Experts and Doctors on gene expression profiling in Brisbane, Queensland, Australia

Summary

Locale: Brisbane, Queensland, Australia
Topic: gene expression profiling

Top Publications

  1. Burger M, Tebay M, Keith P, Samaratunga H, Clements J, Lavin M, et al. Expression analysis of delta-catenin and prostate-specific membrane antigen: their potential as diagnostic markers for prostate cancer. Int J Cancer. 2002;100:228-37 pubmed
    ..Thus we have identified delta-catenin (not previously associated with prostatic adenocarcinoma) and confirmed the potential of PSMA as potential candidates for the diagnosis and management of prostate cancer. ..
  2. McManus D, Le T, Blair D. Genomics of parasitic flatworms. Int J Parasitol. 2004;34:153-8 pubmed
    ..We highlight the remarkable recent progress in gene discovery for schistosomes and the goal of sequencing complete schistosome genomes. ..
  3. Marcellin E, Mercer T, Licona Cassani C, Palfreyman R, Dinger M, Steen J, et al. Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics. 2013;14:15 pubmed publisher
    ..Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes...
  4. Kemp J, Morris J, Medina Gomez C, Forgetta V, Warrington N, Youlten S, et al. Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis. Nat Genet. 2017;49:1468-1475 pubmed publisher
    ..The results implicate GPC6 as a novel determinant of BMD, and also identify abnormal skeletal phenotypes in knockout mice associated with a further 100 prioritized genes. ..
  5. Gobert G, Jones M. Discovering new schistosome drug targets: the role of transcriptomics. Curr Drug Targets. 2008;9:922-30 pubmed
    ..It is hoped that with these approaches the future investigation of complex biological and physiological questions such as drug mode of action or drug resistance in parasitology may be addressed. ..
  6. Srikhanta Y, Dowideit S, Edwards J, Falsetta M, Wu H, Harrison O, et al. Phasevarions mediate random switching of gene expression in pathogenic Neisseria. PLoS Pathog. 2009;5:e1000400 pubmed publisher
    ..This study, in conjunction with our previous work in H. influenzae, indicates that phasevarions may be a common strategy used by host-adapted bacterial pathogens to randomly switch between "differentiated" cell types. ..
  7. Ewen K, Baker M, Wilhelm D, Aitken R, Koopman P. Global survey of protein expression during gonadal sex determination in mice. Mol Cell Proteomics. 2009;8:2624-41 pubmed publisher
  8. Merritt M, Parsons P, Newton T, Martyn A, Webb P, Green A, et al. Expression profiling identifies genes involved in neoplastic transformation of serous ovarian cancer. BMC Cancer. 2009;9:378 pubmed publisher
    ..Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. These results highlight several genes that may play an important role across the spectrum of serous ovarian tumorigenesis. ..
  9. Reverter A, Hudson N, Nagaraj S, Perez Enciso M, Dalrymple B. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics. 2010;26:896-904 pubmed publisher
    ..We argue that RIF has universal applicability, and advocate its use as a promising hypotheses generating tool for the systematic identification of novel TF not yet documented as critical. ..

More Information

Publications113 found, 100 shown here

  1. Le S, Gongora M, Zhang B, Grimmond S, Campbell G, Campbell J, et al. Gene expression profile of the fibrotic response in the peritoneal cavity. Differentiation. 2010;79:232-43 pubmed publisher
  2. Mercer T, Wilhelm D, Dinger M, Soldà G, Korbie D, Glazov E, et al. Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res. 2011;39:2393-403 pubmed publisher
    ..Our findings suggest novel functions for 3'UTRs, as well as caution in the use of 3'UTR sequence probes to analyze gene expression. ..
  3. Buske F, Bauer D, Mattick J, Bailey T. Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res. 2012;22:1372-81 pubmed publisher
    ..With focus on biotechnological applications, we screen mammalian genomes for high-affinity triplex target sites that can be used to target genomic loci specifically and find that triplex formation offers a resolution of ~1300 nt. ..
  4. An J, Lai J, Lehman M, Nelson C. miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res. 2013;41:727-37 pubmed publisher
    ..Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star. ..
