Experts and Doctors on gene expression profiling in Singapore, Central Singapore, Singapore

Summary

Locale: Singapore, Central Singapore, Singapore
Topic: gene expression profiling

Top Publications

  1. Loh Y, Christoffels A, Brenner S, Hunziker W, Venkatesh B. Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes. Genome Res. 2004;14:1248-57 pubmed
  2. Aggarwal A, Guo D, Hoshida Y, Yuen S, Chu K, So S, et al. Topological and functional discovery in a gene coexpression meta-network of gastric cancer. Cancer Res. 2006;66:232-41 pubmed
    ..Thus, besides enhancing our knowledge of gastric cancer, our results show the broad utility of applying meta-analytic approaches to genome-wide data for the purposes of biological discovery. ..
  3. Leong W, Chow V. Transcriptomic and proteomic analyses of rhabdomyosarcoma cells reveal differential cellular gene expression in response to enterovirus 71 infection. Cell Microbiol. 2006;8:565-80 pubmed
    ..Thus, microarray, real-time RT-PCR and proteomic analyses can elucidate the global view of the numerous and complex cellular responses that contribute towards EV71 pathogenesis. ..
  4. Yap D, Smith D, Zhang X, Hill J. Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. BMC Genomics. 2007;8:210 pubmed
    ..It also provides a step towards standardization of experiments relying on cells being in the stem cell or differentiating state. ..
  5. Tan B, Tan L, Yu K, Tan P, Lee M, Sii L, et al. Clinical validation of a customized multiple signature microarray for breast cancer. Clin Cancer Res. 2008;14:461-9 pubmed publisher
    ..2; P = 0.019). The consistency of the MSA platform in an independent patient population suggests that custom microarrays could potentially function as an adjunct to standard immunohistochemistry and FISH in clinical practice. ..
  6. Toh S, Gong J, Du G, Li J, Yang S, Ye J, et al. Up-regulation of mitochondrial activity and acquirement of brown adipose tissue-like property in the white adipose tissue of fsp27 deficient mice. PLoS ONE. 2008;3:e2890 pubmed publisher
    ..Our data thus suggest that Fsp27 acts as a novel regulator in vivo to control WAT identity, mitochondrial activity and insulin sensitivity. ..
  7. Moh M, Zhang T, Lee L, Shen S. Expression of hepaCAM is downregulated in cancers and induces senescence-like growth arrest via a p53/p21-dependent pathway in human breast cancer cells. Carcinogenesis. 2008;29:2298-305 pubmed publisher
    ..Together, the results suggest that the expression of hepaCAM in MCF7 cells not only inhibits cell growth but also induces cellular senescence through the p53/21 pathway. ..
  8. Liu T, Wu Y, Guo X, Hui J, Lee E, Lim B. Effects of ectopic Nanog and Oct4 overexpression on mesenchymal stem cells. Stem Cells Dev. 2009;18:1013-22 pubmed publisher
    ..These results provide insight into the improvement of the stemness of MSCs by genetic modification with stemness-related genes. ..
  9. Hu G, Cabrera A, Kono M, Mok S, Chaal B, Haase S, et al. Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol. 2010;28:91-8 pubmed publisher
    ..Our network may facilitate identification of novel antimalarial drugs and vaccines. ..

More Information

Publications141 found, 100 shown here

  1. Siang A, Doley R, Vonk F, Kini R. Transcriptomic analysis of the venom gland of the red-headed krait (Bungarus flaviceps) using expressed sequence tags. BMC Mol Biol. 2010;11:24 pubmed publisher
    ..Although the venoms of most species of the snake genus Bungarus have been well characterized, a detailed compositional analysis of B. flaviceps is currently lacking...
  2. Ang M, Ooi A, Thike A, Tan P, Zhang Z, Dykema K, et al. Molecular classification of breast phyllodes tumors: validation of the histologic grading scheme and insights into malignant progression. Breast Cancer Res Treat. 2011;129:319-29 pubmed publisher
    ..HOXB13 protein overexpression was found to be correlated with stromal hypercellularity and atypia (P = 0.03, P = 0.039, respectively) and may be implicated in the development of malignant phyllodes tumors. ..
  3. Tan S, Lin Z, Chang C, Varang V, Chng K, Pan Y, et al. AP-2? regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription. EMBO J. 2011;30:2569-81 pubmed publisher
    ..Finally, we show that most ERBS associated with long-range chromatin interactions are colocalized with AP-2? and FoxA1. Together, our results suggest AP-2? is a novel collaborative factor in ER?-mediated transcription. ..
