ..We conclude ATF3 may be an important mediator of optic nerve regeneration-promoting gene expression in fish, a role which merits further investigation. ..
  8. Barth J, Clark C, Fresco V, Knoll E, Lee B, Argraves W, et al. Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis. Dev Dyn. 2010;239:2024-33 pubmed publisher
    ..5 overexpression. Given the role of Jarid2 as a regulator of early cardiac proliferation, these findings highlight Jarid2 as one of several potential mediators of the critical role played by Nkx2.5 during OFT morphogenesis. ..
  9. Miecznikowski J, Wang D, Liu S, Sucheston L, Gold D. Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. BMC Cancer. 2010;10:573 pubmed publisher
    ..These candidate pathways should help to develop a panel of significant biomarkers for the prognosis of breast cancer patients in a clinical setting. ..
  10. Kalhan S, Uppal S, Moorman J, Bennett C, Gruca L, Parimi P, et al. Metabolic and genomic response to dietary isocaloric protein restriction in the rat. J Biol Chem. 2011;286:5266-77 pubmed publisher
    ..These may be related to high methylation demands placed on the organism and caused by possible changes in cellular osmolarity as a result of the efflux of the intracellular taurine. ..
  11. Davis S, Mooney R, Kanin E, Grass J, Landick R, Ansari A. Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide. Methods Enzymol. 2011;498:449-71 pubmed publisher
    ..This approach provides the framework for engineering gene networks and controlling biological output in a desired manner. ..
  12. Wang C, Jedlicka P, Patrick A, Micalizzi D, Lemmer K, Deitsch E, et al. SIX1 induces lymphangiogenesis and metastasis via upregulation of VEGF-C in mouse models of breast cancer. J Clin Invest. 2012;122:1895-906 pubmed publisher
  13. Mukhopadhyay A, Khoury T, Stein L, Shrikant P, Sood A. Prostate derived Ets transcription factor and Carcinoembryonic antigen related cell adhesion molecule 6 constitute a highly active oncogenic axis in breast cancer. Oncotarget. 2013;4:610-21 pubmed
    ..Together, these findings show that PDEF-CEACAM6 is a highly active oncogenic axis in breast cancer and suggest that targeting of these molecules should provide novel treatments for most breast cancer patients. ..
  14. Weinmann A, Yan P, Oberley M, Huang T, Farnham P. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 2002;16:235-44 pubmed
    ..We suggest that human CpG microarrays, in combination with chromatin immunoprecipitation, will allow rapid identification of target promoters for many mammalian transcription factors. ..
  15. Stenzel Poore M, Stevens S, Xiong Z, Lessov N, Harrington C, Mori M, et al. Effect of ischaemic preconditioning on genomic response to cerebral ischaemia: similarity to neuroprotective strategies in hibernation and hypoxia-tolerant states. Lancet. 2003;362:1028-37 pubmed
    ..Preconditioning reprogrammes the response to ischaemic injury. Similar changes reported by others support an evolutionarily conserved endogenous response to decreased blood flow and oxygen limitation such as seen during hibernation. ..
  16. Finlin B, Mosley A, Crump S, Correll R, Ozcan S, Satin J, et al. Regulation of L-type Ca2+ channel activity and insulin secretion by the Rem2 GTPase. J Biol Chem. 2005;280:41864-71 pubmed
  17. Luo W, Fan W, Xie H, Jing L, Ricicki E, Vouros P, et al. Phenotypic anchoring of global gene expression profiles induced by N-hydroxy-4-acetylaminobiphenyl and benzo[a]pyrene diol epoxide reveals correlations between expression profiles and mechanism of toxicity. Chem Res Toxicol. 2005;18:619-29 pubmed
    ..Differences in the transcriptional response of TK6 cells to N-OH-AABP or BPDE exposure may explain the dramatic differences in the toxicity and mutagenicity of these human carcinogens. ..
  18. Mazhawidza W, Winters S, Kaiser U, Kakar S. Identification of gene networks modulated by activin in LbetaT2 cells using DNA microarray analysis. Histol Histopathol. 2006;21:167-78 pubmed publisher
    ..Modulation of expression of genes by activin suggests that activin may mediate its effects through a variety of signaling pathways. ..