  5. You H, McManus D, Hu W, Smout M, Brindley P, Gobert G. Transcriptional responses of in vivo praziquantel exposure in schistosomes identifies a functional role for calcium signalling pathway member CamKII. PLoS Pathog. 2013;9:e1003254 pubmed publisher
    ..Together, these studies comprehensively charted transcriptional changes upon exposure to praziquantel and, notably, identified CamKII as potentially central to the, as yet undefined, mode of action of praziquantel. ..
  6. Carvalhais L, Schenk P. Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities. Methods Enzymol. 2013;531:251-67 pubmed publisher
    ..Here, we describe issues and important considerations of soil sample processing and cDNA preparation for metatranscriptomics from bacteria and archaea and provide a set of methods that can be used in the required experimental steps. ..
  7. Rae F, Hooper J, Nicol D, Clements J. Characterization of a novel gene, STAG1/PMEPA1, upregulated in renal cell carcinoma and other solid tumors. Mol Carcinog. 2001;32:44-53 pubmed
    ..The upregulation of this gene in several solid tumors indicated that it may play an important role in tumorigenesis. ..
  8. Wells C, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, et al. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Res. 2003;13:1360-5 pubmed
  9. Rae F, Martinez G, Gillinder K, Smith A, Shooter G, Forrest A, et al. Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1. Oncogene. 2004;23:3067-79 pubmed
    ..Therefore, the tumour suppressor activities of WT1 may be achieved by repressing the mevalonate pathway, thereby controlling cellular proliferation and promoting terminal differentiation. ..
  10. Trabi M, Craik D. Tissue-specific expression of head-to-tail cyclized miniproteins in Violaceae and structure determination of the root cyclotide Viola hederacea root cyclotide1. Plant Cell. 2004;16:2204-16 pubmed
    ..We propose that cyclotides constitute a new family of plant defense peptides, which might constitute an even larger and, in their biological function, more diverse family than the well-known plant defensins...
  11. He Y, Rothnagel J, Epis M, Leedman P, Smith R. Downstream targets of heterogeneous nuclear ribonucleoprotein A2 mediate cell proliferation. Mol Carcinog. 2009;48:167-79 pubmed publisher
    ..These results reinforce the conclusion that hnRNP A2/B1 is associated with cellular processes that affect the cell cycle and proliferation. ..
  12. Robinson K, Meers J, Gravel J, McCarthy F, Mahony T. The essential and non-essential genes of Bovine herpesvirus 1. J Gen Virol. 2008;89:2851-63 pubmed publisher
    ..However, ORFs encoding glycoprotein K (UL53), regulatory, membrane, tegument and capsid proteins (UL54, UL49.5, UL49, UL35, UL20, UL16 and UL7) were shown to differ in requirement when compared to HHV-1-encoded homologues...
  13. Melino M, Gadd V, Walker G, Skoien R, Barrie H, Jothimani D, et al. Macrophage secretory products induce an inflammatory phenotype in hepatocytes. World J Gastroenterol. 2012;18:1732-44 pubmed publisher
    ..Secreted macrophage products alter the phenotype and function of hepatocytes, with increased expression of inflammatory mediators, suggesting that hepatocytes actively participate in liver injury. ..
  14. Johnson J, Waddell N, Chenevix Trench G. The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes. BMC Cancer. 2012;12:246 pubmed publisher
    ..The application of the GINI method to LCLs to identify transcripts harbouring germline truncating mutations is challenging due to a number of factors related to cell type, microarray sensitivity and variations in NMD efficiency. ..
  15. Tallack M, Magor G, Dartigues B, Sun L, Huang S, Fittock J, et al. Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq. Genome Res. 2012;22:2385-98 pubmed publisher
    ..Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation, and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation. ..
  16. Kumar D, Yadav A, Jia X, Mulvenna J, Dash D. Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation. Mol Cell Proteomics. 2016;15:329-39 pubmed publisher
    ..Our integrative multi-omics data analysis not only enables the discovery of new proteoforms but also generates an improved reference for human disease studies in the rat model. ..
  17. Acuna Hidalgo R, Deriziotis P, Steehouwer M, Gilissen C, Graham S, van Dam S, et al. Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. PLoS Genet. 2017;13:e1006683 pubmed publisher
    ..Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype. ..
