Experts and Doctors on gene expression profiling in United States

Summary

Locale: United States
Topic: gene expression profiling

Top Publications

  1. Raman S, Rathinasabapathi B. beta-alanine N-methyltransferase of Limonium latifolium. cDNA cloning and functional expression of a novel N-methyltransferase implicated in the synthesis of the osmoprotectant beta-alanine betaine. Plant Physiol. 2003;132:1642-51 pubmed
    ..Phylogenetic analyses suggested that beta-Ala NMTase represents a novel family of N-methyltransferases that are evolutionarily related to O-methyltransferases...
  2. Kim E, Chen F, Wang C, Harrison L. CDK5 is a novel regulatory protein in PPARgamma ligand-induced antiproliferation. Int J Oncol. 2006;28:191-4 pubmed
    ..This is the first report of cdk5/p35 expression and kinase activity in colon cancer cells, which is associated with ciglitazone-induced antiproliferation in HT-29 cells. ..
  3. Skalsky R, Samols M, Plaisance K, Boss I, Riva A, Lopez M, et al. Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol. 2007;81:12836-45 pubmed
    ..Together, these findings indicate that KSHV miR-K12-11 is an ortholog of miR-155. ..
  4. Aliota M, Fuchs J, Mayhew G, Chen C, Christensen B. Mosquito transcriptome changes and filarial worm resistance in Armigeres subalbatus. BMC Genomics. 2007;8:463 pubmed
    ..We have initiated transcriptome profiling studies in Ar. subalbatus to identify molecular components involved in B. malayi refractoriness...
  5. Yu K, Li R, Hatanaka T, Hildebrand D. Cloning and functional analysis of two type 1 diacylglycerol acyltransferases from Vernonia galamensis. Phytochemistry. 2008;69:1119-27 pubmed publisher
    ..This data indicates that the two VgDGAT1s are functional, but not likely to be responsible for the selective accumulation of vernolic acid in V. galamensis seed oil. ..
  6. Udagawa T, Nemoto N, Wilkinson C, Narashimhan J, Jiang L, Watt S, et al. Int6/eIF3e promotes general translation and Atf1 abundance to modulate Sty1 MAPK-dependent stress response in fission yeast. J Biol Chem. 2008;283:22063-75 pubmed publisher
    ..Thus, the robust protein synthesis promoted by intact eIF3 appears to be a part of the requisites for sound Sty1 MAPK-dependent signaling governed by the activity of the Atf1 transcription factor. ..
  7. Bauer D, Gupta D, Harotunian V, Meador Woodruff J, McCullumsmith R. Abnormal expression of glutamate transporter and transporter interacting molecules in prefrontal cortex in elderly patients with schizophrenia. Schizophr Res. 2008;104:108-20 pubmed publisher
    ..These data indicate that proteins involved in glutamate reuptake and cycling are altered in the cortex in schizophrenia, and may provide potential targets for future treatment strategies. ..
  8. Pelz C, Kulesz Martin M, Bagby G, Sears R. Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data. BMC Bioinformatics. 2008;9:520 pubmed publisher
  9. Amarasinghe J, Scannapieco F, Haase E. Transcriptional and translational analysis of biofilm determinants of Aggregatibacter actinomycetemcomitans in response to environmental perturbation. Infect Immun. 2009;77:2896-907 pubmed publisher
    ..Thus, anaerobic conditions, nutrient stress, and iron limitation each upregulate known biofilm determinants of A. actinomycetemcomitans to contribute to biofilm formation. ..

More Information

Publications775 found, 100 shown here

  1. Benakanakere M, Li Q, Eskan M, Singh A, Zhao J, Galicia J, et al. Modulation of TLR2 protein expression by miR-105 in human oral keratinocytes. J Biol Chem. 2009;284:23107-15 pubmed publisher
    ..Further understanding of the role of miRNA in host responses may elucidate disease susceptibility and suggest new anti-inflammatory therapeutics. ..
  2. Zhang J, Li J, Deng H. Identifying gene interaction enrichment for gene expression data. PLoS ONE. 2009;4:e8064 pubmed publisher
  3. Ling I, Estus S. Role of SFRS13A in low-density lipoprotein receptor splicing. Hum Mutat. 2010;31:702-9 pubmed publisher
    ..We interpret these results as suggesting that SFRS13A regulates LDLR splicing efficiency and may therefore emerge as a modulator of cholesterol homeostasis. ..
