Analysis options for high-throughput sequencing in miRNA expression profiling.

PubWeight™: 0.96‹?› | Rank: Top 15%

🔗 View Article (PMC 4007773)

Published in BMC Res Notes on March 13, 2014

Authors

Tomasz Stokowy, Markus Eszlinger, Michał Świerniak, Krzysztof Fujarewicz, Barbara Jarząb, Ralf Paschke, Knut Krohn1

Author Affiliations

1: Interdisciplinary Center for Clinical Research (IZKF), University of Leipzig, Liebigstr, 21, 04103 Leipzig, Germany. krok@medizin.uni-leipzig.de.

Articles citing this

Exosomes from bulk and stem cells from human prostate cancer have a differential microRNA content that contributes cooperatively over local and pre-metastatic niche. Oncotarget (2016) 0.84

Dietary RNAs: New Stories Regarding Oral Delivery. Nutrients (2015) 0.82

Reciprocal control of miR-197 and IL-6/STAT3 pathway reveals miR-197 as potential therapeutic target for hepatocellular carcinoma. Oncoimmunology (2015) 0.81

Mini but mighty: microRNAs in the pathobiology of periodontal disease. Periodontol 2000 (2015) 0.80

Circulating microRNAs found dysregulated in ex-exposed asbestos workers and pleural mesothelioma patients as potential new biomarkers. Oncotarget (2016) 0.79

Mitochondrial poly(A) polymerase is involved in tRNA repair. Nucleic Acids Res (2015) 0.78

Cancer stem cells as a potential therapeutic target in thyroid carcinoma. Oncol Lett (2016) 0.77

Oligoadenylation of 3' decay intermediates promotes cytoplasmic mRNA degradation in Drosophila cells. RNA (2016) 0.77

MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae. BMC Genomics (2015) 0.77

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression. BMC Genomics (2016) 0.76

Novel genes on rat chromosome 10 are linked to body fat mass, preadipocyte number and adipocyte size. Int J Obes (Lond) (2016) 0.75

Regulation of human adipogenesis by miR125b-5p. Adipocyte (2016) 0.75

Identification of CHEK1, SLC26A4, c-KIT, TPO and TG as new biomarkers for human follicular thyroid carcinoma. Oncotarget (2016) 0.75

MicroRNA biomarkers for early detection of embryonic malformations in pregnancy. J Biomol Res Ther (2014) 0.75

Evaluation of microRNA alignment techniques. RNA (2016) 0.75

Associations of Il-1 Family-Related Polymorphisms With Gastric Cancer Risk and the Role of Mir-197 In Il-1f5 Expression. Medicine (Baltimore) (2015) 0.75

miRNA expression and function in thyroid carcinomas: a comparative and critical analysis and a model for other cancers. Oncotarget (2016) 0.75

Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA (2017) 0.75

Transcriptome analysis in primary colorectal cancer tissues from patients with and without liver metastases using next-generation sequencing. Cancer Med (2017) 0.75

Articles cited by this

The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79

MicroRNA expression profiles classify human cancers. Nature (2005) 69.12

Differential expression analysis for sequence count data. Genome Biol (2010) 64.56

BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23

miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res (2010) 25.85

Principles of microRNA-target recognition. PLoS Biol (2005) 23.70

A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol (2010) 22.10

A uniform system for microRNA annotation. RNA (2003) 20.28

Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet (2011) 9.79

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics (2009) 8.69

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83

MicroRNA profiling: approaches and considerations. Nat Rev Genet (2012) 4.39

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature (2010) 3.87

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA (2010) 3.85

MicroRNA expression profiling of thyroid tumors: biological significance and diagnostic utility. J Clin Endocrinol Metab (2008) 3.40

Expression profiling of microRNAs by deep sequencing. Brief Bioinform (2009) 2.71

Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics (2009) 2.39

A limited set of human MicroRNA is deregulated in follicular thyroid carcinoma. J Clin Endocrinol Metab (2006) 2.10

Proliferation and tumorigenesis of a murine sarcoma cell line in the absence of DICER1. Cancer Cell (2012) 2.04

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA (2009) 1.96

MicroRNAs in tumorigenesis: a primer. Am J Pathol (2007) 1.83

Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol (2008) 1.75

MicroRNAs in thyroid cancer. J Clin Endocrinol Metab (2011) 1.35

microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA (2011) 1.26

Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques (2010) 1.26

Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues. PLoS One (2013) 1.24

Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma. J Mol Endocrinol (2012) 1.10

Current state and future perspective of molecular diagnosis of fine-needle aspiration biopsy of thyroid nodules. J Clin Endocrinol Metab (2011) 1.06