  18. Georgas K, Bowles J, Yamada T, Koopman P, Little M. Characterisation of Crim1 expression in the developing mouse urogenital tract reveals a sexually dimorphic gonadal expression pattern. Dev Dyn. 2000;219:582-7 pubmed
    ..Crim1 also displays a striking male-specific expression pattern in the fetal gonads, its expression strongest in the Sertoli cells of the developing testis. ..
  19. Chai M, McManus D, McInnes R, Moertel L, Tran M, Loukas A, et al. Transcriptome profiling of lung schistosomula,in vitro cultured schistosomula and adult Schistosoma japonicum. Cell Mol Life Sci. 2006;63:919-29 pubmed
    ..Thus caution is urged when using in vitro-cultured schistosomes and mechanically transformed/cultured schistosomula in molecular, biochemical and immunological studies. ..
  20. Waddell N, Ten Haaf A, Marsh A, Johnson J, Walker L, Gongora M, et al. BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression. PLoS Genet. 2008;4:e1000080 pubmed publisher
    ..This study indicates that mutation effect, and presence of rare variants possibly associated with a low risk of cancer, must be considered in the development of array-based assays of variant pathogenicity. ..
  21. Gibson G. The environmental contribution to gene expression profiles. Nat Rev Genet. 2008;9:575-81 pubmed publisher
    ..Incorporating estimates of genetic relationships into study designs will facilitate genomic analysis of environmental plasticity by aiding the identification of major regulatory loci in natural populations. ..
  22. Allsopp L, Beloin C, Ulett G, Valle J, Totsika M, Sherlock O, et al. Molecular characterization of UpaB and UpaC, two new autotransporter proteins of uropathogenic Escherichia coli CFT073. Infect Immun. 2012;80:321-32 pubmed publisher
    ..This attenuated phenotype was also observed in single-challenge experiments, where deletion of the upaB gene in CFT073 significantly reduced early colonization of the bladder. ..
  23. Burel J, Apte S, Doolan D. Systems Approaches towards Molecular Profiling of Human Immunity. Trends Immunol. 2016;37:53-67 pubmed publisher
    ..Recognizing that the field is still in its infancy, we also discuss current limitations of systems immunology, as well as the need for validation of key findings for the discipline to fulfill its promise. ..
  24. Minelli C, Dean C, Hind M, Alves A, Amaral A, Siroux V, et al. Association of Forced Vital Capacity with the Developmental Gene NCOR2. PLoS ONE. 2016;11:e0147388 pubmed publisher
    ..Our findings also support SERPINE2, a COPD gene with weak previous evidence of association with FVC, and suggest WNT16 as a further promising candidate. ..
  25. Polkinghorne A, Hogan R, Vaughan L, Summersgill J, Timms P. Differential expression of chlamydial signal transduction genes in normal and interferon gamma-induced persistent Chlamydophila pneumoniae infections. Microbes Infect. 2006;8:61-72 pubmed
    ..pneumoniae persistence, likely as part of the IFN-gamma response stimulon as described for C. trachomatis, but with considerable differences in the transcriptional profile. ..
  26. Gobert G, McInnes R, Moertel L, Nelson C, Jones M, Hu W, et al. Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling. Exp Parasitol. 2006;114:160-72 pubmed
    ..This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome. ..
  27. Swagell C, Henly D, Morris C. Regulation of human hepatocyte gene expression by fatty acids. Biochem Biophys Res Commun. 2007;362:374-80 pubmed
    ..5h) transcriptional regulation by palmitate, oleate, and eicosapentaenoic acid (EPA) identified that oleate and EPA initiated similar changes in the pattern of hepatic gene regulation, whereas palmitate had little effect. ..
  28. Dinger M, Amaral P, Mercer T, Mattick J. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic. 2009;8:407-23 pubmed publisher
  29. Caragata E, Poinsignon A, Moreira L, Johnson P, Leong Y, Ritchie S, et al. Improved accuracy of the transcriptional profiling method of age grading in Aedes aegypti mosquitoes under laboratory and semi-field cage conditions and in the presence of Wolbachia infection. Insect Mol Biol. 2011;20:215-24 pubmed publisher
    ..Our findings suggest that the new model is a robust and powerful tool for age determination in Australian Ae. aegypti populations. ..