  4. Wong T, Zhou L, Li J, Tong L, Zhao S, Li X, et al. Proteomic profiling of inflammatory signaling molecules in the tears of patients on chronic glaucoma medication. Invest Ophthalmol Vis Sci. 2011;52:7385-91 pubmed publisher
    ..To identify the tear proteins associated with the long-term use of glaucoma medication by using proteomic analysis and to compare these proteins to those previously reported in primary dry eye disease...
  5. Tolfvenstam T, Lindblom A, Schreiber M, Ling L, Chow A, Ooi E, et al. Characterization of early host responses in adults with dengue disease. BMC Infect Dis. 2011;11:209 pubmed publisher
    ..Several of the early transcripts identified may be affected by or mediate the pathogenesis and deserve further assessment at this timepoint in correlation to severe disease. ..
  6. Wang S, Ooi L, Hui K. Upregulation of Rac GTPase-activating protein 1 is significantly associated with the early recurrence of human hepatocellular carcinoma. Clin Cancer Res. 2011;17:6040-51 pubmed publisher
    ..Besides being an independent informative prognostic biomarker, RACGAP1 could also be a potential molecular target for designing therapeutic strategies for HCC. ..
  7. Chandrasekaran K, Karolina D, Sepramaniam S, Armugam A, Wintour E, Bertram J, et al. Role of microRNAs in kidney homeostasis and disease. Kidney Int. 2012;81:617-27 pubmed publisher
    ..In addition, we highlight the need for further investigations on miRNA-based studies in the development of diagnostic, prognostic, and therapeutic tools for renal diseases. ..
  8. Bozdech Z, Mok S, Gupta A. DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods Mol Biol. 2013;923:189-211 pubmed
  9. Ho V, Yeo S, Kunasegaran K, De Silva D, Tarulli G, Voorhoeve P, et al. Expression analysis of rare cellular subsets: direct RT-PCR on limited cell numbers obtained by FACS or soft agar assays. Biotechniques. 2013;54:208-12 pubmed publisher
  10. Wen Y, Lim G, Wong S. Profiling of genes related to cross protection and competition for NbTOM1 by HLSV and TMV. PLoS ONE. 2013;8:e73725 pubmed publisher
    ..These results indicate that host genes involved in the plant defense response and virus multiplication are up-regulated by challenge virus TMV but not by protecting virus HLSV during cross protection. ..
  11. Qian F, Zhen F, Ong C, Jin S, Meng Soo H, Stainier D, et al. Microarray analysis of zebrafish cloche mutant using amplified cDNA and identification of potential downstream target genes. Dev Dyn. 2005;233:1163-72 pubmed
    ..Our study provides valuable information for studying hematopoiesis and vessel formation. The method described here offers a powerful tool for gene expression profiling of zebrafish mutants in general. ..
  12. Fong C, Chua M, McKie A, Ling S, Mason V, Li R, et al. Sprouty 2, an inhibitor of mitogen-activated protein kinase signaling, is down-regulated in hepatocellular carcinoma. Cancer Res. 2006;66:2048-58 pubmed
  13. Lian Q, Yeo K, Que J, Tan E, Yu F, Yin Y, et al. Establishing clonal cell lines with endothelial-like potential from CD9(hi), SSEA-1(-) cells in embryonic stem cell-derived embryoid bodies. PLoS ONE. 2006;1:e6 pubmed
    ..By combining empirical and rational evidence-based methods, we identified definitive selectable surface antigens for the isolation and propagation of lineage-restricted stem cells with endothelial-like potential from mouse ESCs. ..
  14. Lee K, Goh W, Xu M, Kua N, Lunny D, Wong J, et al. Detection of the p53 response in zebrafish embryos using new monoclonal antibodies. Oncogene. 2008;27:629-40 pubmed
  15. Tan K, Zhu Y, Tan H, Rajasegaran V, Aggarwal A, Wu J, et al. Amplification and overexpression of PPFIA1, a putative 11q13 invasion suppressor gene, in head and neck squamous cell carcinoma. Genes Chromosomes Cancer. 2008;47:353-62 pubmed publisher
    ..This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. ..
  16. Ho I, Chan K, Ng W, Guo C, Hui K, Cheang P, et al. Matrix metalloproteinase 1 is necessary for the migration of human bone marrow-derived mesenchymal stem cells toward human glioma. Stem Cells. 2009;27:1366-75 pubmed publisher
    ..Taken together, this study provides, for the first time, supporting evidence that MMP1 is critically involved in the migration capacity of MSCs, acting through the MMP1/PAR1 axis. ..