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing. Methods (2012) 1.04

Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS One (2012) 1.01

Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match. RNA (2012) 0.95

Evaluation of candidate diagnostic microRNAs in thyroid fine-needle aspiration biopsy samples. Thyroid (2012) 0.95

Differences in microRNA detection levels are technology and sequence dependent. RNA (2013) 0.93

High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation. PLoS One (2013) 0.90

Molecular signatures of thyroid follicular neoplasia. Endocr Relat Cancer (2010) 0.88

Inverse correlation of miRNA and cell cycle-associated genes suggests influence of miRNA on benign thyroid nodule tumorigenesis. J Clin Endocrinol Metab (2012) 0.84

Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis. Gene (2013) 0.80

Dynamic linear model for the identification of miRNAs in next-generation sequencing data. Biometrics (2011) 0.80

Articles by these authors

The management of thyroid nodules: a retrospective analysis of health insurance data. Dtsch Arztebl Int (2013) 2.97

American Association of Clinical Endocrinologists, Associazione Medici Endocrinologi, and EuropeanThyroid Association Medical Guidelines for Clinical Practice for the Diagnosis and Management of Thyroid Nodules. Endocr Pract (2010) 2.97

Pituitary adenoma predisposition caused by germline mutations in the AIP gene. Science (2006) 2.24

Hormonal regulation of adiponectin gene expression in 3T3-L1 adipocytes. Biochem Biophys Res Commun (2002) 1.86

Adiponectin gene expression and secretion is inhibited by interleukin-6 in 3T3-L1 adipocytes. Biochem Biophys Res Commun (2003) 1.82

Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res (2005) 1.77

Effect of a 4 week physical training program on plasma concentrations of inflammatory markers in patients with abnormal glucose tolerance. Eur J Endocrinol (2006) 1.76

Evaluation of small-molecule modulators of the luteinizing hormone/choriogonadotropin and thyroid stimulating hormone receptors: structure-activity relationships and selective binding patterns. J Med Chem (2006) 1.71

Altered fiber distribution and fiber-specific glycolytic and oxidative enzyme activity in skeletal muscle of patients with type 2 diabetes. Diabetes Care (2006) 1.63

American Association of Clinical Endocrinologists, Associazione Medici Endocrinologi, and European Thyroid Association Medical guidelines for clinical practice for the diagnosis and management of thyroid nodules: executive summary of recommendations. Endocr Pract (2010) 1.57

[Diagnosis and treatment of thyroid cancer - Polish guidelines]. Endokrynol Pol (2010) 1.56

A low molecular weight agonist signals by binding to the transmembrane domain of thyroid-stimulating hormone receptor (TSHR) and luteinizing hormone/chorionic gonadotropin receptor (LHCGR). J Biol Chem (2006) 1.38

Potential biomarkers of nonobstructive azoospermia identified in microarray gene expression analysis. Fertil Steril (2013) 1.38

[Heart failure due to chronic hypoparathyroidism in patient with acute coronary syndrome]. Kardiol Pol (2013) 1.37

Cellularity and adipogenic profile of the abdominal subcutaneous adipose tissue from obese adolescents: association with insulin resistance and hepatic steatosis. Diabetes (2010) 1.35

Molecular pathogenesis of euthyroid and toxic multinodular goiter. Endocr Rev (2004) 1.33

Association of FTO variants with BMI and fat mass in the self-contained population of Sorbs in Germany. Eur J Hum Genet (2010) 1.26

Clinical characteristics and therapeutic responses in patients with germ-line AIP mutations and pituitary adenomas: an international collaborative study. J Clin Endocrinol Metab (2010) 1.24

Isoproterenol, TNFalpha, and insulin downregulate adipose triglyceride lipase in 3T3-L1 adipocytes. Mol Cell Endocrinol (2005) 1.20

Analysis of the relationship between the Pro12Ala variant in the PPAR-gamma2 gene and the response rate to therapy with pioglitazone in patients with type 2 diabetes. Diabetes Care (2003) 1.17

Molecular diagnosis of pituitary adenoma predisposition caused by aryl hydrocarbon receptor-interacting protein gene mutations. Proc Natl Acad Sci U S A (2007) 1.16

Interleukin-6 is a negative regulator of visfatin gene expression in 3T3-L1 adipocytes. Am J Physiol Endocrinol Metab (2005) 1.15

Pancreatic neuroendocrine tumor with ectopic adrenocorticotropin production upon second recurrence. J Clin Endocrinol Metab (2004) 1.14

Identification of a novel epitope in the thyroid-stimulating hormone receptor ectodomain acting as intramolecular signaling interface. J Biol Chem (2004) 1.14