  30. Cummings M, Simpson P, Reid L, Jayanthan J, Skerman J, Song S, et al. Metastatic progression of breast cancer: insights from 50 years of autopsies. J Pathol. 2014;232:23-31 pubmed publisher
  31. Truong G, Guanzon D, Kinhal V, Elfeky O, Lai A, Longo S, et al. Oxygen tension regulates the miRNA profile and bioactivity of exosomes released from extravillous trophoblast cells - Liquid biopsies for monitoring complications of pregnancy. PLoS ONE. 2017;12:e0174514 pubmed publisher
  32. de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol. 2017;35:872-878 pubmed publisher
    ..We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions. ..
  33. Williams S, Gotley D, Antalis T. Human trypsinogen in colorectal cancer. Int J Cancer. 2001;93:67-73 pubmed
    ..6%) as well as in primary tumor tissues (65% vs. 15%). These data demonstrate that TRY2 is the dominant TRY in colon tissue and suggest that up-regulation of TRY1 expression in colon tumors may be associated with a metastatic phenotype. ..
  34. Da Silva L, Parry S, Reid L, Keith P, Waddell N, Kossai M, et al. Aberrant expression of E-cadherin in lobular carcinomas of the breast. Am J Surg Pathol. 2008;32:773-83 pubmed publisher
    ..Misclassification of tumors may lead to mismanagement of patients in clinical practice, particularly in the context of in situ disease at margins. ..
  35. Ju X, Zenke M, Hart D, Clark G. CD300a/c regulate type I interferon and TNF-alpha secretion by human plasmacytoid dendritic cells stimulated with TLR7 and TLR9 ligands. Blood. 2008;112:1184-94 pubmed publisher
    ..These data indicate that CD300a and CD300c play an important role in the cross-regulation of TNF-alpha and IFN-alpha secretion from pDCs. ..
  36. Watts R, Hancock V, Ong C, Vejborg R, Mabbett A, Totsika M, et al. Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties. J Clin Microbiol. 2010;48:2449-58 pubmed publisher
    ..coli strain, 83972. This is the first global gene expression analysis of E. coli CA-ABU strains. Overall, our data suggest that nosocomial ABU and CA-ABU E. coli isolates possess similar virulence profiles...
  37. Gobert G. Applications for profiling the schistosome transcriptome. Trends Parasitol. 2010;26:434-9 pubmed publisher
    ..Finally, the relevance of transcriptomics for exploring and contrasting different parasite populations or species is discussed. ..
  38. Doolan D. Plasmodium immunomics. Int J Parasitol. 2011;41:3-20 pubmed publisher
    ..Herein, current progress and perspectives regarding Plasmodium immunomics are reviewed. ..
  39. Schroder W, Gardner J, Le T, Duke M, Burke M, Jones M, et al. SerpinB2 deficiency modulates Th1?Th2 responses after schistosome infection. Parasite Immunol. 2010;32:764-8 pubmed
    ..SerpinB2-/- mice immunized with soluble egg antigen (SEA) also showed reduced levels of SEA-specific IgG1. SerpinB2 deficiency thus promoted certain Th1 and reduced certain Th2 responses in response to this Th2 immunogen. ..
  40. Rolland A, Lehmann K, Johnson K, Gaido K, Koopman P. Uncovering gene regulatory networks during mouse fetal germ cell development. Biol Reprod. 2011;84:790-800 pubmed publisher
  41. Hemani G, Shakhbazov K, Westra H, Esko T, Henders A, McRae A, et al. Detection and replication of epistasis influencing transcription in humans. Nature. 2014;508:249-53 pubmed publisher
    ..This study presents the first evidence, to our knowledge, for many instances of segregating common polymorphisms interacting to influence human traits. ..
  42. Sternberg I, Vela I, Scardino P. Molecular Profiles of Prostate Cancer: To Treat or Not to Treat. Annu Rev Med. 2016;67:119-35 pubmed publisher
  43. Constantinoiu C, Molloy J, Jorgensen W, Coleman G. Antibody response against endogenous stages of an attenuated strain of Eimeria tenella. Vet Parasitol. 2008;154:193-204 pubmed publisher
    ..The time-courses of the antibody response to sporozoite and merozoite antigens were similar but varied depending on the inoculation regime and the degree of oocyst recirculation...
