Experts and Doctors on gene expression profiling in Sweden


Locale: Sweden
Topic: gene expression profiling

Top Publications

  1. von Gertten C, Flores Morales A, Holmin S, Mathiesen T, Nordqvist A. Genomic responses in rat cerebral cortex after traumatic brain injury. BMC Neurosci. 2005;6:69 pubmed
    ..Since trauma is a risk factor for development of neurodegenerative disease, this knowledge may also reduce late negative effects. ..
  2. Ryden P, Andersson H, Landfors M, Näslund L, Hartmanová B, Noppa L, et al. Evaluation of microarray data normalization procedures using spike-in experiments. BMC Bioinformatics. 2006;7:300 pubmed
    ..If bias is not a major problem; we recommend the use of either the CM-procedure or partial filtration. ..
  3. Persson H, Flicker S, Sadegh M, Greiff L, Valenta R, Ohlin M. A common idiotype in IgE and its relation to recognition of the grass pollen allergen Phl p 2. Mol Immunol. 2008;45:2715-20 pubmed publisher
    ..Such a restriction may contribute to the limited molecular diversity observed in some IgE populations. ..
  4. Kindlund B, Sjoling A, Hansson M, Edebo A, Hansson L, Sjovall H, et al. FOXP3-expressing CD4(+) T-cell numbers increase in areas of duodenal gastric metaplasia and are associated to CD4(+) T-cell aggregates in the duodenum of Helicobacter pylori-infected duodenal ulcer patients. Helicobacter. 2009;14:192-201 pubmed publisher
    ..The numbers of CD4(+)FOXP3(+) T cells are increased and localized in CD4(+) T-cell aggregates in areas of duodenal gastric metaplasia in duodenal ulcer patients. ..
  5. Banduseela V, Ochala J, Chen Y, Göransson H, Norman H, Radell P, et al. Gene expression and muscle fiber function in a porcine ICU model. Physiol Genomics. 2009;39:141-59 pubmed publisher
    ..To our knowledge, this is the first study that isolates the effect of immobilization and mechanical ventilation in an ICU condition from various other cofactors...
  6. Nishikubo N, Takahashi J, Roos A, Derba Maceluch M, Piens K, Brumer H, et al. Xyloglucan endo-transglycosylase-mediated xyloglucan rearrangements in developing wood of hybrid aspen. Plant Physiol. 2011;155:399-413 pubmed publisher
    ..XET overexpression promoted vessel element growth but not fiber expansion. We suggest that the amount of nascent xyloglucan relative to XET is an important determinant of whether XET strengthens or loosens the cell wall. ..
  7. JORNSTEN R, Abenius T, Kling T, Schmidt L, Johansson E, Nordling T, et al. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol. 2011;7:486 pubmed publisher
    ..We conclude that large-scale network modeling of the effects of CNAs on gene expression may provide insights into the biology of human cancer. Free software in MATLAB and R is provided. ..
  8. Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B. Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure. PLoS ONE. 2017;12:e0181084 pubmed publisher
    ..The results point to a lack of strong and consistent expression alterations in the NAc after alcohol exposure, suggesting that transcriptional effects of alcohol are weak or transient, or occur primarily in brain regions other than NAc. ..
  9. Ståhlberg A, Kubista M, Pfaffl M. Comparison of reverse transcriptases in gene expression analysis. Clin Chem. 2004;50:1678-80 pubmed

More Information

Publications157 found, 100 shown here

  1. Wright D, Johansson T, Le Quéré A, Söderström B, Tunlid A. Spatial patterns of gene expression in the extramatrical mycelium and mycorrhizal root tips formed by the ectomycorrhizal fungus Paxillus involutus in association with birch (Betula pendula) seedlings in soil microcosms. New Phytol. 2005;167:579-96 pubmed
    ..Differential expression of genes among the extramatrical mycelium and mycorrhizal tips indicates functional specialization of tissues forming ECM associations. ..
  2. Gustafsson A, Kupershmidt I, Edlundh Rose E, Greco G, Serafino A, Krasnowska E, et al. Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro. BMC Cancer. 2005;5:75 pubmed
    ..The responses are largely related to inhibition of proliferation and stimulation of differentiation in both cell types but are almost completely lineage specific. ID-1 is indicated as an early mediator of NAC action. ..