  19. Kutuzova G, DeLuca H. 1,25-Dihydroxyvitamin D3 regulates genes responsible for detoxification in intestine. Toxicol Appl Pharmacol. 2007;218:37-44 pubmed
    ..There is also an increased expression of antioxidant genes. These results support the idea that vitamin D is a significant factor in detoxification and protection against environmental toxins. ..
  20. Myles M, Dieckgraefe B, Criley J, Franklin C. Characterization of cecal gene expression in a differentially susceptible mouse model of bacterial-induced inflammatory bowel disease. Inflamm Bowel Dis. 2007;13:822-36 pubmed
    ..Collectively, these findings provide a foundation for understanding the immunological mechanisms that confer resistance or susceptibility to H. hepaticus-induced typhlitis. ..
  21. Posey T, Weng T, Chen Z, Chintagari N, Wang P, Jin N, et al. Arsenic-induced changes in the gene expression of lung epithelial L2 cells: implications in carcinogenesis. BMC Genomics. 2008;9:115 pubmed publisher
    ..Our findings provide important insight for the future studies of arsenic-mediated lung cancer. ..
  22. Emmons J, Townley Tilson W, Deleault K, Skinner S, Gross R, Whitfield M, et al. Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation. RNA. 2008;14:888-902 pubmed publisher
    ..The data implicate TTP as having a broader role in regulating and limiting the immune response than previously suspected. ..
  23. Turner D, Findlay V, Kirven A, Moussa O, Watson D. Global gene expression analysis identifies PDEF transcriptional networks regulating cell migration during cancer progression. Mol Biol Cell. 2008;19:3745-57 pubmed publisher
  24. Yang Y, Zhu M, Wu L, Zhou J. Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference. BMC Genomics. 2008;9 Suppl 2:S5 pubmed publisher
    ..This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference. ..
  25. Estler M, Boskovic G, Denvir J, Miles S, Primerano D, Niles R. Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma. BMC Genomics. 2008;9:478 pubmed publisher
    ..Pathway analysis suggests that CDC2, CHEK1, CDC45L and MCM6 are key players in mediating the biological activity of RA in B16 melanoma cells. ..
  26. Damron T, Zhang M, Pritchard M, Middleton F, Horton J, Margulies B, et al. Microarray cluster analysis of irradiated growth plate zones following laser microdissection. Int J Radiat Oncol Biol Phys. 2009;74:949-56 pubmed publisher
  27. De S, Cipriano R, Jackson M, Stark G. Overexpression of kinesins mediates docetaxel resistance in breast cancer cells. Cancer Res. 2009;69:8035-42 pubmed publisher
    ..Our finding that kinesins can mediate docetaxel resistance might lead to novel therapeutic approaches in which kinesin inhibitors are paired with taxanes. ..
  28. Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley R, Bilgin D, et al. Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol. 2010;152:541-52 pubmed publisher
    ..Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes, supporting their rapid specialization. ..
  29. Yalcin M, Dyskin E, Lansing L, Bharali D, Mousa S, Bridoux A, et al. Tetraiodothyroacetic acid (tetrac) and nanoparticulate tetrac arrest growth of medullary carcinoma of the thyroid. J Clin Endocrinol Metab. 2010;95:1972-80 pubmed publisher
    ..Tetrac also inhibits angiogenesis initiated by vascular endothelial growth factor and basic fibroblast growth factor...
  30. Spillman M, Manning N, Dye W, Sartorius C, Post M, Harrell J, et al. Tissue-specific pathways for estrogen regulation of ovarian cancer growth and metastasis. Cancer Res. 2010;70:8927-36 pubmed publisher
    ..Because breast cancer selective ER modulators (SERM) are therapeutically ineffective in EOC, we suggest that our EOC-specific E2-regulated genes can assist pharmacologic discovery of ovarian-targeted SERM. ..
  31. Rogers T, Ataide S, Dare K, Katz A, Seveau S, Roy H, et al. A pseudo-tRNA modulates antibiotic resistance in Bacillus cereus. PLoS ONE. 2012;7:e41248 pubmed publisher
    ..These findings illustrate that while integration of genomic islands often leaves tRNA genes intact and functional, in other instances inactivation may generate tRNA-like elements that are then recruited to other functions in the cell. ..