  4. Kwon N, Garzia A, Espeso E, Ugalde U, Yu J. FlbC is a putative nuclear C2H2 transcription factor regulating development in Aspergillus nidulans. Mol Microbiol. 2010;77:1203-19 pubmed publisher
    ..In summary, FlbC is a putative nuclear transcription factor necessary for proper activation of conidiation, and its balanced activity is crucial for governing growth and development in A. nidulans. ..
  5. Rawls K, Yacovone S, Maupin Furlow J. GlpR represses fructose and glucose metabolic enzymes at the level of transcription in the haloarchaeon Haloferax volcanii. J Bacteriol. 2010;192:6251-60 pubmed publisher
    ..The results presented here provide genetic and biochemical evidence that GlpR controls both fructose and glucose metabolic enzymes through transcriptional repression of the glpR-pfkB operon and kdgK1 during growth on glycerol...
  6. Rosenthal A, Matson E, Eldar A, Leadbetter J. RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture. ISME J. 2011;5:1133-42 pubmed publisher
    ..The results suggest that staggeringly intricate networks of metabolic and gene interactions drive lignocellulose degradation and co-evolution of termite gut microbiota...
  7. Liu Y, Patwardhan G, Xie P, Gu X, Giuliano A, Cabot M. Glucosylceramide synthase, a factor in modulating drug resistance, is overexpressed in metastatic breast carcinoma. Int J Oncol. 2011;39:425-31 pubmed publisher
    ..Although a small study, these data suggest that GCS may be a prognostic indicator and potential target for the treatment of chemotherapy-refractory breast cancer. ..
  8. Qiu H, Lizano P, Laure L, Sui X, Rashed E, Park J, et al. H11 kinase/heat shock protein 22 deletion impairs both nuclear and mitochondrial functions of STAT3 and accelerates the transition into heart failure on cardiac overload. Circulation. 2011;124:406-15 pubmed publisher
  9. Atamian H, Eulgem T, Kaloshian I. SlWRKY70 is required for Mi-1-mediated resistance to aphids and nematodes in tomato. Planta. 2012;235:299-309 pubmed publisher
    ..This indicates that some aspects of WRKY70 regulation are conserved among distantly related eudicots...
  10. Chung M, Peyrot S, Leboeuf S, Park T, McGary K, Marcotte E, et al. RFX2 is broadly required for ciliogenesis during vertebrate development. Dev Biol. 2012;363:155-65 pubmed publisher
    ..Furthermore, we show that Rfx2 is essential for expression of several ciliogenic genes, including TTC25, which we show here is required for ciliogenesis, HH signaling, and left-right patterning. ..
  11. Kruzel E, Giles S, Hull C. Analysis of Cryptococcus neoformans sexual development reveals rewiring of the pheromone-response network by a change in transcription factor identity. Genetics. 2012;191:435-49 pubmed publisher
    ..gene regulatory components during eukaryotic evolution. ..
  12. 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
  13. Lis M, Bhatt S, Schoenly N, Lee A, Nislow C, Bobek L. Chemical genomic screening of a Saccharomyces cerevisiae genomewide mutant collection reveals genes required for defense against four antimicrobial peptides derived from proteins found in human saliva. Antimicrob Agents Chemother. 2013;57:840-7 pubmed publisher
    ..cerevisiae cells and consequently a high degree of similarity between their modes of action. ..
  14. Wang H, Ru Y, Sanchez Carbayo M, Wang X, Kieft J, Theodorescu D. Translation initiation factor eIF3b expression in human cancer and its role in tumor growth and lung colonization. Clin Cancer Res. 2013;19:2850-60 pubmed publisher
    ..eIF3b expression relates to human bladder and prostate cancer prognosis, is required for tumor growth, and thus a candidate therapeutic target. ..
  15. Guo L, Frost M, He L, Siegwart J, Norton T. Gene expression signatures in tree shrew sclera in response to three myopiagenic conditions. Invest Ophthalmol Vis Sci. 2013;54:6806-19 pubmed publisher
    ..We compared gene expression signatures in tree shrew sclera produced by three different visual conditions that all produce ocular elongation and myopia: minus-lens wear, form deprivation, and dark treatment...