AMERICAN ASSOCIATION OF CLINICAL ENDOCRINOLOGISTS, AMERICAN COLLEGE OF ENDOCRINOLOGY, AND ASSOCIAZIONE MEDICI ENDOCRINOLOGI MEDICAL GUIDELINES FOR CLINICAL PRACTICE FOR THE DIAGNOSIS AND MANAGEMENT OF THYROID NODULES - 2016 UPDATE. Endocr Pract (2016) 1.13

SRGAP1 is a candidate gene for papillary thyroid carcinoma susceptibility. J Clin Endocrinol Metab (2013) 1.12

Hypercalcemia as a result of sarcoidosis with normal serum concentrations of vitamin D. Med Sci Monit (2007) 1.11

Contacts between extracellular loop two and transmembrane helix six determine basal activity of the thyroid-stimulating hormone receptor. J Biol Chem (2006) 1.08

Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet (2011) 1.07

Monocyte chemoattractant protein 1 expression is stimulated by growth hormone and interleukin-6 in 3T3-L1 adipocytes. Biochem Biophys Res Commun (2004) 1.07

Current state and future perspective of molecular diagnosis of fine-needle aspiration biopsy of thyroid nodules. J Clin Endocrinol Metab (2011) 1.06

Adiponectin, obesity, and cardiovascular disease. Biochimie (2004) 1.05

Extended hormone binding site of the human thyroid stimulating hormone receptor: distinctive acidic residues in the hinge region are involved in bovine thyroid stimulating hormone binding and receptor activation. J Biol Chem (2008) 1.03

Molecular fine-needle aspiration biopsy diagnosis of thyroid nodules by tumor specific mutations and gene expression patterns. Mol Cell Endocrinol (2010) 1.02

Interleukin-6 is a positive regulator of tumor necrosis factor alpha-induced adipose-related protein in 3T3-L1 adipocytes. FEBS Lett (2004) 1.00

Structural determinants for G-protein activation and specificity in the third intracellular loop of the thyroid-stimulating hormone receptor. J Mol Med (Berl) (2006) 0.98

Hormonal regulation of the novel adipocytokine visfatin in 3T3-L1 adipocytes. J Endocrinol (2005) 0.97

Mechanisms of disease: hydrogen peroxide, DNA damage and mutagenesis in the development of thyroid tumors. Nat Clin Pract Endocrinol Metab (2007) 0.97

Functional desensitization of the extracellular calcium-sensing receptor is regulated via distinct mechanisms: role of G protein-coupled receptor kinases, protein kinase C and beta-arrestins. Endocrinology (2007) 0.97

Impact of molecular screening for point mutations and rearrangements in routine air-dried fine-needle aspiration samples of thyroid nodules. Thyroid (2013) 0.97

Ectopic Cushing' syndrome caused by a neuroendocrine carcinoma of the mesentery. BMC Cancer (2006) 0.96

The superagonistic activity of bovine thyroid-stimulating hormone (TSH) and the human TR1401 TSH analog is determined by specific amino acids in the hinge region of the human TSH receptor. J Biol Chem (2009) 0.96

Significance of ectodomain cysteine boxes 2 and 3 for the activation mechanism of the thyroid-stimulating hormone receptor. J Biol Chem (2006) 0.95

A multi-gene approach to differentiate papillary thyroid carcinoma from benign lesions: gene selection using support vector machines with bootstrapping. Endocr Relat Cancer (2007) 0.95

Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors. Endocr Rev (2007) 0.95

Diagnostic and therapeutic guidelines for gastro-entero-pancreatic neuroendocrine neoplasms (recommended by the Polish Network of Neuroendocrine Tumours). Endokrynol Pol (2013) 0.95

The human thyrotropin receptor is predominantly internalized by beta-arrestin 2. Endocrinology (2006) 0.93

Stable feature selection and classification algorithms for multiclass microarray data. Biol Direct (2012) 0.93

Evidence for cooperative signal triggering at the extracellular loops of the TSH receptor. FASEB J (2008) 0.93

Somatic VHL gene alterations in MEN2-associated medullary thyroid carcinoma. BMC Cancer (2006) 0.93

Similar prevalence of somatic TSH receptor and Gsalpha mutations in toxic thyroid nodules in geographical regions with different iodine supply in Turkey. Eur J Endocrinol (2006) 0.93

Selenium and goiter prevalence in borderline iodine sufficiency. Eur J Endocrinol (2006) 0.93

Evaluation of a computer based interactive diabetes education program designed to train the estimation of the energy or carbohydrate contents of foods. Patient Educ Couns (2002) 0.92

Large genomic deletions in AIP in pituitary adenoma predisposition. J Clin Endocrinol Metab (2008) 0.92