  32. Preuss K, Lopez J, Colbourne J, Wade M. Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum. BMC Genomics. 2012;13:671 pubmed publisher
    ..These transcriptionally active regions represent novel exons of potentially unknown genes for future study. Our results lay a foundation for utilizing T. castaneum as a model for understanding the role of maternal genes in evolution. ..
  33. Alimova I, Birks D, Harris P, Knipstein J, Venkataraman S, Marquez V, et al. Inhibition of EZH2 suppresses self-renewal and induces radiation sensitivity in atypical rhabdoid teratoid tumor cells. Neuro Oncol. 2013;15:149-60 pubmed publisher
    ..Our observations provide evidence that EZH2 disruption alters cell cycle progression and may be an important new therapeutic target, particularly in combination with radiation, in ATRT. ..
  34. Kanaan Z, Roberts H, Eichenberger M, Billeter A, Ocheretner G, Pan J, et al. A plasma microRNA panel for detection of colorectal adenomas: a step toward more precise screening for colorectal cancer. Ann Surg. 2013;258:400-8 pubmed publisher
    ..This miRNA panel warrants study in larger cohorts. Plasma-based assays could provide better screening compliance compared to fecal occult blood or endoscopic screening. ..
  35. Askovich P, Sanders C, Rosenberger C, Diercks A, Dash P, Navarro G, et al. Differential host response, rather than early viral replication efficiency, correlates with pathogenicity caused by influenza viruses. PLoS ONE. 2013;8:e74863 pubmed publisher
    ..Because influenza infection extending into the lung generally results in severe disease, early activation of these pathways may be one factor distinguishing high- and low-pathogenicity strains. ..
  36. Askree S, Chin E, Bean L, Coffee B, Tanner A, Hegde M. Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genet. 2013;14:116 pubmed publisher
    ..Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. ..
  37. Fotinos A, Nagarajan N, Martins A, Fritz D, Garsetti D, Lee A, et al. Bone morphogenetic protein-focused strategies to induce cytotoxicity in lung cancer cells. Anticancer Res. 2014;34:2095-104 pubmed
    ..The observed cytotoxicity suggests that reducing BMP signaling is a useful line of attack for therapy of lung cancer. ..
  38. Lee Y, Lewis J, Ippolito D, Hussainzada N, Lein P, Jackson D, et al. Repeated exposure to neurotoxic levels of chlorpyrifos alters hippocampal expression of neurotrophins and neuropeptides. Toxicology. 2016;340:53-62 pubmed publisher
    ..An equally significant finding is that subchronic exposure to CPF at a level that produces more moderate inhibition of hippocampal cholinesterase (approximately 50% of control) does not produce a discernable change in gene expression. ..
  39. Morgan R, Sofer L, Anderson A, Bernberg E, Cui J, Burnside J. Induction of host gene expression following infection of chicken embryo fibroblasts with oncogenic Marek's disease virus. J Virol. 2001;75:533-9 pubmed
  40. Okinaka Y, Yang C, Perna N, Keen N. Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol Plant Microbe Interact. 2002;15:619-29 pubmed
    ..Among these, mutations of Bacillus subtilis pps1, Escherichia coli purU, and Pseudomonas aeruginosa pheC homologues reduced virulence on African violet leaves. Thus, new insights were obtained into genes important in bacterial virulence...
  41. Fisher R, Slayton W, Chien C, Guthrie S, Bray C, Scott E. PU.1 supports proliferation of immature erythroid progenitors. Leuk Res. 2004;28:83-9 pubmed
    ..1 target genes known to affect cytokine signaling and gene regulation in the erythroid lineage. These data suggest that PU.1 plays an important role in regulating the proliferation of immature erythroid progenitors. ..