  16. Anselmo M, Dalvin S, Prodhan P, Komatsuzaki K, Aidlen J, Schnitzer J, et al. Slit and robo: expression patterns in lung development. Gene Expr Patterns. 2003;3:13-9 pubmed
    ..We conclude Slit/Robo are expressed in temporo-spatially adjacent domains suggesting interactive roles in pulmonary bronchiolar development. ..
  17. Lee Y, Eum S, Chen K, Hennig B, Toborek M. Gene expression profile in interleukin-4-stimulated human vascular endothelial cells. Mol Med. 2004;10:19-27 pubmed
    ..In addition, a better understanding of IL-4-induced vascular injury at the level of gene expression could lead to the identification of new therapeutic strategies for atherosclerosis. ..
  18. Ponomarev I, Maiya R, Harnett M, Schafer G, Ryabinin A, Blednov Y, et al. Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci. 2006;26:5673-83 pubmed
  19. Ge X, Wu Q, Wang S. SAGE detects microRNA precursors. BMC Genomics. 2006;7:285 pubmed
    ..The observation that some orphan longSAGE tags uniquely match miRNA precursors provides information about the expression of some known and predicted miRNAs. ..
  20. Hulshizer R, Blalock E. Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data. BMC Bioinformatics. 2007;8:240 pubmed
  21. Rock J, Lopez M, Baker H, Harfe B. Identification of genes expressed in the mouse limb using a novel ZPA microarray approach. Gene Expr Patterns. 2007;8:19-26 pubmed
    ..The expression of two other genes was confirmed by rtPCR. The methods described in this report will be applicable for identifying genes enriched in Shh-expressing cells throughout development. ..
  22. Hsu K, Gildersleeve J, Mahal L. A simple strategy for the creation of a recombinant lectin microarray. Mol Biosyst. 2008;4:654-62 pubmed publisher
    ..This work opens the door to the establishment of a vast set of defined lectins via high-throughout approaches, advancing lectin microarray technology for glycomic analysis. ..
  23. Zhang J, Addepalli B, Yun K, Hunt A, Xu R, Rao S, et al. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS ONE. 2008;3:e2410 pubmed publisher
    ..These results implicate the Arabidopsis CPSF30 protein in the posttranscriptional control of the responses of plants to stress, and in particular to the expression of a set of genes that suffices to confer tolerance to oxidative stress. ..
  24. McKenzie S, Sakamoto S, Kyprianou N. Maspin modulates prostate cancer cell apoptotic and angiogenic response to hypoxia via targeting AKT. Oncogene. 2008;27:7171-9 pubmed publisher
    ..This study may have significance in the identification of maspin-driven therapeutic targeting in advanced metastatic prostate cancer. ..
  25. Gandhi A, Kang J, Capone L, Parton A, Wu L, Zhang L, et al. Dexamethasone synergizes with lenalidomide to inhibit multiple myeloma tumor growth, but reduces lenalidomide-induced immunomodulation of T and NK cell function. Curr Cancer Drug Targets. 2010;10:155-67 pubmed
  26. Pattanaik S, Kong Q, Zaitlin D, Werkman J, Xie C, Patra B, et al. Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta. 2010;231:1061-76 pubmed publisher
    ..These results suggest that NtAn2 is a key gene controlling anthocyanin production in reproductive tissues of tobacco...
  27. 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. ..
  28. Benoit S, Maier R. Mua (HP0868) is a nickel-binding protein that modulates urease activity in Helicobacter pylori. MBio. 2011;2:e00039-11 pubmed publisher
    ..This mechanism would counterbalance the NikR-mediated activation of urease and ensure that, in the presence of a high nickel concentration, urease activation is limited and does not lead to massive production of detrimental ammonia. ..
  29. Hensley M, Gunasekera T, Easton J, Sigdel T, Sugarbaker S, Klingbeil L, et al. Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli. J Inorg Biochem. 2012;111:164-72 pubmed publisher
    ..These results are discussed in light of Zn(II) starvation model that has been postulated for B. subtilis...
  30. Choi Y, Fuchs J, Mayhew G, Yu H, Christensen B. Tissue-enriched expression profiles in Aedes aegypti identify hemocyte-specific transcriptome responses to infection. Insect Biochem Mol Biol. 2012;42:729-38 pubmed publisher
  31. Wolf B, Schwarzer A, Côté A, Hampton T, Schwaab T, Huarte E, et al. Gene expression profile of peripheral blood lymphocytes from renal cell carcinoma patients treated with IL-2, interferon-? and dendritic cell vaccine. PLoS ONE. 2012;7:e50221 pubmed publisher
    ..This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC...