  3. Bengtsson A, Bengtsson H. Microarray image analysis: background estimation using quantile and morphological filters. BMC Bioinformatics. 2006;7:96 pubmed
    ..However, in order to get unbiased estimates these filters have to be implemented with great care. The performance of morphological opening is in general poor with a substantial spatial-dependent bias. ..
  4. Ekman M, Tollbäck P, Klint J, Bergman B. Protein expression profiles in an endosymbiotic cyanobacterium revealed by a proteomic approach. Mol Plant Microbe Interact. 2006;19:1251-61 pubmed
    ..This is the first comprehensive analysis of proteins in the symbiotic state. ..
  5. Staaf J, Vallon Christersson J, Lindgren D, Juliusson G, Rosenquist R, Hoglund M, et al. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics. 2008;9:409 pubmed publisher
    ..The proposed normalization strategy represents a valuable tool that improves the quality of data obtained from Illumina Infinium arrays, in particular when used for LOH and copy number variation studies. ..
  6. Boij P, Patel R, Garcia C, Jarvis P, Aronsson H. In vivo studies on the roles of Tic55-related proteins in chloroplast protein import in Arabidopsis thaliana. Mol Plant. 2009;2:1397-409 pubmed publisher
    ..Thus, we conclude that atTic55-II and AtPTC52 are not strictly required for functional protein import in Arabidopsis. ..
  7. Rundlöf A, Carlsten M, Giacobini M, Arner E. Prominent expression of the selenoprotein thioredoxin reductase in the medullary rays of the rat kidney and thioredoxin reductase mRNA variants differing at the 5' untranslated region. Biochem J. 2000;347 Pt 3:661-8 pubmed
    ..It can therefore be concluded that TrxR1 mRNA is expressed in at least three different variants that differ at their 5' UTRs. ..
  8. Yang X, Jansson P, Nagaev I, Jack M, Carvalho E, Sunnerhagen K, et al. Evidence of impaired adipogenesis in insulin resistance. Biochem Biophys Res Commun. 2004;317:1045-51 pubmed
    ..Our findings suggest that insulin resistance is associated with an impaired adipogenesis. ..
  9. Lundgren J, Masson P, Mirzaei Z, Young P. Identification and characterization of a Drosophila proteasome regulatory network. Mol Cell Biol. 2005;25:4662-75 pubmed
    ..Transfer of the 5' UTR from the proteasome subunit Rpn1/S2 to a noninducible promoter was sufficient to confer transcriptional upregulation of the reporter mRNA after proteasome inhibition. ..
  10. Breslin T, Krogh M, Peterson C, Troein C. Signal transduction pathway profiling of individual tumor samples. BMC Bioinformatics. 2005;6:163 pubmed
    ..This study shows that it is feasible to infer signal transduction pathway activity, in individual samples, from gene expression data. Furthermore, these pathway activities are biologically relevant in the three cancer data sets. ..
  11. Nyman U, Sobczak Pluta A, Vlachos P, Perlmann T, Zhivotovsky B, Joseph B. Full-length p73alpha represses drug-induced apoptosis in small cell lung carcinoma cells. J Biol Chem. 2005;280:34159-69 pubmed
    ..In conclusion, the reported overexpression of p73alpha in certain tumor types, and our findings that p73alpha exerts anti-apoptotic functions, indicate a potential oncogenic activity for p73. ..
  12. Hansson S, Chen Y, Brodszki J, Chen M, Hernandez Andrade E, Inman J, et al. Gene expression profiling of human placentas from preeclamptic and normotensive pregnancies. Mol Hum Reprod. 2006;12:169-79 pubmed
  13. Karlsson S, Holmberg E, Askerlund A, Levan K. Altered transforming growth factor-beta pathway expression pattern in rat endometrial cancer. Cancer Genet Cytogenet. 2007;177:43-50 pubmed
    ..We propose that the irregularities present in TGF-beta pathway among the majority of the EAC tumor cell lines may affect EAC carcinogenesis. ..