  17. Zhao C, Zhang H, Wong W, Sem X, Han H, Ong S, et al. Identification of novel functional differences in monocyte subsets using proteomic and transcriptomic methods. J Proteome Res. 2009;8:4028-38 pubmed publisher
    ..These functional differences would provide new insights into the different roles of the two monocyte subsets in regulating innate and adaptive immune responses. ..
  18. Tong L, Diebold Y, Calonge M, Gao J, Stern M, Beuerman R. Comparison of gene expression profiles of conjunctival cell lines with primary cultured conjunctival epithelial cells and human conjunctival tissue. Gene Expr. 2009;14:265-78 pubmed
  19. Wang M, Wang X, Ching C, Chen W. Proteomic profiling of cellular responses to Carvedilol enantiomers in vascular smooth muscle cells by iTRAQ-coupled 2-D LC-MS/MS. J Proteomics. 2010;73:1601-11 pubmed publisher
    ..Our findings thus provided molecular evidence on a comprehensive protein profile on Carvedilol-cell interaction, which may shed new light in molecular events underlying Carvedilol treatment...
  20. Low D, Chen K. Genome-wide gene expression profiling of the Angelman syndrome mice with Ube3a mutation. Eur J Hum Genet. 2010;18:1228-35 pubmed publisher
    ..These observation help in providing insights into the genesis of neurodevelopmental phenotype of AS and highlight specific area for future research. ..
  21. Kuss C, Gan C, Gunalan K, Bozdech Z, Sze S, Preiser P. Quantitative proteomics reveals new insights into erythrocyte invasion by Plasmodium falciparum. Mol Cell Proteomics. 2012;11:M111.010645 pubmed publisher
    ..These results demonstrate a so far unrecognized mechanism by which the malaria parasite is able to adapt to variations in the host cell environment by post-transcriptional regulation. ..
  22. Kumar P, Hu Y, Yamamoto Y, Hoe N, Wei T, Mu D, et al. Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection. Cell. 2011;147:525-38 pubmed publisher
  23. Li Z, Zheng W, Wang Z, Zeng Z, Zhan H, Li C, et al. A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors. Dis Model Mech. 2013;6:414-23 pubmed publisher
    ..Thus, our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. ..
  24. Zhang S, Guo T, Chan H, Sze S, Koh C. Integrative transcriptome and proteome study to identify the signaling network regulated by POPX2 phosphatase. J Proteome Res. 2013;12:2525-36 pubmed publisher
    ..Taken together, our data suggest that POPX2 might regulate cell motility through its regulation of the MAPK1/3, leading to changes in the cytoskeleton and cell motility. ..
  25. Hu Y, Hase T, Li H, Prabhakar S, Kitano H, Ng S, et al. A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data. BMC Genomics. 2016;17:1025 pubmed publisher
    ..It is believed to be extensible and applicable to other single-cell RNA-seq expression profiles like that of the study of the cancer progression and treatment within a highly heterogeneous tumour. ..
  26. Morrison J, Rathore A, Mantri C, Aman S, Nishida A, St John A. Transcriptional Profiling Confirms the Therapeutic Effects of Mast Cell Stabilization in a Dengue Disease Model. J Virol. 2017;91: pubmed publisher
    ..The use of the mast cell stabilization drug ketotifen reversed many of these responses and induced additional changes in the transcriptome and immune cell repertoire that contribute to decreased dengue disease. ..
  27. Cao B, Loh K. Catabolic pathways and cellular responses of Pseudomonas putida P8 during growth on benzoate with a proteomics approach. Biotechnol Bioeng. 2008;101:1297-312 pubmed publisher
    ..Based on the data obtained, physiological changes of P. putida in response to growth on benzoate at different concentrations were discussed. ..
  28. Leo J, Wang S, Guo C, Aw S, Zhao Y, Li J, et al. Gene regulation profile reveals consistent anticancer properties of progesterone in hormone-independent breast cancer cells transfected with progesterone receptor. Int J Cancer. 2005;117:561-8 pubmed
    ..The identification of many novel progesterone target genes open up new avenues for in-depth elucidation of progesterone-mediated molecular networks. ..
  29. Jiang X, Tan J, Li J, Kivimäe S, Yang X, Zhuang L, et al. DACT3 is an epigenetic regulator of Wnt/beta-catenin signaling in colorectal cancer and is a therapeutic target of histone modifications. Cancer Cell. 2008;13:529-41 pubmed publisher
    ..Our study identifies DACT3 as an important regulator of Wnt/beta-catenin signaling in colorectal cancer and suggests a potential strategy for therapeutic control of Wnt/beta-catenin signaling in colorectal cancer. ..