  32. Meznarich J, Malchodi L, Helterline D, Ramsey S, Bertko K, Plummer T, et al. Urokinase plasminogen activator induces pro-fibrotic/m2 phenotype in murine cardiac macrophages. PLoS ONE. 2013;8:e57837 pubmed publisher
    ..Understanding the mechanisms by which uPA modulates macrophage function may reveal insights into diverse pathologic processes. ..
  33. Zhang K, Zhao S, Wang Q, Yang H, Zhu J, Ma R. Identification of microRNAs in Nipple Discharge as Potential Diagnostic Biomarkers for Breast Cancer. Ann Surg Oncol. 2015;22 Suppl 3:S536-44 pubmed publisher
    ..miRNAs could serve as potential tumor biomarkers that can assist in breast cancer screening. Up-regulation of miR-4484, miR-K12-5-5p, and miR-3646 in nipple discharge may be a predictor of malignant breast cancer. ..
  34. Drummond C, Hill M, Shi H, Fan X, Xie J, Haller S, et al. Na/K-ATPase signaling regulates collagen synthesis through microRNA-29b-3p in cardiac fibroblasts. Physiol Genomics. 2016;48:220-9 pubmed publisher
    ..Additionally, these data indicate that miR-29b-3p expression plays an important role in the formation of cardiac fibrosis in CKD. ..
  35. McNulty S, Strube C, Rosa B, Martin J, Tyagi R, Choi Y, et al. Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. Sci Rep. 2016;6:20316 pubmed publisher
  36. Rahman M, MacNeil S, Jenkins D, Shrestha G, Wyatt S, McQuerry J, et al. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Med. 2017;9:40 pubmed publisher
    ..These phenotypes correlate to unique mechanisms of apoptosis and drug response and have the potential of pinpointing targetable aberration(s) for more effective breast cancer treatments. ..
  37. Wang J, Saha T, Zhang Y, Zhang C, Raikhel A. Juvenile hormone and its receptor methoprene-tolerant promote ribosomal biogenesis and vitellogenesis in the Aedes aegypti mosquito. J Biol Chem. 2017;292:10306-10315 pubmed publisher
    ..In summary, our results indicate that JH is critical for inducing the expression of ribosomal protein genes and demonstrate that RRS1 mediates the JH signal to enhance both ribosomal biogenesis and vitellogenesis. ..
  38. Romano R, Li H, Tummala R, Maul R, Sinha S. Identification of Basonuclin2, a DNA-binding zinc-finger protein expressed in germ tissues and skin keratinocytes. Genomics. 2004;83:821-33 pubmed
    ..Moreover, the structural and functional similarities with Basonuclin1 suggest that Basonuclin2 may play an analogous function in germ cells and skin keratinocytes. ..
  39. Vemuri G, Minning T, Altman E, Eiteman M. Physiological response of central metabolism in Escherichia coli to deletion of pyruvate oxidase and introduction of heterologous pyruvate carboxylase. Biotechnol Bioeng. 2005;90:64-76 pubmed
    ..The physiological and expression changes resulting from these genetic perturbations demonstrate the importance of the pyruvate node in respiration and its impact on acetate overflow during aerobic growth. ..
  40. Robalino J, Almeida J, McKillen D, Colglazier J, Trent H, Chen Y, et al. Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiol Genomics. 2007;29:44-56 pubmed
  41. Jain M, Chourey P, Li Q, Pring D. Expression of cell wall invertase and several other genes of sugar metabolism in relation to seed development in sorghum (Sorghum bicolor). J Plant Physiol. 2008;165:331-44 pubmed
    ..This trait is unique to sorghum among cereals and may facilitate its survival in drought environment. ..
  42. Bullard T, Protack T, Aguilar F, Bagwe S, Massey H, Blaxall B. Identification of Nogo as a novel indicator of heart failure. Physiol Genomics. 2008;32:182-9 pubmed
    ..To our knowledge, this is the first report to demonstrate the relationship between Nogo expression and HF, including cell-type specificity, in both mouse and human HF and phenotypic rescue. ..
  43. Chikina M, Huttenhower C, Murphy C, Troyanskaya O. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol. 2009;5:e1000417 pubmed publisher
    ..To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data. ..