  14. Lee J, Au A, Foukakis T, Barbaro M, Kiss N, Clifton Bligh R, et al. Array-CGH identifies cyclin D1 and UBCH10 amplicons in anaplastic thyroid carcinoma. Endocr Relat Cancer. 2008;15:801-15 pubmed publisher
    ..In summary, the recurrent chromosomal copy number changes and molecular alterations identified in this study may provide an insight into the pathogenesis and development of ATC. ..
  15. Kalm M, Fukuda A, Fukuda H, Ohrfelt A, Lannering B, Bjork Eriksson T, et al. Transient inflammation in neurogenic regions after irradiation of the developing brain. Radiat Res. 2009;171:66-76 pubmed publisher
    ..It remains to be elucidated whether these transient changes are involved in the persistent effects of radiation observed on neurogenesis and cognition in rodents. ..
  16. Ahlin G, Hilgendorf C, Karlsson J, Szigyarto C, Uhlen M, Artursson P. Endogenous gene and protein expression of drug-transporting proteins in cell lines routinely used in drug discovery programs. Drug Metab Dispos. 2009;37:2275-83 pubmed publisher
  17. Olivares Hernández R, Usaite R, Nielsen J. Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level. Biotechnol Bioeng. 2010;107:865-75 pubmed publisher
  18. Yadav M, Zhang J, Fischer H, Huang W, Lutay N, Cirl C, et al. Inhibition of TIR domain signaling by TcpC: MyD88-dependent and independent effects on Escherichia coli virulence. PLoS Pathog. 2010;6:e1001120 pubmed publisher
    ..Dysregulation of the host response by microbial TcpC thus appears to impair the protective effects of innate immunity, while promoting inflammation and tissue damage. ..
  19. Mangelsen E, Kilian J, Harter K, Jansson C, Wanke D, Sundberg E. Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis. Mol Plant. 2011;4:97-115 pubmed publisher
    ..Summarized, our data provide an important basis for further investigation of gene functions in order to aid an improved heat tolerance and reduced losses of yield in barley as a model for cereal crops. ..
  20. Walser M, Hansen A, Svensson P, Jernas M, Oscarsson J, Isgaard J, et al. Peripheral administration of bovine GH regulates the expression of cerebrocortical beta-globin, GABAB receptor 1, and the Lissencephaly-1 protein (LIS-1) in adult hypophysectomized rats. Growth Horm IGF Res. 2011;21:16-24 pubmed publisher
    ..These transcripts represent potential novel mechanisms by which GH can interact with the brain. ..
  21. Väremo L, Nielsen J, Nookaew I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 2013;41:4378-91 pubmed publisher
    ..As a consequence of this, we suggest to use a consensus scoring approach, based on multiple GSA runs. In combination with the directionality classes, this constitutes a more thorough basis for an enriched biological interpretation. ..
  22. Kristiansson E, Osterlund T, Gunnarsson L, Arne G, Larsson D, Nerman O. A novel method for cross-species gene expression analysis. BMC Bioinformatics. 2013;14:70 pubmed publisher
    ..The method has been implemented in R and is freely available at ..
  23. Harbst K, Lauss M, Cirenajwis H, Winter C, Howlin J, Torngren T, et al. Molecular and genetic diversity in the metastatic process of melanoma. J Pathol. 2014;233:39-50 pubmed publisher
  24. Thorell K, Bengtsson Palme J, Liu O, Palacios Gonzales R, Nookaew I, Rabeneck L, et al. In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis. Infect Immun. 2017;85: pubmed publisher
  25. Danielsson F, Wiking M, Mahdessian D, Skogs M, Ait Blal H, Hjelmare M, et al. RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins. J Proteome Res. 2013;12:299-307 pubmed publisher
    ..The results show a path to combine transcriptomics with affinity proteomics to characterize the proteins in a gene- or chromosome-centric manner. ..
  26. Pathak S, Meng W, Nandy S, Ping J, Bisgin A, Helmfors L, et al. Radiation and SN38 treatments modulate the expression of microRNAs, cytokines and chemokines in colon cancer cells in a p53-directed manner. Oncotarget. 2015;6:44758-80 pubmed publisher
    ..These miRNAs have the potential for use in colon cancer therapy as they are related to p53, pro- or anti-inflammatory cyto- or chemokines after the radiation and SN38 treatment. ..