  42. Kapoun A, Liang F, O Young G, Damm D, Quon D, White R, et al. B-type natriuretic peptide exerts broad functional opposition to transforming growth factor-beta in primary human cardiac fibroblasts: fibrosis, myofibroblast conversion, proliferation, and inflammation. Circ Res. 2004;94:453-61 pubmed
  43. Chu T, Deng S, Wolfinger R, Paules R, Hamadeh H. Cross-site comparison of gene expression data reveals high similarity. Environ Health Perspect. 2004;112:449-55 pubmed
  44. Ito T, Wellmer F, Yu H, Das P, Ito N, Alves Ferreira M, et al. The homeotic protein AGAMOUS controls microsporogenesis by regulation of SPOROCYTELESS. Nature. 2004;430:356-60 pubmed
  45. Higgs B, Elashoff M, Richman S, Barci B. An online database for brain disease research. BMC Genomics. 2006;7:70 pubmed
  46. Conlon E, Song J, Liu J. Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics. 2006;7:247 pubmed
    ..We assume that each study contains only two conditions: an experimental and a control sample. We demonstrated our model's suitability for a small number of studies that have been either pre-scaled or have no outliers. ..
  47. Yao Z, Zhao B, Hoffman E, Ghimbovschi S, Dubois D, Almon R, et al. Application of scaling factors in simultaneous modeling of microarray data from diverse chips. Pharm Res. 2007;24:643-9 pubmed
    ..Modeling of pharmacodynamic/pharmacogenomic (PD/PG) data from diverse chips should be performed with caution due to differential probe set intensities. In such circumstances, a power scaling factor can be applied in the modeling. ..
  48. Pavel E, Nadella K, Towns W, Kirschner L. Mutation of Prkar1a causes osteoblast neoplasia driven by dysregulation of protein kinase A. Mol Endocrinol. 2008;22:430-40 pubmed
    ..Tumor cells exhibited enhanced growth in response to PKA-stimulating agents, suggesting that tumorigenesis in osteoblast precursor cells is driven by effects directly mediated by the dysregulation of PKA. ..
  49. Douard V, Cui X, Soteropoulos P, Ferraris R. Dexamethasone sensitizes the neonatal intestine to fructose induction of intestinal fructose transporter (Slc2A5) function. Endocrinology. 2008;149:409-23 pubmed
    ..Thus, dexamethasone, which allows dietary fructose to precociously stimulate intestinal fructose absorption, can mimic the effect of age and modify developmental timing mechanisms regulating GLUT5. ..
  50. Lee M, El Shewy H, Luttrell D, Luttrell L. Role of beta-arrestin-mediated desensitization and signaling in the control of angiotensin AT1a receptor-stimulated transcription. J Biol Chem. 2008;283:2088-97 pubmed
  51. Rustad T, Harrell M, Liao R, Sherman D. The enduring hypoxic response of Mycobacterium tuberculosis. PLoS ONE. 2008;3:e1502 pubmed publisher
    ..Analysis of the EHR should help elucidate the key regulatory factors and enzymatic machinery exploited by M. tuberculosis for long-term bacteriostasis in the face of oxygen deprivation. ..
  52. Bajak E, Hagedorn C. Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA. Methods Mol Biol. 2008;419:147-60 pubmed publisher
    ..The length of the 3' poly(A) ends can be defined using a rapid polymerase chain reaction (PCR)- based approach. ..
  53. Fernandez D, Telarico T, Bonilla E, Li Q, Banerjee S, Middleton F, et al. Activation of mammalian target of rapamycin controls the loss of TCRzeta in lupus T cells through HRES-1/Rab4-regulated lysosomal degradation. J Immunol. 2009;182:2063-73 pubmed publisher
    ..The results suggest that activation of mTOR causes the loss of TCRzeta in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation. ..
  54. Lanaspa M, Andres Hernando A, Rivard C, Dai Y, Li N, Berl T. ZAC1 is up-regulated by hypertonicity and decreases sorbitol dehydrogenase expression, allowing accumulation of sorbitol in kidney cells. J Biol Chem. 2009;284:19974-81 pubmed publisher
    ..Taken together, these data strongly suggest that ZAC1 is up-regulated under hypertonic stress and negatively regulates expression of SDH, allowing for accumulation of sorbitol as a compatible organic osmolyte...