  44. Senf A, Chen X. Identification of genes involved in the same pathways using a Hidden Markov Model-based approach. Bioinformatics. 2009;25:2945-54 pubmed publisher
    ..The algorithm performed very well compared to the Signature Algorithm and a purely correlation-based approach. Java source codes and data sets are available at http://www.ittc.ku.edu/~xwchen/software.htm ..
  45. Morrissey C, Lai J, Brown L, Wang Y, Roudier M, Coleman I, et al. The expression of osteoclastogenesis-associated factors and osteoblast response to osteolytic prostate cancer cells. Prostate. 2010;70:412-24 pubmed publisher
    ..IL-6 may have an important role in promoting osteoclastogenesis in PCa bone metastasis through its' interaction with sIL-6R. ..
  46. Mukhopadhyay P, Horn K, Greene R, Michele Pisano M. Prenatal exposure to environmental tobacco smoke alters gene expression in the developing murine hippocampus. Reprod Toxicol. 2010;29:164-75 pubmed publisher
  47. Hampton T, Stanton B. A novel approach to analyze gene expression data demonstrates that the DeltaF508 mutation in CFTR downregulates the antigen presentation pathway. Am J Physiol Lung Cell Mol Physiol. 2010;298:L473-82 pubmed publisher
    ..Additional studies are required to determine whether MHC class I gene repression in CF reduces antigen presentation at the protein level and whether repression impairs immune function. ..
  48. Moorman J, Zhang C, Ni L, Ma C, Zhang Y, Wu X, et al. Impaired hepatitis B vaccine responses during chronic hepatitis C infection: involvement of the PD-1 pathway in regulating CD4(+) T cell responses. Vaccine. 2011;29:3169-76 pubmed publisher
  49. Dong C, Wu Y, Yao J, Wang Y, Yu Y, Rychahou P, et al. G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer. J Clin Invest. 2012;122:1469-86 pubmed publisher
    ..Our study not only reveals a critical mechanism underlying the epigenetic regulation of EMT but also paves a way for the development of new treatment strategies for CLBC. ..
  50. Kumar P, Dezso Z, Mackenzie C, Oestreicher J, Agoulnik S, Byrne M, et al. Circulating miRNA biomarkers for Alzheimer's disease. PLoS ONE. 2013;8:e69807 pubmed publisher
    ..05. Pathway analysis, taking into account enriched target mRNAs for these signature miRNAs was also carried out, suggesting that the disturbance of multiple enzymatic pathways including lipid metabolism could play a role in AD etiology. ..
  51. Song R, Koyuncu O, Greco T, Diner B, Cristea I, Enquist L. Two Modes of the Axonal Interferon Response Limit Alphaherpesvirus Neuroinvasion. MBio. 2016;7:e02145-15 pubmed publisher
    ..The response to type II interferon (IFN-γ) involves long-distance signaling to the PNS cell body. These responses to two interferons erect an efficient and rapid barrier to PNS infection. ..
  52. Mruthyunjaya P, Seider M, Stinnett S, Schefler A. Association between Tumor Regression Rate and Gene Expression Profile after Iodine 125 Plaque Radiotherapy for Uveal Melanoma. Ophthalmology. 2017;124:1532-1539 pubmed publisher
    ..05). Class 1 UM tumors tend to regress more rapidly than class 2 tumors in the first 6 months after plaque radiotherapy. Class 1A and 1B tumors regress at similar rates after plaque radiotherapy. ..
  53. Seroude L, Brummel T, Kapahi P, Benzer S. Spatio-temporal analysis of gene expression during aging in Drosophila melanogaster. Aging Cell. 2002;1:47-56 pubmed
  54. Getchell T, Peng X, Green C, Stromberg A, Chen K, Mattson M, et al. In silico analysis of gene expression profiles in the olfactory mucosae of aging senescence-accelerated mice. J Neurosci Res. 2004;77:430-52 pubmed
  55. Kumar S, Leontovich A, Coenen M, Bahn R. Gene expression profiling of orbital adipose tissue from patients with Graves' ophthalmopathy: a potential role for secreted frizzled-related protein-1 in orbital adipogenesis. J Clin Endocrinol Metab. 2005;90:4730-5 pubmed
    ..These results support the concept that orbital adipogenesis is enhanced in GO and suggest that elevated levels of sFRP-1 in the GO orbit may be involved in stimulating this pathogenic process. ..