  27. Garbom S, Olofsson M, Björnfot A, Srivastava M, Robinson V, Oyston P, et al. Phenotypic characterization of a virulence-associated protein, VagH, of Yersinia pseudotuberculosis reveals a tight link between VagH and the type III secretion system. Microbiology. 2007;153:1464-73 pubmed
    ..In conclusion, the vagH mutant exhibits a virulence phenotype similar to that of a T3SS-negative mutant, indicating a tight link between VagH and type III secretion in Y. pseudotuberculosis. ..
  28. Vizlin Hodzic D, Ryme J, Simonsson S, Simonsson T. Developmental studies of Xenopus shelterin complexes: the message to reset telomere length is already present in the egg. FASEB J. 2009;23:2587-94 pubmed publisher
  29. Tyo K, Kocharin K, Nielsen J. Toward design-based engineering of industrial microbes. Curr Opin Microbiol. 2010;13:255-62 pubmed publisher
    ..Genome-scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward Design-based Engineering. ..
  30. Levan K, Partheen K, Osterberg L, Olsson B, Delle U, Eklind S, et al. Identification of a gene expression signature for survival prediction in type I endometrial carcinoma. Gene Expr. 2010;14:361-70 pubmed
  31. Willems E, Guerrero Bosagna C, Decuypere E, Janssens S, Buyse J, Buys N, et al. Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model. Sci Rep. 2016;6:20837 pubmed publisher
    ..In conclusion, these results demonstrated that prenatal protein undernutrition by albumen removal leads to long-term alterations of the hepatic transcriptome in the chicken. ..
  32. Kultima K, Scholz B, Alm H, Sköld K, Svensson M, Crossman A, et al. Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: a proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE. BMC Bioinformatics. 2006;7:475 pubmed
    ..Individual proteins may be interesting as such, but by studying sets of proteins the interpretation of the results are probably more accurate and biologically informative. ..
  33. Haas U, Raschperger E, Hamberg M, Samuelsson B, Tryggvason K, Haeggstrom J. Targeted knock-down of a structurally atypical zebrafish 12S-lipoxygenase leads to severe impairment of embryonic development. Proc Natl Acad Sci U S A. 2011;108:20479-84 pubmed publisher
    ..Hence, we have identified a unique vertebrate 12S-LO that breaks the current structure-function paradigms for S and R stereo-specificity and with critical roles in normal embryonic development. ..
  34. Hultström M, Leh S, Paliege A, Bachmann S, Skogstrand T, Iversen B. Collagen-binding proteins in age-dependent changes in renal collagen turnover: microarray analysis of mRNA expression. Physiol Genomics. 2012;44:576-86 pubmed publisher
    ..Collagen stabilizing proteins may be essential for the control of renal ECM turnover and the pathogenesis of kidney fibrosis. ..
  35. Dunaeva M, Adamska I. Identification of genes expressed in response to light stress in leaves of Arabidopsis thaliana using RNA differential display. Eur J Biochem. 2001;268:5521-9 pubmed
    ..Three ORFs homologous to the Lsr5 gene were found on chromosome I and IV of Arabidopsis indicating that a multigene family of these proteins exists in plants. The possible role of Lsr gene products in light stress defences is discussed. ..
  36. Sun X, Wei L, Liden J, Hui G, Dahlman Wright K, Hjerpe A, et al. Molecular characterization of tumour heterogeneity and malignant mesothelioma cell differentiation by gene profiling. J Pathol. 2005;207:91-101 pubmed
    ..These differences in the molecular phenotype may give a better basis for diagnosis and for designing novel therapies. ..
  37. Stadelmann B, Hanevik K, Andersson M, Bruserud O, Svard S. The role of arginine and arginine-metabolizing enzymes during Giardia - host cell interactions in vitro. BMC Microbiol. 2013;13:256 pubmed publisher
    ..Giardia affects the host's arginine metabolism on many different levels. Many of the effects can be reversed by addition of arginine or citrulline, which could be a beneficial supplement in oral rehydration therapy. ..