  30. Anand A, Suganthan P. Multiclass cancer classification by support vector machines with class-wise optimized genes and probability estimates. J Theor Biol. 2009;259:533-40 pubmed publisher
    ..This study demonstrates successful implementation of the framework of class-wise feature selection and multiclass classification for prediction of cancer subtypes on six datasets. ..
  31. Wong K, Tai J, Wong W, Han H, Sem X, Yeap W, et al. Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets. Blood. 2011;118:e16-31 pubmed publisher
    ..By comprehensively defining the 3 monocyte subsets during healthy conditions, we facilitate target identification and detailed analyses of aberrations that may occur to monocyte subsets during diseases. ..
  32. Zhang C, McFarlane C, Lokireddy S, Masuda S, Ge X, Gluckman P, et al. Inhibition of myostatin protects against diet-induced obesity by enhancing fatty acid oxidation and promoting a brown adipose phenotype in mice. Diabetologia. 2012;55:183-93 pubmed publisher
    ..Taken together, our data suggest that anti-myostatin therapeutics could be beneficial in alleviating obesity. ..
  33. Chin A, Fong W, Goh L, Philp R, Oh S, Choo A. Identification of proteins from feeder conditioned medium that support human embryonic stem cells. J Biotechnol. 2007;130:320-8 pubmed
    ..Using proteomic tools, important proteins from CM that supports hESC culture have been identified, which when replaced with recombinant proteins, continue to support undifferentiated hESC growth in a feeder-free culture platform. ..
  34. Fu X, Toh W, Liu H, Lu K, Li M, Cao T. Establishment of clinically compliant human embryonic stem cells in an autologous feeder-free system. Tissue Eng Part C Methods. 2011;17:927-37 pubmed publisher
    ..Overall, this study suggested a strategy for efficient propagation of clinically compliant hESCs in an autologous feeder-free culture system. ..
  35. Yeo H, Beh T, Quek J, Koh G, Chan K, Lee D. Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells. PLoS ONE. 2011;6:e27231 pubmed publisher
    ..In addition, we proposed a core self-renewal module of regulatory interplay between E2F and, WNT and FGF pathways in these cells. Thus, we conclude that E2F plays a significant role in influencing the self-renewal capabilities of hPSCs. ..
  36. Carpentier S, Vu Manh T, Chelbi R, Henri S, Malissen B, Haniffa M, et al. Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1(+) DCs in mouse and human and distinguishes them from Langerhans cells. J Immunol Methods. 2016;432:35-49 pubmed publisher
    ..This analysis demonstrates the equivalence between human and mouse skin XCR1(+) DCs, and between mouse and human Langerhans cells. ..
  37. Tan F, Ooi A, Huang D, Wong J, Qian C, Chao C, et al. p38delta/MAPK13 as a diagnostic marker for cholangiocarcinoma and its involvement in cell motility and invasion. Int J Cancer. 2010;126:2353-61 pubmed publisher
    ..In summary, p38delta may serve as a novel diagnostic marker for CC and may also serve as a new target for molecular based therapy of this disease. ..
  38. Li Y, Patra J. Integration of multiple data sources to prioritize candidate genes using discounted rating system. BMC Bioinformatics. 2010;11 Suppl 1:S20 pubmed publisher
    ..The proposed DRS algorithm is a powerful and effective framework for candidate gene prioritization. If weights of different data sources are proper given, the DRS algorithm will perform better. ..
  39. Ng F, Toh T, Ting E, Koh G, Sandanaraj E, Phong M, et al. Progenitor-like traits contribute to patient survival and prognosis in oligodendroglial tumors. Clin Cancer Res. 2012;18:4122-35 pubmed
    ..Collectively, these data highlight the limitation of morphology-based histologic analyses in tumor classification, consequently impacting on treatment decisions. ..
  40. Wan G, Yang K, Lim Q, Zhou L, He B, Wong H, et al. Identification and validation of reference genes for expression studies in a rat model of neuropathic pain. Biochem Biophys Res Commun. 2010;400:575-80 pubmed publisher
    ..These genes may contribute to the development of neuropathic pain pathology and may serve as candidate biomarkers for potential diagnosis. ..
  41. Chen W, Salto Tellez M, Palanisamy N, Ganesan K, Hou Q, Tan L, et al. Targets of genome copy number reduction in primary breast cancers identified by integrative genomics. Genes Chromosomes Cancer. 2007;46:288-301 pubmed
    ..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. ..
  42. Yu S, Ma H, Ow J, Goh Z, Chiang R, Yang H, et al. Zfp553 Is Essential for Maintenance and Acquisition of Pluripotency. Stem Cells Dev. 2016;25:55-67 pubmed publisher
    ..Together, our preliminary findings provide novel insights to a newly identified pluripotency factor Zfp553 and its role in pluripotency regulation. ..