  56. Eide D, Clark S, Nair T, Gehl M, Gribskov M, Guerinot M, et al. Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol. 2005;6:R77 pubmed
    ..Our results indicate the power of ionomics to identify new aspects of mineral homeostasis and how these data can be used to develop hypotheses regarding the functions of previously uncharacterized genes. ..
  57. Németh Z, Csóka B, Wilmanski J, Xu D, Lu Q, Ledent C, et al. Adenosine A2A receptor inactivation increases survival in polymicrobial sepsis. J Immunol. 2006;176:5616-26 pubmed
    ..Similar to observations with A(2A)R KO mice, an A(2A)R antagonist increased survival even when administered in a delayed fashion. These studies demonstrate that A(2A)R blockade may be useful in the treatment of infection and sepsis. ..
  58. Jaworski D, Beem Miller M, Lluri G, Barrantes Reynolds R. Potential regulatory relationship between the nested gene DDC8 and its host gene tissue inhibitor of metalloproteinase-2. Physiol Genomics. 2007;28:168-78 pubmed
    ..That TIMP-2 transcripts in wild-type brain contain DDC8 sequence suggests alternative splicing between the two genes. ..
  59. Wooley S, Donaldson J, Stevens M, Gusse A, Lindroth R. Extrafloral nectaries in aspen (Populus tremuloides): heritable genetic variation and herbivore-induced expression. Ann Bot. 2007;100:1337-46 pubmed
    ..The relationship between EFNs and predators likely varies in relation to multiple temporal and environmental factors. ..
  60. Miller C, Page McCaw A, Broihier H. Matrix metalloproteinases promote motor axon fasciculation in the Drosophila embryo. Development. 2008;135:95-109 pubmed
    ..These data demonstrate that MMP activity is essential for embryonic motor axon fasciculation. ..
  61. Anway M, Skinner M. Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease. Prostate. 2008;68:517-29 pubmed publisher
    ..Potential epigenetic transgenerational alteration of prostate gene expression by environmental compounds may be important to consider in the etiology of adult onset prostate disease. ..
  62. Ge G, Wong G. Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles. BMC Bioinformatics. 2008;9:275 pubmed publisher
    ..Additionally, the use of feature selection method allows us to select biomarkers with potentially important roles in cancer development, therefore highlighting the validity of this method. ..
  63. Graham A, Kiss D, Andrulis E. Core exosome-independent roles for Rrp6 in cell cycle progression. Mol Biol Cell. 2009;20:2242-53 pubmed publisher
    ..Collectively, these data support the idea that dRrp6 has a core exosome-independent role in cell cycle and mitotic progression. ..
  64. Yu J, Hu K, Smuga Otto K, Tian S, Stewart R, Slukvin I, et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science. 2009;324:797-801 pubmed publisher
    ..These results demonstrate that reprogramming human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors and removes one obstacle to the clinical application of human iPS cells. ..
  65. Slonim D, Koide K, Johnson K, Tantravahi U, Cowan J, Jarrah Z, et al. Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Proc Natl Acad Sci U S A. 2009;106:9425-9 pubmed publisher
    ..Our results suggest that there are secondary adverse consequences of DS evident in the second trimester, leading to testable hypotheses about possible antenatal therapy for DS. ..
  66. Filichkin S, Priest H, Givan S, Shen R, Bryant D, Fox S, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010;20:45-58 pubmed publisher
    ..Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression. ..
  67. Hickey J, Weldon L, Hefty P. The atypical OmpR/PhoB response regulator ChxR from Chlamydia trachomatis forms homodimers in vivo and binds a direct repeat of nucleotide sequences. J Bacteriol. 2011;193:389-98 pubmed publisher
    ..Taken together, these observations support the conclusion that ChxR, in the absence of phosphorylation, exhibits many of the characteristics of a phosphorylated (active) OmpR/PhoB subfamily response regulator. ..
  68. Meyer E, Aglyamova G, Matz M. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol Ecol. 2011;20:3599-616 pubmed publisher
    ..Future studies of gene expression in corals will have to address this genetic variation, which could have important adaptive consequences for corals during global climate change. ..