  38. Zubarev R, Nielsen M, Fung E, Savitski M, Kel Margoulis O, Wingender E, et al. Identification of dominant signaling pathways from proteomics expression data. J Proteomics. 2008;71:89-96 pubmed publisher
    ..Pathway search engines can find application in a variety of proteomics-related fields, from fundamental molecular biology to search for novel types of disease biomarkers. ..
  39. Caren H, Djos A, Nethander M, Sjöberg R, Kogner P, Enström C, et al. Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma. BMC Cancer. 2011;11:66 pubmed publisher
    ..It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas. ..
  40. Kokosar M, Benrick A, Perfilyev A, Fornes R, Nilsson E, Maliqueo M, et al. Epigenetic and Transcriptional Alterations in Human Adipose Tissue of Polycystic Ovary Syndrome. Sci Rep. 2016;6:22883 pubmed publisher
    ..Together, these novel findings show that women with PCOS have multiple transcriptional and epigenetic changes in adipose tissue that are relevant for development of the disease. ..
  41. Nookaew I, Gabrielsson B, Holmang A, Sandberg A, Nielsen J. Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice. PLoS ONE. 2010;5:e12361 pubmed publisher
    ..This could be applied to improve diets for subjects exposed to health risks associated with obesity. ..
  42. Lindvall C, Hou M, Komurasaki T, Zheng C, Henriksson M, Sedivy J, et al. Molecular characterization of human telomerase reverse transcriptase-immortalized human fibroblasts by gene expression profiling: activation of the epiregulin gene. Cancer Res. 2003;63:1743-7 pubmed
  43. Johansson U, Olsson A, Gabrielsson S, Nilsson B, Korsgren O. Inflammatory mediators expressed in human islets of Langerhans: implications for islet transplantation. Biochem Biophys Res Commun. 2003;308:474-9 pubmed
    ..In conclusion, several inflammatory mediators were expressed in isolated islets, particularly at an early stage after isolation, indicating that a few days of culture could be beneficial for the outcome of islet transplantation. ..
  44. Hao L, Johnsen R, Lauter G, Baillie D, Burglin T. Comprehensive analysis of gene expression patterns of hedgehog-related genes. BMC Genomics. 2006;7:280 pubmed
    ..They might interact with the Patched or the Patched-related proteins in a manner similar to the interaction of Hedgehog with its receptor Patched. ..
  45. Carlsson J, Lagercrantz U, Sundström J, Teixeira R, Wellmer F, Meyerowitz E, et al. Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers. Plant J. 2007;49:452-62 pubmed
    ..These results suggest that AP3 expression in stamens depends on proper mt function and a correct nuclear-mt interaction, and that mt alterations cause the male sterility phenotype of the CMS line. ..
  46. Soneson C, Lilljebjörn H, Fioretos T, Fontes M. Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. BMC Bioinformatics. 2010;11:191 pubmed publisher
    ..We conclude that regularized dual CCA as well as PCA+CCA are useful methods for exploratory analysis of paired genetic data sets, and can be efficiently implemented also when the number of variables is very large. ..
  47. Svensson P, Englund M, Markström E, Ohlsson B, Jernas M, Billig H, et al. Copper induces the expression of cholesterogenic genes in human macrophages. Atherosclerosis. 2003;169:71-6 pubmed
    ..The effect of copper on cholesterogenic genes may also have implications for liver steatosis in early stages of Wilson's disease. ..
  48. Zhao H, Granberg F, Pettersson U. How adenovirus strives to control cellular gene expression. Virology. 2007;363:357-75 pubmed
    ..The struggle of the virus to gain control of TGF-beta and Wnt signaling, as well as the apoptotic pathways, was conspicuous. ..
  49. Aberg A, Shingler V, Balsalobre C. Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo. Mol Microbiol. 2008;67:1223-41 pubmed publisher
  50. Ingvarsson P. Molecular evolution of synonymous codon usage in Populus. BMC Evol Biol. 2008;8:307 pubmed publisher
    ..tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula. ..
  51. Andersson E, Swärd C, Stenman G, Ahlman H, Nilsson O. High-resolution genomic profiling reveals gain of chromosome 14 as a predictor of poor outcome in ileal carcinoids. Endocr Relat Cancer. 2009;16:953-66 pubmed publisher
    ..Predictive fluorescence in situ hybridization analysis of chromosome 14 status in patients with ileal carcinoids is suggested. ..