  55. Bhaskaran M, Wang Y, Zhang H, Weng T, Baviskar P, Guo Y, et al. MicroRNA-127 modulates fetal lung development. Physiol Genomics. 2009;37:268-78 pubmed publisher
    ..These findings suggest that miR-127 may have an important role in fetal lung development. ..
  56. Kim S, Bhat P, Cui X, Walia H, Xu J, Wanamaker S, et al. Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. BMC Plant Biol. 2009;9:65 pubmed publisher
    ..The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis. ..
  57. Smythies L, Shen R, Bimczok D, Novak L, Clements R, Eckhoff D, et al. Inflammation anergy in human intestinal macrophages is due to Smad-induced IkappaBalpha expression and NF-kappaB inactivation. J Biol Chem. 2010;285:19593-604 pubmed publisher
    ..Our findings implicate stromal transforming growth factor-beta-induced dysregulation of NF-kappaB proteins and Smad signaling in the differentiation of pro-inflammatory blood monocytes into noninflammatory intestinal macrophages. ..
  58. Wang X, Bao X, Pal R, Agbas A, Michaelis E. Transcriptomic responses in mouse brain exposed to chronic excess of the neurotransmitter glutamate. BMC Genomics. 2010;11:360 pubmed publisher
    ..The patterns observed were characterized by a combination of responses to stress and stimulation of nerve growth, intracellular transport and recovery. ..
  59. Chang Z, Ling C, Yamashita M, Welham N. Microarray-driven validation of reference genes for quantitative real-time polymerase chain reaction in a rat vocal fold model of mucosal injury. Anal Biochem. 2010;406:214-21 pubmed publisher
    ..The stable reference genes identified here are suitable for accurate normalization of target gene expression in vocal fold mucosal injury experiments. ..
  60. Rao X, Di Leva G, Li M, Fang F, Devlin C, Hartman Frey C, et al. MicroRNA-221/222 confers breast cancer fulvestrant resistance by regulating multiple signaling pathways. Oncogene. 2011;30:1082-97 pubmed publisher
  61. Sukumaran S, Jusko W, Dubois D, Almon R. Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action. J Appl Physiol (1985). 2011;110:1732-47 pubmed publisher
  62. Pietersen C, Lim M, Macey L, Woo T, Sonntag K. Neuronal type-specific gene expression profiling and laser-capture microdissection. Methods Mol Biol. 2011;755:327-43 pubmed publisher
  63. Panguluri S, Kuwabara N, Kang Y, Cooper N, Lundy R. Conditioned taste aversion dependent regulation of amygdala gene expression. Physiol Behav. 2012;105:996-1006 pubmed publisher
    ..Together, these results support the notion that we have identified downstream genes in the amygdala that contribute to CTA learning. ..
  64. Wang D, Yan L, Hu Q, Sucheston L, Higgins M, Ambrosone C, et al. IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. Bioinformatics. 2012;28:729-30 pubmed publisher
    ..IMA is implemented in the R language and is freely available from http://www.rforge.net/IMA. ..
  65. Charizanis K, Lee K, Batra R, Goodwin M, Zhang C, Yuan Y, et al. Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron. 2012;75:437-50 pubmed publisher
    ..Importantly, the majority of the Mbnl2-regulated exons examined were similarly misregulated in DM. We propose that major pathological features of the DM brain result from disruption of the MBNL2-mediated developmental splicing program...
  66. Tomov V, Palko O, Lau C, Pattekar A, Sun Y, Tacheva R, et al. Differentiation and Protective Capacity of Virus-Specific CD8+ T Cells Suggest Murine Norovirus Persistence in an Immune-Privileged Enteric Niche. Immunity. 2017;47:723-738.e5 pubmed publisher
    ..Our studies revealed a strategy of immune evasion by MNV via the induction of a CD8+ T cell program normally reserved for latent pathogens and persistence in an immune-privileged enteric niche. ..
  67. Said Salim B, Dunman P, McAleese F, Macapagal D, Murphy E, McNamara P, et al. Global regulation of Staphylococcus aureus genes by Rot. J Bacteriol. 2003;185:610-9 pubmed
    ..aureus genes. Our data also indicate that Rot and agr have opposing effects on select target genes. These results provide further insight into the role of Rot in the regulatory cascade of S. aureus virulence gene expression. ..