  43. Richards M, Tan S, Tan J, Chan W, Bongso A. The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells. 2004;22:51-64 pubmed
  44. Xu X, Soo S, Sun W, Zweigerdt R. Global expression profile of highly enriched cardiomyocytes derived from human embryonic stem cells. Stem Cells. 2009;27:2163-74 pubmed publisher
  45. Dheen S, Hao A, Fu J, Gopalakrishnakone P, Ling E. Identification of differentially expressed genes in fetal rat forebrain exposed to a teratogen by cDNA microarray analysis. Histol Histopathol. 2007;22:729-42 pubmed publisher
    ..The present results suggest that a vigorous inflammatory response involving amoeboid microglia/brain macrophages primarily is an important component in CP-induced prenatal development disorder. ..
  46. Kong S, Chui P, Lim B, Salto Tellez M. Elucidating the molecular physiopathology of acute respiratory distress syndrome in severe acute respiratory syndrome patients. Virus Res. 2009;145:260-9 pubmed publisher
    ..Ultimately, this study may serve as a model for future, tissue-based analyses of fibroinflammatory conditions affecting the lung...
  47. Heng J, Feng B, Han J, Jiang J, Kraus P, Ng J, et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell. 2010;6:167-74 pubmed publisher
    ..We also show that Nr5a2 works in part through activating Nanog. Together, we show that unrelated transcription factors can replace Oct4 and uncovers an exogenous Oct4-free reprogramming code. ..
  48. Gwee P, Tay B, Brenner S, Venkatesh B. Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes. BMC Evol Biol. 2009;9:47 pubmed publisher
    ..We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae)...
  49. Li J, Tan J, Zhuang L, Banerjee B, Yang X, Chau J, et al. Ribosomal protein S27-like, a p53-inducible modulator of cell fate in response to genotoxic stress. Cancer Res. 2007;67:11317-26 pubmed
    ..Thus, RPS27L modulates DNA damage response and functions as a part of the control switch to determine cell fate to DNA damage-p53 response. ..
  50. Shei W, Liu J, Htoon H, Aung T, Vithana E. Differential expression of the Slc4 bicarbonate transporter family in murine corneal endothelium and cell culture. Mol Vis. 2013;19:1096-106 pubmed
    ..Moreover, as cell culture can affect expression levels of Slc4 genes, caution and careful design of experiments are necessary when undertaking studies of Slc4-mediated ion transport in cultured cells. ..
  51. Li H, Courtois E, Sengupta D, Tan Y, Chen K, Goh J, et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet. 2017;49:708-718 pubmed publisher
    ..Overall, our results demonstrate that unbiased single-cell RNA-seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor. ..
  52. Low Y, Blöcker C, McPherson J, Tang S, Cheng Y, Wong J, et al. A formalin-fixed paraffin-embedded (FFPE)-based prognostic signature to predict metastasis in clinically low risk stage I/II microsatellite stable colorectal cancer. Cancer Lett. 2017;403:13-20 pubmed publisher
    ..92, design-set; HR = 2.05, test-set). Thus, early-stage CRC patients who test positive may be considered for adjuvant therapy after surgery. ..
  53. Chu Z, Li J, Eshaghi M, Karuturi R, Lin K, Liu J. Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome. BMC Genomics. 2007;8:323 pubmed
    ..pombe. ..
  54. Zhou J, Pan M, Xie Z, Loh S, Bi C, Tai Y, et al. Synergistic antileukemic effects between ABT-869 and chemotherapy involve downregulation of cell cycle-regulated genes and c-Mos-mediated MAPK pathway. Leukemia. 2008;22:138-46 pubmed
    ..Thus, a clinical trial using sequence-dependent combination therapy with ABT-869 in AML is warranted. ..
  55. Sui J, Zhang J, Tan T, Ching C, Chen W. Comparative proteomics analysis of vascular smooth muscle cells incubated with S- and R-enantiomers of atenolol using iTRAQ-coupled two-dimensional LC-MS/MS. Mol Cell Proteomics. 2008;7:1007-18 pubmed publisher
    ..Our preliminary results thus provide molecular evidence on the metabolic effect and possible link of calcium-binding proteins with treatment of hypertension associated with atenolol. ..
  56. Orban L, Sreenivasan R, Olsson P. Long and winding roads: testis differentiation in zebrafish. Mol Cell Endocrinol. 2009;312:35-41 pubmed publisher
    ..New approaches and methodologies provide hope that answers to a number of important questions will be deciphered in the future. ..