  52. Johansson I, Nilsson C, Berglund P, Lauss M, Ringner M, Olsson H, et al. Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker. Breast Cancer Res. 2012;14:R31 pubmed
    ..Finally, we identified NAT1 as a possible prognostic biomarker for MBC, as suggested by NAT1 positivity corresponding to better outcome. ..
  53. Henriksson E, Olsson A, Johannesson H, Johansson H, Hanson J, Engström P, et al. Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiol. 2005;139:509-18 pubmed
    ..In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals. ..
  54. Johansson P, Häkkinen J. Improving missing value imputation of microarray data by using spot quality weights. BMC Bioinformatics. 2006;7:306 pubmed
    ..Including a measure of spot quality improves the accuracy of the missing value imputation. WeNNI, the proposed method is more accurate and less sensitive to parameters than the widely used kNNimpute and LSimpute algorithms. ..
  55. Mok B, Ribacke U, Winter G, Yip B, Tan C, Fernandez V, et al. Comparative transcriptomal analysis of isogenic Plasmodium falciparum clones of distinct antigenic and adhesive phenotypes. Mol Biochem Parasitol. 2007;151:184-92 pubmed
    ..The present data provides evidence for complex transcriptional differences between closely related isogenic P. falciparum of distinct adhesive and antigenic characteristics. ..
  56. Brolinson A, Fourcade S, Jakobsson A, Pujol A, Jacobsson A. Steroid hormones control circadian Elovl3 expression in mouse liver. Endocrinology. 2008;149:3158-66 pubmed publisher
  57. Lönnroth C, Andersson M, Arvidsson A, Nordgren S, Brevinge H, Lagerstedt K, et al. Preoperative treatment with a non-steroidal anti-inflammatory drug (NSAID) increases tumor tissue infiltration of seemingly activated immune cells in colorectal cancer. Cancer Immun. 2008;8:5 pubmed
    ..These findings agree with previous information that high prostanoid activities in colorectal cancer increase the risk for reduced disease-specific survival following tumor resection. ..
  58. Barrenas F, Andersson B, Cardell L, Langston M, Mobini R, Perkins A, et al. Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine. 2008;42:325-9 pubmed publisher
    ..Further studies are warranted to examine if such differences have diagnostic and therapeutic implications in allergic diseases. ..
  59. Tormin A, Brune J, Olsson E, Valcich J, Neuman U, Olofsson T, et al. Characterization of bone marrow-derived mesenchymal stromal cells (MSC) based on gene expression profiling of functionally defined MSC subsets. Cytotherapy. 2009;11:114-28 pubmed publisher
    ..Furthermore, this study shows that cell sorting based on proliferation characteristics and gene expression profiling can be utilized to identify surface markers for the characterization of MSC subpopulations. ..
  60. Abramsson A, Westman Brinkmalm A, Pannee J, Gustavsson M, von Otter M, Blennow K, et al. Proteomics profiling of single organs from individual adult zebrafish. Zebrafish. 2010;7:161-8 pubmed publisher
  61. Andersson M, Ahlberg V, Jensen Waern M, Fossum C. Intestinal gene expression in pigs experimentally co-infected with PCV2 and PPV. Vet Immunol Immunopathol. 2011;142:72-80 pubmed publisher
  62. Takahashi Y, Li L, Kamiryo M, Asteriou T, Moustakas A, Yamashita H, et al. Hyaluronan fragments induce endothelial cell differentiation in a CD44- and CXCL1/GRO1-dependent manner. J Biol Chem. 2005;280:24195-204 pubmed
    ..Our data show that hyaluronan fragments and FGF-2 affect endothelial cell morphogenesis by the induction of overlapping but also by distinct sets of genes. ..
  63. Mellberg S, Dimberg A, Bahram F, Hayashi M, Rennel E, Ameur A, et al. Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis. FASEB J. 2009;23:1490-502 pubmed publisher
    ..In conclusion, we have identified genes, which may serve critical functions in formation of the vascular tube. One of these, VE-PTP, regulates VEGFR2 activity thereby modulating the VEGF-response during angiogenesis. ..