  44. Ranjit N, Zhan B, Stenzel D, Mulvenna J, Fujiwara R, Hotez P, et al. A family of cathepsin B cysteine proteases expressed in the gut of the human hookworm, Necator americanus. Mol Biochem Parasitol. 2008;160:90-9 pubmed publisher
    ..These data show that N. americanus expresses a family of intestinal CatBs, many of which are likely to be involved in nutrient acquisition and therefore are potential targets for chemotherapies and vaccines...
  45. Waddell N, Cocciardi S, Johnson J, Healey S, Marsh A, Riley J, et al. Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay. J Pathol. 2010;221:452-61 pubmed publisher
  46. Ewen K, Jackson A, Wilhelm D, Koopman P. A male-specific role for p38 mitogen-activated protein kinase in germ cell sex differentiation in mice. Biol Reprod. 2010;83:1005-14 pubmed publisher
    ..These data suggest that p38 MAPK signaling antagonizes entry into meiosis in XY germ cells, instead directing them toward mitotic quiescence and a spermatogenic fate. ..
  47. Hayward A, Vighnesh G, Delay C, Samian M, Manoli S, Stiller J, et al. Second-generation sequencing for gene discovery in the Brassicaceae. Plant Biotechnol J. 2012;10:750-9 pubmed publisher
    ..We hypothesize that Brassica NSP genes may function in the root in other plant-microbe interaction pathways that were recruited for mycorrhizal and rhizobial symbioses during evolution...
  48. Francis S, Larsen J, Pavey S, Bowman R, Hayward N, Fong K, et al. Expression profiling identifies genes involved in emphysema severity. Respir Res. 2009;10:81 pubmed publisher
    ..Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3. ..
  49. Hudson N, Reverter A, Wang Y, Greenwood P, Dalrymple B. Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PLoS ONE. 2009;4:e7249 pubmed publisher
    ..Together with a simple examination of a co-expression module's contents, these three gene expression approaches are starting to illuminate the in vivo transcriptional regulation of skeletal muscle development. ..
  50. Perry C, Burke M, Stenzel D, McManus D, Ramm G, Gobert G. Differential expression of chemokine and matrix re-modelling genes is associated with contrasting schistosome-induced hepatopathology in murine models. PLoS Negl Trop Dis. 2011;5:e1178 pubmed publisher
    ..This improved understanding of the immunopathogenesis in the murine model schistosomiasis provides the basis for a better appreciation of the complexities associated with chronic human schistosomiasis...
  51. Bonazzi V, Stark M, Hayward N. MicroRNA regulation of melanoma progression. Melanoma Res. 2012;22:101-13 pubmed publisher
    ..On the basis of the current literature, we present a network of miRNA interactions involved in melanoma progression. Some of these key miRNAs may have utility as diagnostic markers or in targeted treatments...
  52. Bromham L, Clark F, McKee J. Discovery of a novel murine type C retrovirus by data mining. J Virol. 2001;75:3053-7 pubmed
    ..This virus is present in multiple copies in the mouse genome and expressed in a range of mouse tissues...
  53. Liew A, Xian J, Wu S, Smith D, Yan H. Spectral estimation in unevenly sampled space of periodically expressed microarray time series data. BMC Bioinformatics. 2007;8:137 pubmed
    ..The method can also be used as an effective tool for gene expression time series interpolation or resampling. ..
  54. Feigl B, Cao D, Morris C, Zele A. Persons with age-related maculopathy risk genotypes and clinically normal eyes have reduced mesopic vision. Invest Ophthalmol Vis Sci. 2011;52:1145-50 pubmed publisher
  55. Vitale A, Matigian N, Ravishankar S, Bellette B, Wood S, Wolvetang E, et al. Variability in the generation of induced pluripotent stem cells: importance for disease modeling. Stem Cells Transl Med. 2012;1:641-50 pubmed publisher
  56. Brennan T, Krömer J, Nielsen L. Physiological and transcriptional responses of Saccharomyces cerevisiae to d-limonene show changes to the cell wall but not to the plasma membrane. Appl Environ Microbiol. 2013;79:3590-600 pubmed publisher
    ..We show that limonene can alter the structure and function of the cell wall, which has a clear effect on cytokinesis...