  68. Gu J, Wang J, Stockton A, Lokitz B, Henegar L, Hall J. Cytokine gene expression profiles in kidney medulla and cortex of obese hypertensive dogs. Kidney Int. 2004;66:713-21 pubmed
    ..The molecular mechanisms linking abnormal kidney function and obesity hypertension are poorly understood. This study compared gene expression profiles in the kidney medulla and cortex of obese and lean dogs...
  69. Offner H. Neuroimmunoprotective effects of estrogen and derivatives in experimental autoimmune encephalomyelitis: therapeutic implications for multiple sclerosis. J Neurosci Res. 2004;78:603-24 pubmed
    ..Alternatively, one might envision using EE or fluasterone metabolites alone or in combination therapies in both male and female MS patients. ..
  70. Chinnaiyan P, Huang S, Vallabhaneni G, Armstrong E, Varambally S, Tomlins S, et al. Mechanisms of enhanced radiation response following epidermal growth factor receptor signaling inhibition by erlotinib (Tarceva). Cancer Res. 2005;65:3328-35 pubmed
    ..These data suggest that the erlotinib/radiation combination represents a strategy worthy of further examination in clinical trials. ..
  71. Xiao X, Grove K, Lau S, McWeeney S, Smith M. Deoxyribonucleic acid microarray analysis of gene expression pattern in the arcuate nucleus/ventromedial nucleus of hypothalamus during lactation. Endocrinology. 2005;146:4391-8 pubmed
  72. Chen L, Bush C, Necela B, Su W, Yanagisawa M, Anastasiadis P, et al. RS5444, a novel PPARgamma agonist, regulates aspects of the differentiated phenotype in nontransformed intestinal epithelial cells. Mol Cell Endocrinol. 2006;251:17-32 pubmed
    ..Many nuclear receptors regulate differentiation. However, our results point to novel effects of PPARgamma on cell-cell and cell-matrix interactions, which are not typical of other nuclear receptors. ..
  73. Lai Z, Gross B, Zou Y, Andrews J, Rieseberg L. Microarray analysis reveals differential gene expression in hybrid sunflower species. Mol Ecol. 2006;15:1213-27 pubmed
    ..deserticola habitat. One gene (a G protein-coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat. ..
  74. Meng Q, Gideon K, Harbo S, Renne R, Lee M, Brys A, et al. Gene expression profiling in lung tissues from mice exposed to cigarette smoke, lipopolysaccharide, or smoke plus lipopolysaccharide by inhalation. Inhal Toxicol. 2006;18:555-68 pubmed
    ..In addition, an LPS-compromised mouse model showed potential as a useful tool for studying cigarette smoke-associated COPD. ..
  75. Hersh B, Nelson C, Stoll S, Norton J, Albert T, Carroll S. The UBX-regulated network in the haltere imaginal disc of D. melanogaster. Dev Biol. 2007;302:717-27 pubmed
    ..The evolution of haltere morphology involved changes in UBX-regulated target genes, both positive and negative, throughout the wing genetic regulatory network. ..
  76. Lee I, Li Z, Marcotte E. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS ONE. 2007;2:e988 pubmed
    ..YeastNet is available from http://www.yeastnet.org. ..
  77. Yang Y, Harris D, Luo F, Wu L, Parsons A, Palumbo A, et al. Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response. BMC Genomics. 2008;9 Suppl 1:S11 pubmed publisher
    ..oneidensis Fur is involved in iron acquisition and acid tolerance response. In addition, analyzing genome-wide transcriptional profiles provides useful information for the characterization of Fur and iron response in S. oneidensis...
  78. Haveman S, DiDonato R, Villanueva L, Shelobolina E, Postier B, Xu B, et al. Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production. Appl Environ Microbiol. 2008;74:4277-84 pubmed publisher
    ..This contrasts with the direct reduction of Fe(III) that has been proposed for Geobacter species...