  69. Sha W, Martins A, Laubenbacher R, Mendes P, Shulaev V. The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PLoS ONE. 2013;8:e74939 pubmed publisher
    ..Genes up-regulated only by cumene hydroperoxide are mainly related to the cell membrane and cell wall, and proteolysis process, while those down-regulated only by this aromatic peroxide are involved in mitochondrial function. ..
  70. Simões Costa M, Tan Cabugao J, Antoshechkin I, Sauka Spengler T, Bronner M. Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. Genome Res. 2014;24:281-90 pubmed publisher
    ..Taken together, our analysis provides unprecedented characterization of the migratory CNC transcriptome and identifies new links in the gene regulatory network responsible for development of this critical cell population. ..
  71. Zhao S, Evans J, Kothari V, Sun G, Larm A, Mondine V, et al. The Landscape of Prognostic Outlier Genes in High-Risk Prostate Cancer. Clin Cancer Res. 2016;22:1777-86 pubmed publisher
  72. Zanotelli M, Ardalani H, Zhang J, Hou Z, Nguyen E, Swanson S, et al. Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels. Acta Biomater. 2016;35:32-41 pubmed publisher
    ..Human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) cultured in synthetic hydrogels self-assemble into capillary networks through mechanisms consistent with in vivo vascular morphogenesis. ..
  73. Toh S, Treves D, Barati M, Perlin M. Reliable transformation system for Microbotryum lychnidis-dioicae informed by genome and transcriptome project. Arch Microbiol. 2016;198:813-25 pubmed publisher
    ..The technique thus provides for the first time the ability to stably introduce transgenes and over-express target M. lychnidis-dioicae genes. ..
  74. Rogina B, Helfand S. Cu, Zn superoxide dismutase deficiency accelerates the time course of an age-related marker in Drosophila melanogaster. Biogerontology. 2000;1:163-9 pubmed
  75. Liang P, Jones C, Bisgrove B, Song L, Glenn S, Yost H, et al. Genomic characterization and expression analysis of the first nonmammalian renin genes from zebrafish and pufferfish. Physiol Genomics. 2004;16:314-22 pubmed publisher
  76. Sung S, Amasino R. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature. 2004;427:159-64 pubmed
    ..Here we identify a gene with a function in the measurement of the duration of cold exposure and in the establishment of the vernalized state. We show that this silencing involves changes in the modification of histones in FLC chromatin. ..
  77. Krystofova S, Borkovich K. The heterotrimeric G-protein subunits GNG-1 and GNB-1 form a Gbetagamma dimer required for normal female fertility, asexual development, and galpha protein levels in Neurospora crassa. Eukaryot Cell. 2005;4:365-78 pubmed publisher
    ..Direct evidence for a physical association between GNB-1 and GNG-1 in vivo was provided by coimmunoprecipitation...
  78. Roden J, King B, Trout D, Mortazavi A, Wold B, Hart C. Mining gene expression data by interpreting principal components. BMC Bioinformatics. 2006;7:194 pubmed
    ..This approach also shows promise in other topic domains such as multi-spectral imaging datasets. ..
  79. Sun X, Song Q. PKC-mediated USP phosphorylation is required for 20E-induced gene expression in the salivary glands of Drosophila melanogaster. Arch Insect Biochem Physiol. 2006;62:116-27 pubmed
    ..The composite data suggest that PKC-mediated USP phosphorylation is required for 20E-induced gene expression in the salivary glands of Drosophila melanogaster. ..
  80. Liu Y, Das S, Olszewski R, Carpenter D, Culiat C, Sundberg J, et al. The near-naked hairless (Hr(N)) mutation disrupts hair formation but is not due to a mutation in the Hairless coding region. J Invest Dermatol. 2007;127:1605-14 pubmed
    ..Therefore, Hr(N) does not appear to be an allele of Hr but may result from a mutation in a closely linked gene or from a regulatory mutation in Hr. ..
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    ..Furthermore, there was an overall pattern of tissue specifically methylated CpG islands that distinguished neural tissues from non-neural. ..
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    ..We propose that CRY2/PHOT2 negatively regulate the proteasome-mediated degradation of HRT, likely via COP1, and blue-light relieves this repression resulting in HRT degradation...
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    ..In light of these results, we examined the evolution of morphological characters and found support for advanced cephalization and shells as possibly having multiple origins within Mollusca. ..
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    ..This approach to health status classification shows promise for disease identification in a clinical setting, and assessment of health status of wildlife...