  57. Topkas E, Cai N, Cumming A, Hazar Rethinam M, Gannon O, Burgess M, et al. Auranofin is a potent suppressor of osteosarcoma metastasis. Oncotarget. 2016;7:831-44 pubmed publisher
    ..Thus, TXNRD2 may represent a novel druggable target that could be deployed to reduce the development of fatal pulmonary metastases in patients with OS. ..
  58. Schepers G, Bullejos M, Hosking B, Koopman P. Cloning and characterisation of the Sry-related transcription factor gene Sox8. Nucleic Acids Res. 2000;28:1473-80 pubmed
    ..Sox8 maps to the t complex on mouse chromosome 17 and to human chromosome 16p13.3, a region associated with the microphthalmia-cataract syndrome CATM and the alpha-thalassemia/mental retardation syndrome ATR-16. ..
  59. Arnold J, Huggard P, Cummings M, Ramm G, Chenevix Trench G. Reduced expression of chemokine (C-C motif) ligand-2 (CCL2) in ovarian adenocarcinoma. Br J Cancer. 2005;92:2024-31 pubmed
    ..These data support the hypothesis that CCL2 may play a role in the pathobiology of ovarian cancers, but additional studies will be required to evaluate this possibility. ..
  60. Simpson P, Reis Filho J, Lambros M, Jones C, Steele D, Mackay A, et al. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas. J Pathol. 2008;215:231-44 pubmed publisher
  61. Walker L, Thompson B, Waddell N, Grimmond S, Spurdle A. Use of DNA-damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients. PLoS Genet. 2010;6:e1000850 pubmed publisher
  62. Wang S, Myers S, Eriksson N, Fitzsimmons R, Muscat G. Nr4a1 siRNA expression attenuates ?-MSH regulated gene expression in 3T3-L1 adipocytes. Mol Endocrinol. 2011;25:291-306 pubmed publisher
    ..We conclude that Nur77 expression is necessary for MSH-mediated induction of gene expression in differentiated adipocytes. Furthermore, this study demonstrates cross talk between MSH and Nr4a signaling in adipocytes. ..
  63. Houghton C, Fassett R, Coombes J. Sulforaphane and Other Nutrigenomic Nrf2 Activators: Can the Clinician's Expectation Be Matched by the Reality?. Oxid Med Cell Longev. 2016;2016:7857186 pubmed publisher
    ..Both its high bioavailability and significant Nrf2 inducer capacity contribute to the therapeutic potential of sulforaphane-yielding supplements. ..
  64. Faulkner G, Forrest A, Chalk A, Schroder K, Hayashizaki Y, Carninci P, et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics. 2008;91:281-8 pubmed publisher
    ..These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone. ..
  65. Trusov Y, Zhang W, Assmann S, Botella J. Ggamma1 + Ggamma2 not equal to Gbeta: heterotrimeric G protein Ggamma-deficient mutants do not recapitulate all phenotypes of Gbeta-deficient mutants. Plant Physiol. 2008;147:636-49 pubmed publisher
  66. Beverdam A, Svingen T, Bagheri Fam S, Bernard P, McClive P, Robson M, et al. Sox9-dependent expression of Gstm6 in Sertoli cells during testis development in mice. Reproduction. 2009;137:481-6 pubmed publisher
    ..Our data suggest that Gstm6 plays a male-specific role in gonad development or function, possibly by modulating the exposure of somatic tissue and/or germ cells to endogenous or exogenous toxicants. ..
  67. Cristino A, Nunes F, Barchuk A, Aguiar Coelho V, Simões Z, Bitondi M. Organization, evolution and transcriptional profile of hexamerin genes of the parasitic wasp Nasonia vitripennis (Hymenoptera: Pteromalidae). Insect Mol Biol. 2010;19 Suppl 1:137-46 pubmed publisher
    ..Temporal and spatial transcriptional profiles of N. vitripennis hexamerins suggest that they have physiological functions other than metamorphosis, which are arguably coupled with its lifestyle. ..