  57. Koh W, Sheng C, Tan B, Lee Q, Kuznetsov V, Kiang L, et al. Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. BMC Genomics. 2010;11 Suppl 1:S6 pubmed publisher
  58. Choy M, Chen M, Manikandan J, Peng Z, Jenner A, Melendez A, et al. Up-regulation of endoplasmic reticulum stress-related genes during the early phase of treatment of cultured cortical neurons by the proteasomal inhibitor lactacystin. J Cell Physiol. 2011;226:494-510 pubmed publisher
  59. Ivan F, Rajapakse J, Welsch R, Rozen S, Narasaraju T, Xiong G, et al. Differential pulmonary transcriptomic profiles in murine lungs infected with low and highly virulent influenza H3N2 viruses reveal dysregulation of TREM1 signaling, cytokines, and chemokines. Funct Integr Genomics. 2012;12:105-17 pubmed publisher
    ..Overall, our comparative transcriptomic study provided insights into key host factors that influence the dynamics, pathogenesis, and outcome of severe influenza. ..
  60. Chu Q, Cai L, Fu Y, Chen X, Yan Z, Lin X, et al. Dkk2/Frzb in the dermal papillae regulates feather regeneration. Dev Biol. 2014;387:167-78 pubmed publisher
    ..Our results suggest that the Wnt signaling in the proximal feather follicle is fine-tuned to accommodate feather regeneration and axis formation. ..
  61. Hegde A, Qiu N, Qiu X, Ho S, Tay K, George J, et al. Genomewide expression analysis in zebrafish mind bomb alleles with pancreas defects of different severity identifies putative Notch responsive genes. PLoS ONE. 2008;3:e1479 pubmed publisher
  62. Zhang H, Chong H, Ching C, Song H, Jiang R. Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Appl Microbiol Biotechnol. 2012;94:1107-17 pubmed publisher
    ..In conclusion, direct manipulation of the transcript profile through engineering global transcription factor CRP can provide a useful tool in strain engineering. ..
  63. Zheng W, Xu H, Lam S, Luo H, Karuturi R, Gong Z. Transcriptomic analyses of sexual dimorphism of the zebrafish liver and the effect of sex hormones. PLoS ONE. 2013;8:e53562 pubmed publisher
    ..The information obtained in this study provides comprehensive insights into the sexual dimorphism of zebrafish liver transcriptome and will facilitate further development of the zebrafish as a human liver disease model. ..
  64. Silambarasan M, Tan J, Karolina D, Armugam A, Kaur C, Jeyaseelan K. MicroRNAs in Hyperglycemia Induced Endothelial Cell Dysfunction. Int J Mol Sci. 2016;17:518 pubmed publisher
    ..These miRNAs were also found to be involved in endothelial dysfunction. At least seven of them, miR-29b-3p, -29c-3p, -125b-1-3p, -130b-3p, -221-3p, -320a and -192-5p, can be correlated to endothelial cell apoptosis. ..
  65. Ng F, Boucher S, Koh S, Sastry K, Chase L, Lakshmipathy U, et al. PDGF, TGF-beta, and FGF signaling is important for differentiation and growth of mesenchymal stem cells (MSCs): transcriptional profiling can identify markers and signaling pathways important in differentiation of MSCs into adipogenic, chondrogenic, . Blood. 2008;112:295-307 pubmed publisher
    ..Thus, this study illustrates it is possible to predict signaling pathways active in cellular differentiation and growth using microarray data and experimentally verify these predictions. ..
  66. Ong S, Tan Y, Beretta O, Jiang D, Yeap W, Tai J, et al. Macrophages in human colorectal cancer are pro-inflammatory and prime T cells towards an anti-tumour type-1 inflammatory response. Eur J Immunol. 2012;42:89-100 pubmed publisher
    ..These new findings would contribute to the development of future cancer immunotherapies based on enhancing the tumour-suppressive properties of TAMs to boost anti-tumour immune responses. ..
  67. Yew E, Cheung N, Choy M, Qi R, Lee A, Peng Z, et al. Proteasome inhibition by lactacystin in primary neuronal cells induces both potentially neuroprotective and pro-apoptotic transcriptional responses: a microarray analysis. J Neurochem. 2005;94:943-56 pubmed
  68. Hu W, Tay S, Zhao Y. Endometriosis-specific genes identified by real-time reverse transcription-polymerase chain reaction expression profiling of endometriosis versus autologous uterine endometrium. J Clin Endocrinol Metab. 2006;91:228-38 pubmed
    ..Some of these genes, known to participate in estrogen activities and antiapoptosis, may play a role in the pathogenesis of endometriosis and may represent potential diagnostic markers or therapeutic targets for endometriosis. ..