  64. Blomberg K, Boucheron N, Lindvall J, Yu L, Raberger J, Berglof A, et al. Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells. BMC Genomics. 2009;10:233 pubmed publisher
    ..Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk. ..
  65. Israelsson C, Bengtsson H, Lobell A, Nilsson L, Kylberg A, Isaksson M, et al. Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders. Eur J Neurosci. 2010;31:852-63 pubmed publisher
    ..It is concluded that the Cxcl10(+) cells appear in the inflamed central nervous system and may represent a novel population of cells that it may be possible to target pharmacologically in a broad range of neurodegenerative conditions. ..
  66. Eklund M, Spjuth O, Wikberg J. An eScience-Bayes strategy for analyzing omics data. BMC Bioinformatics. 2010;11:282 pubmed publisher
    ..The eScience-Bayes thus approach permits us to fully leverage on the advantages of Bayesian methods, resulting in models with improved predictive performance that gives more information about the underlying biological system. ..
  67. Naurin S, Hansson B, Hasselquist D, Kim Y, Bensch S. The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds. BMC Genomics. 2011;12:37 pubmed publisher
    ..Such differences might correspond to genes with different rates of evolution related to sexual dimorphism in the avian brain, and might therefore be correlated with differences between the species in sex-specific behaviours. ..
  68. Chau M, Forcinito P, Andrade A, Hegde A, Ahn S, Lui J, et al. Organization of the Indian hedgehog--parathyroid hormone-related protein system in the postnatal growth plate. J Mol Endocrinol. 2011;47:99-107 pubmed publisher
    ..The findings support the hypothesis that the embryonic Ihh–PTHrP feedback loop is maintained in the postnatal growth plate except that the source of PTHrP has shifted to a more proximal location in the resting zone. ..
  69. Erdogdu O, Eriksson L, Nystrom T, Sjoholm A, Zhang Q. Exendin-4 restores glucolipotoxicity-induced gene expression in human coronary artery endothelial cells. Biochem Biophys Res Commun. 2012;419:790-5 pubmed publisher
  70. Rentoft M, Coates P, Laurell G, Nylander K. Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes. PLoS ONE. 2012;7:e35276 pubmed publisher
  71. Jernas M, Malmeström C, Axelsson M, Nookaew I, Wadenvik H, Lycke J, et al. MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS). BMC Immunol. 2013;14:32 pubmed publisher
    ..The differential expression of mir-494, mir-197 and the predicted microRNA target gene TNFSF14 was verified by real-time PCR and ELISA. These findings indicate that microRNA may be important regulatory molecules in T-cells in MS. ..
  72. Mårtensson U, Bristulf J, Owman C, Olde B. The mouse chemerin receptor gene, mcmklr1, utilizes alternative promoters for transcription and is regulated by all-trans retinoic acid. Gene. 2005;350:65-77 pubmed
    ..The results emphasise a possible role of cmklr1 in bone modelling. ..
  73. Nelander S, Larsson E, Kristiansson E, Mansson R, Nerman O, Sigvardsson M, et al. Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. BMC Genomics. 2005;6:68 pubmed
    ..Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design. ..
  74. Granberg F, Svensson C, Pettersson U, Zhao H. Adenovirus-induced alterations in host cell gene expression prior to the onset of viral gene expression. Virology. 2006;353:1-5 pubmed
    ..A time course analysis showed that the induction of these immediate-early response genes was transient and suppressed after the onset of the adenovirus early gene expression. ..
  75. Rubin C, Lindberg J, Fitzsimmons C, Savolainen P, Jensen P, Lundeberg J, et al. Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits. BMC Genomics. 2007;8:208 pubmed
    ..Information derived from this study could be relevant to the bone research field and may also aid in further inference of genetic changes accompanying animal domestication. ..
  76. Vallon Christersson J, Staaf J, Kvist A, Medstrand P, Borg A, Rovira C. Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray. BMC Genomics. 2007;8:295 pubmed
  77. Gummesson A, Hagg D, Olson F, Hulthe J, Carlsson L, Fagerberg B. Adipose tissue is not an important source for matrix metalloproteinase-9 in the circulation. Scand J Clin Lab Invest. 2009;69:636-42 pubmed publisher
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