  68. Petsch K, Mylne J, Botella J. Cosuppression of eukaryotic release factor 1-1 in Arabidopsis affects cell elongation and radial cell division. Plant Physiol. 2005;139:115-26 pubmed
    ..This is the first attempt at functional characterization of a release factor in vivo in plants and demonstrates the importance of eRF1-1 function in Arabidopsis. ..
  69. Roberts D, Newton R, Beaumont K, Helen Leonard J, Sturm R. Quantitative analysis of MC1R gene expression in human skin cell cultures. Pigment Cell Res. 2006;19:76-89 pubmed
  70. Choi J, Xu M, Makowski M, Zhang T, Law M, Kovacs M, et al. A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF. Nat Genet. 2017;49:1326-1335 pubmed publisher
    ..PARP1-mediated senescence rescue was accompanied by transcriptional activation of the melanocyte-lineage survival oncogene MITF, highlighting a new role for PARP1 in melanomagenesis. ..
  71. Rae F, Hooper J, Eyre H, Sutherland G, Nicol D, Clements J. TTYH2, a human homologue of the Drosophila melanogaster gene tweety, is located on 17q24 and upregulated in renal cell carcinoma. Genomics. 2001;77:200-7 pubmed
    ..In addition to a putative role in brain and testis, the over-expression of TTYH2 in renal cell carcinoma suggests that it may have an important role in kidney tumorigenesis. ..
  72. Coussens A, Wilkinson C, Hughes I, Morris C, van Daal A, Anderson P, et al. Unravelling the molecular control of calvarial suture fusion in children with craniosynostosis. BMC Genomics. 2007;8:458 pubmed
    ..Expression differences were also analysed between each unfused suture type, between sutures from syndromic and non-syndromic craniosynostosis patients, and between unfused sutures from individuals with and without craniosynostosis...
  73. Mellick G, Silburn P, Sutherland G, Siebert G. Exploiting the potential of molecular profiling in Parkinson's disease: current practice and future probabilities. Expert Rev Mol Diagn. 2010;10:1035-50 pubmed publisher
  74. Edwards D, Batley J, Snowdon R. Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet. 2013;126:1-11 pubmed publisher
  75. Spadaro P, Flavell C, Widagdo J, Ratnu V, Troup M, Ragan C, et al. Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice. Biol Psychiatry. 2015;78:848-59 pubmed publisher
    ..Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders. ..
  76. Himes S, Tagoh H, Goonetilleke N, Sasmono T, Oceandy D, Clark R, et al. A highly conserved c-fms gene intronic element controls macrophage-specific and regulated expression. J Leukoc Biol. 2001;70:812-20 pubmed
    ..Removal of FIRE abolished reporter gene expression, revealing a suppressive activity in the remaining intronic sequences. Hence, FIRE is shown to be a key regulatory element in the fms gene. ..
  77. Dowhan D, Harrison M, Eriksson N, Bailey P, Pearen M, Fuller P, et al. Protein arginine methyltransferase 6-dependent gene expression and splicing: association with breast cancer outcomes. Endocr Relat Cancer. 2012;19:509-26 pubmed publisher
    ..These results suggest that dysregulation of PRMT6-dependent transcription and alternative splicing may be involved in breast cancer pathophysiology and the molecular consequences identifying a unique and informative biomarker profile. ..
  78. Gobert G, Moertel L, Brindley P, McManus D. Developmental gene expression profiles of the human pathogen Schistosoma japonicum. BMC Genomics. 2009;10:128 pubmed publisher
    ..Advanced analyses including ANOVA, principal component analysis, and hierarchal clustering provided a global synopsis of gene expression relationships among the different developmental stages of the schistosome parasite...
  79. Davidson M, Larsen J, Yang I, Hayward N, Clarke B, Duhig E, et al. MicroRNA-218 is deleted and downregulated in lung squamous cell carcinoma. PLoS ONE. 2010;5:e12560 pubmed publisher
  80. Schroder K, Irvine K, Taylor M, Bokil N, Lê Cao K, Masterman K, et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A. 2012;109:E944-53 pubmed publisher
    ..Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change. ..