  69. Nasirudeen A, Liu D. Gene expression profiling by microarray analysis reveals an important role for caspase-1 in dengue virus-induced p53-mediated apoptosis. J Med Virol. 2009;81:1069-81 pubmed publisher
    ..Gene silencing of caspase-1 or inhibition of caspase-1 activity led to reduction in dengue virus-induced apoptosis with minimal effect on virus replication. ..
  70. Grinchuk O, Motakis E, Kuznetsov V. Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression. BMC Genomics. 2010;11 Suppl 1:S9 pubmed publisher
    ..Co-expression pattern of this module correlates with histological grades and a poor prognosis in breast cancer when over-expressed. TNFAIP1/POLDIP2 CSAGA maps the risks of breast cancer relapse onto the complex genomic locus on 17q11.2. ..
  71. Kiener T, Sleptsova Friedrich I, Hunziker W. Identification, tissue distribution and developmental expression of tjp1/zo-1, tjp2/zo-2 and tjp3/zo-3 in the zebrafish, Danio rerio. Gene Expr Patterns. 2007;7:767-76 pubmed
    ..Interestingly, the differential tissue and developmental expression of the two tjp1 and tjp2 genes indicates that the duplicated genes have been adapted for distinct transcriptional regulations during evolution. ..
  72. Ma M, Nevalainen T, Yeo J, Ong W. Expression profile of multiple secretory phospholipase A(2) isoforms in the rat CNS: enriched expression of sPLA(2)-IIA in brainstem and spinal cord. J Chem Neuroanat. 2010;39:242-7 pubmed publisher
    ..The expression of sPLA(2)-IIA in the dorsal horn and spinal trigeminal nucleus is consistent with previous results which showed an important role of CNS sPLA(2) in nociceptive transmission. ..
  73. Ung C, Lam S, Hlaing M, Winata C, Korzh S, Mathavan S, et al. Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation. BMC Genomics. 2010;11:212 pubmed publisher
    ..The molecular conservation of mercury-induced hepatotoxicity between zebrafish and human cell line reveals the feasibility of using zebrafish to model molecular toxicity in human for toxicant risk assessments. ..
  74. Guo G, Huss M, Tong G, Wang C, Li Sun L, Clarke N, et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell. 2010;18:675-85 pubmed publisher
    ..These results illustrate the power of single-cell expression analysis to provide insight into developmental mechanisms. The technique should be widely applicable to other biological systems. ..
  75. Yang P, Wang M, He C, Yao S. Proteomic profiling and potential cellular target identification of K11777, a clinical cysteine protease inhibitor, in Trypanosoma brucei. Chem Commun (Camb). 2012;48:835-7 pubmed publisher
    ..We report herein the design, synthesis and application of K11777-derived activity-based probes (ABPs) allowing in situ profiling and identification of potential cellular targets of K11777 in Trypanosoma brucei. ..
  76. Zhang H, Chong H, Ching C, Jiang R. Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance. Biotechnol Bioeng. 2012;109:1165-72 pubmed publisher
    ..Scanning electron microscopy images confirmed the elongation of both WT and MT6 when exposed to NaCl but the cell surface of MT6 was relatively smooth. ..
  77. Ivanova T, Zouridis H, Wu Y, Cheng L, Tan I, Gopalakrishnan V, et al. Integrated epigenomics identifies BMP4 as a modulator of cisplatin sensitivity in gastric cancer. Gut. 2013;62:22-33 pubmed publisher
    ..Targeting BMP4 may sensitise GC cells to cisplatin. Oxaliplatin, a clinically acceptable cisplatin alternative, may represent a potential therapeutic option for BMP4-positive GCs. ..
  78. Wang X, Emelyanov A, Korzh V, Gong Z. Zebrafish atonal homologue zath3 is expressed during neurogenesis in embryonic development. Dev Dyn. 2003;227:587-92 pubmed
    ..In addition, these mutants also affect expression of zath3 in the neuroretina. ..
  79. Wang H, Tan J, Emelyanov A, Korzh V, Gong Z. Hepatic and extrahepatic expression of vitellogenin genes in the zebrafish, Danio rerio. Gene. 2005;356:91-100 pubmed
    ..In situ hybridization experiments confirmed that the extrahepatic expression was actually in adipocytes associated with several organs such as the intestine, ovary, and E2-induced testis. ..
  80. Soh D, Dong D, Guo Y, Wong L. Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics. 2010;11:449 pubmed publisher
    ..We accumulated sufficient data to create such an aggregated resource with the convenience of an API to access its information. This unified resource can be accessed at http://www.pathwayapi.com. ..