  79. Ford G, Ford B, Steele E, Gates A, Hood D, Matthews M, et al. Analysis of transcriptional profiles and functional clustering of global cerebellar gene expression in PCD3J mice. Biochem Biophys Res Commun. 2008;377:556-561 pubmed publisher
  80. Zhang X, Zarbl H. Chemopreventive doses of methylselenocysteine alter circadian rhythm in rat mammary tissue. Cancer Prev Res (Phila). 2008;1:119-27 pubmed publisher
  81. Yang S, Tschaplinski T, Engle N, Carroll S, Martin S, Davison B, et al. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics. 2009;10:34 pubmed publisher
    ..Z. mobilis performs best under anaerobic conditions, but is an aerotolerant organism. However, the genetic and physiological basis of ZM4's response to various stresses is understood poorly...
  82. Pascal L, Vencio R, Goo Y, Page L, Shadle C, Liu A. Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells. Prostate. 2009;69:1353-65 pubmed publisher
  83. Hwang D, Hong S, Jeong J, Choi S, Kim H, Kim J, et al. Vesicular monoamine transporter 2 and dopamine transporter are molecular targets of Pitx3 in the ventral midbrain dopamine neurons. J Neurochem. 2009;111:1202-12 pubmed publisher
  84. Miclaus K, Wolfinger R, Vega S, Chierici M, Furlanello C, Lambert C, et al. Batch effects in the BRLMM genotype calling algorithm influence GWAS results for the Affymetrix 500K array. Pharmacogenomics J. 2010;10:336-46 pubmed publisher
  85. FOSTER C, Singh M, Subramanian V, Singh K. Ataxia telangiectasia mutated kinase plays a protective role in ?-adrenergic receptor-stimulated cardiac myocyte apoptosis and myocardial remodeling. Mol Cell Biochem. 2011;353:13-22 pubmed publisher
    ..MMP-9 protein levels were increased in WT-ISO, not in hKO hearts. In conclusion, ATM plays a protective role in cardiac remodeling in response to ?-AR stimulation. ..
  86. Jayadev S, Nesser N, Hopkins S, Myers S, Case A, Lee R, et al. Transcription factor p53 influences microglial activation phenotype. Glia. 2011;59:1402-13 pubmed publisher
  87. Shi F, Kong B, Song J, Lee J, Dienglewicz R, Erf G. Understanding mechanisms of vitiligo development in Smyth line of chickens by transcriptomic microarray analysis of evolving autoimmune lesions. BMC Immunol. 2012;13:18 pubmed publisher
  88. Panicker S, Ganguly T, Consolo M, Price V, Mirmirani P, Honda K, et al. Sterol intermediates of cholesterol biosynthesis inhibit hair growth and trigger an innate immune response in cicatricial alopecia. PLoS ONE. 2012;7:e38449 pubmed publisher
  89. Bowers J, Nambeesan S, Corbi J, Barker M, Rieseberg L, Knapp S, et al. Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms. PLoS ONE. 2012;7:e51360 pubmed publisher
  90. Li M, Tang Y, Wu L, Mo F, Wang X, Li H, et al. The hepatocyte-specific HNF4?/miR-122 pathway contributes to iron overload-mediated hepatic inflammation. Blood. 2017;130:1041-1051 pubmed publisher
    ..Our findings indicate the direct involvement of hepatocytes in IO-induced hepatic inflammation and are informative for developing new molecular targets and preventative therapies for patients with major hemoglobinopathy. ..
  91. Gonzalez Cabrera P, Gaivin R, Yun J, Ross S, Papay R, McCune D, et al. Genetic profiling of alpha 1-adrenergic receptor subtypes by oligonucleotide microarrays: coupling to interleukin-6 secretion but differences in STAT3 phosphorylation and gp-130. Mol Pharmacol. 2003;63:1104-16 pubmed
    ..These results suggest that the alpha(1B)-AR has differential effects on the phosphorylation status of the STAT3 pathway and may not be as prohypertrophic as the other two subtypes. ..
  92. Wang X, Southard R, Kilgore M. The increased expression of peroxisome proliferator-activated receptor-gamma1 in human breast cancer is mediated by selective promoter usage. Cancer Res. 2004;64:5592-6 pubmed
    ..Thus, the increase in PPARgamma expression seen in breast cancer cells results from promoter recruitment, providing new insights into the expression and actions of PPARgamma in breast cancer. ..