  81. Cummins S, Erpenbeck D, Zou Z, Claudianos C, Moroz L, Nagle G, et al. Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia. BMC Biol. 2009;7:28 pubmed publisher
  82. Zhang W, Li J, Jones M, Zhang Z, Zhao L, Blair D, et al. The Echinococcus granulosus antigen B gene family comprises at least 10 unique genes in five subclasses which are differentially expressed. PLoS Negl Trop Dis. 2010;4:e784 pubmed publisher
    ..It is generally accepted that EgAgB is comprised of a gene family of five subfamilies which are highly polymorphic, but the actual number of genes present is unknown...
  83. King T, Lucchini S, Hinton J, Gobius K. Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses. Appl Environ Microbiol. 2010;76:6514-28 pubmed publisher
    ..While E. coli K-12 was most resistant to lactic and hydrochloric acid, O157:H7 may have a greater ability to survive in more complex acidic environments, such as those encountered in the host and during food processing...
  84. Villani R, Adolphe C, Palmer J, Waters M, Wainwright B. Patched1 inhibits epidermal progenitor cell expansion and basal cell carcinoma formation by limiting Igfbp2 activity. Cancer Prev Res (Phila). 2010;3:1222-34 pubmed publisher
    ..We propose that Igfbp2 mediates epidermal progenitor cell expansion and therefore represents an epidermal progenitor cell-specific target of Hh signaling that promotes BCC development. ..
  85. Zhao L, Glazov E, Pattabiraman D, Al Owaidi F, Zhang P, Brown M, et al. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res. 2011;39:4664-79 pubmed publisher
  86. Gardner L, Mills D, Wiegand A, Leavesley D, Elizur A. Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima. BMC Genomics. 2011;12:455 pubmed publisher
    ..The development of PmaxArray 1.0, and the spatial map of its ESTs expression in the mantle has begun characterizing the molecular mechanisms linking the organics and inorganics of the molluscan shell. ..
  87. Gascoigne D, Cheetham S, Cattenoz P, Clark M, Amaral P, Taft R, et al. Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics. 2012;28:3042-50 pubmed publisher
    ..Pinstripe is written in C# and runs under the Mono framework on Linux or Mac OS X, and both under Mono and .Net under Windows. m.dinger@garvan.org.au or j.mattick@garvan.org.au Supplementary data are available at Bioinformatics online. ..
  88. Voisey J, Kelly G, van Daal A. Agouti signal protein regulation in human melanoma cells. Pigment Cell Res. 2003;16:65-71 pubmed
    ..Results identify five genes, namely PPARbeta, eIF-4B, RRM2, MINOR and EVI2B that are down-regulated by ASIP, indicating a likely role for ASIP in human melanogenesis. ..
  89. Smith J, Rangaraj K, Simpson R, Maclean D, Nathanson L, Stuart K, et al. Quantitative analysis of the expression of ACAT genes in human tissues by real-time PCR. J Lipid Res. 2004;45:686-96 pubmed
    ..These results demonstrate quantitatively that ACAT-1 transcripts predominate in human liver and ACAT-2 transcripts predominate in human duodenum and support the notion that ACAT-2 has an important regulatory role in liver and intestine. ..
  90. Himes S, Sester D, Ravasi T, Cronau S, Sasmono T, Hume D. The JNK are important for development and survival of macrophages. J Immunol. 2006;176:2219-28 pubmed
    ..This pattern of expression may underlie the novel role of JNK in macrophages. ..
  91. Walker L, Waddell N, Ten Haaf A, Grimmond S, Spurdle A. Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers. Breast Cancer Res Treat. 2008;112:229-36 pubmed
    ..Similar approaches may be used to identify genes and underlying genetic risk factors that interact with exogenous stimulants to cause or modify any disease, without a priori knowledge of the pathways involved. ..
  92. Stephens A, Gardiner D, White R, Munn A, Manners J. Phases of infection and gene expression of Fusarium graminearum during crown rot disease of wheat. Mol Plant Microbe Interact. 2008;21:1571-81 pubmed publisher
    ..These results indicate that CR disease development involves distinct phases of colonization, each of which is associated with a different fungal gene expression program. ..