  81. Conforti Andreoni C, Beretta O, Licandro G, Qian H, Urbano M, Vitulli F, et al. Synergism of NOD2 and NLRP3 activators promotes a unique transcriptional profile in murine dendritic cells. J Leukoc Biol. 2010;88:1207-16 pubmed publisher
    ..As a whole, the results indicate that two different NLR activators synergize at the transcriptional level, leading to unique differential expression of genes involved in the innate immune response. ..
  82. Ho Y, Xu W, Too H. Direct quantification of mRNA and miRNA from cell lysates using reverse transcription real time PCR: a multidimensional analysis of the performance of reagents and workflows. PLoS ONE. 2013;8:e72463 pubmed publisher
  83. Fan Q, Verhoeven V, Wojciechowski R, Barathi V, Hysi P, Guggenheim J, et al. Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error. Nat Commun. 2016;7:11008 pubmed publisher
    ..5 × 10(-5)), whereas the interactions are less evident in Europeans. The discovery of these loci represents an important advance in understanding how gene and environment interactions contribute to the heterogeneity of myopia. ..
  84. Wang J, Xu Monette Z, Jabbar K, Shen Q, Manyam G, Tzankov A, et al. AKT Hyperactivation and the Potential of AKT-Targeted Therapy in Diffuse Large B-Cell Lymphoma. Am J Pathol. 2017;187:1700-1716 pubmed publisher
    ..This study demonstrates the clinical and therapeutic implications of AKT hyperactivation in DLBCL and suggests that AKT inhibitors need to be combined with other targeted agents for DLBCL to achieve optimal clinical efficacy. ..
  85. Babu D, Fullwood M. Expanding the effects of ERG on chromatin landscapes and dysregulated transcription in prostate cancer. Nat Genet. 2017;49:1294-1295 pubmed publisher
    ..The overexpression of ERG is further assisted by the development of a super-enhancer in the ERG locus. ..
  86. Tong G, Heng B, Tan L, Ng S. Aberrant profile of gene expression in cloned mouse embryos derived from donor cumulus nuclei. Cell Tissue Res. 2006;325:231-43 pubmed
    ..To improve the efficiency of somatic cell nuclear transfer, strategies to rectify aberrant gene expression in cloned embryos should be investigated. ..
  87. Han N, Wen J, Lin Q, Tan P, Liou Y, Sheu F. Proteomics analysis of the expression of neurogranin in murine neuroblastoma (Neuro-2a) cells reveals its involvement for cell differentiation. Int J Biol Sci. 2007;3:263-73 pubmed
    ..Ng may be involved in neuronal growth and differentiation via PKC and ERK1/2 signaling pathways. ..
  88. Zhang D, Lim S, Koay E. Proteomic identification of down-regulation of oncoprotein DJ-1 and proteasome activator subunit 1 in hepatitis B virus-infected well-differentiated hepatocellular carcinoma. Int J Oncol. 2007;31:577-84 pubmed
    ..These findings elucidate, at least in part, the molecular events underlying the mechanism and the potential roles of DJ-1 and PA28alpha in the onset of hepatocarcinogenesis. ..
  89. Tam W, Lim C, Han J, Zhang J, Ang Y, Ng H, et al. T-cell factor 3 regulates embryonic stem cell pluripotency and self-renewal by the transcriptional control of multiple lineage pathways. Stem Cells. 2008;26:2019-31 pubmed publisher
    ..These data demonstrate an important role for Tcf3 in modulating the appropriate level of gene transcription in ESCs and during embryonic development. Disclosure of potential conflicts of interest is found at the end of this article. ..
  90. Ramamoorthy R, Jiang S, Ramachandran S. Oryza sativa cytochrome P450 family member OsCYP96B4 reduces plant height in a transcript dosage dependent manner. PLoS ONE. 2011;6:e28069 pubmed publisher
    ..The oscyp96b4 mutant is a novel rice semi-dwarf mutant. Our data suggest that OsCYP96B4 might be involved in lipid metabolism and regulate cell elongation. ..
  91. Hou Q, Tan H, Lim K, Lim T, Khoo A, Tan I, et al. Identification and functional validation of caldesmon as a potential gastric cancer metastasis-associated protein. J Proteome Res. 2013;12:980-90 pubmed publisher
    ..This study has thus established the potential role of caldesmon in gastric cancer metastasis, and further functional studies are underway to delineate the underlying mechanism of action of this protein. ..
  92. Nguyen T, Nguyen T, Vu T, Farrar J, Hoang T, Dong T, et al. Corticosteroids for dengue - why don't they work?. PLoS Negl Trop Dis. 2013;7:e2592 pubmed publisher
    ..Dysregulated immune responses may contribute to the clinical complications that occur in some patients with dengue...