The hinge region: an important receptor component for GPHR function. Trends Endocrinol Metab (2009) 0.91

Regulation of adiponectin receptor R1 and R2 gene expression in adipocytes of C57BL/6 mice. Biochem Biophys Res Commun (2005) 0.91

Is there a place for thyroidectomy in older patients with thyrotoxic storm and cardiorespiratory failure? Thyroid (2003) 0.91

Thyroid stimulating hormone receptor (TSHR) intron 1 variants are major risk factors for Graves' disease in three European Caucasian cohorts. PLoS One (2010) 0.90

Tissue inhibitor of metalloproteinase-1 predicts adiposity in humans. Eur J Endocrinol (2007) 0.90

Perspectives for improved and more accurate classification of thyroid epithelial tumors. J Clin Endocrinol Metab (2008) 0.90

Modulation of TSHR signaling by posttranslational modifications. Trends Endocrinol Metab (2007) 0.89

Functional significance of the thyrotropin receptor germline polymorphism D727E. Biochem Biophys Res Commun (2003) 0.89

Growth hormone is a positive regulator of adiponectin receptor 2 in 3T3-L1 adipocytes. FEBS Lett (2004) 0.88

A hydrophobic cluster in the center of the third extracellular loop is important for thyrotropin receptor signaling. Endocrinology (2005) 0.88

TFF3-based candidate gene discrimination of benign and malignant thyroid tumors in a region with borderline iodine deficiency. J Clin Endocrinol Metab (2008) 0.88

Principles and determinants of G-protein coupling by the rhodopsin-like thyrotropin receptor. PLoS One (2010) 0.87

Impaired enteral levothyroxine absorption in hypothyroidism refractory to oral therapy after thyroid ablation for papillary thyroid cancer: case report and kinetic studies. Thyroid (2006) 0.87

Two novel mutations in the sixth transmembrane segment of the thyrotropin receptor gene causing hyperfunctioning thyroid nodules. Thyroid (2005) 0.87

MALDI-typing of infectious algae of the genus Prototheca using SOM portraits. J Microbiol Methods (2011) 0.87

Interactions between the extracellular domain and the extracellular loops as well as the 6th transmembrane domain are necessary for TSH receptor activation. Eur J Endocrinol (2005) 0.86

Novel genome-wide association study-based candidate loci for differentiated thyroid cancer risk. J Clin Endocrinol Metab (2014) 0.86

Genetics and phenomics of inherited and sporadic non-autoimmune hyperthyroidism. Mol Cell Endocrinol (2010) 0.85

Variants in the ATM-CHEK2-BRCA1 axis determine genetic predisposition and clinical presentation of papillary thyroid carcinoma. Genes Chromosomes Cancer (2014) 0.85

RET germline mutation in codon 791 in a family representing 3 generations from age 5 to age 70 years: should thyroidectomy be performed? Endocr Pract (2004) 0.85

Gene expression analysis reveals evidence for increased expression of cell cycle-associated genes and Gq-protein-protein kinase C signaling in cold thyroid nodules. J Clin Endocrinol Metab (2004) 0.85

Serum amyloid A3 expression is stimulated by dexamethasone and interleukin-6 in 3T3-L1 adipocytes. J Endocrinol (2004) 0.84

Somatic mutations in thyroid nodular disease. Mol Genet Metab (2002) 0.84

Inverse correlation of miRNA and cell cycle-associated genes suggests influence of miRNA on benign thyroid nodule tumorigenesis. J Clin Endocrinol Metab (2012) 0.84

Molecular testing of thyroid fine-needle aspirations improves presurgical diagnosis and supports the histologic identification of minimally invasive follicular thyroid carcinomas. Thyroid (2015) 0.84

Meta- and reanalysis of gene expression profiles of hot and cold thyroid nodules and papillary thyroid carcinoma for gene groups. J Clin Endocrinol Metab (2006) 0.84

Aryl hydrocarbon receptor interacting protein (AIP) gene mutation analysis in children and adolescents with sporadic pituitary adenomas. Clin Endocrinol (Oxf) (2008) 0.84

Structural determinants for g protein activation and selectivity in the second intracellular loop of the thyrotropin receptor. Endocrinology (2004) 0.84

Lack of correlation for sodium iodide symporter mRNA and protein expression and analysis of sodium iodide symporter promoter methylation in benign cold thyroid nodules. Thyroid (2004) 0.83

A patient with a large recurrent pheochromocytoma demonstrating the pitfalls of diagnosis. Nat Rev Endocrinol (2011) 0.83

Defining structural and functional dimensions of the extracellular thyrotropin receptor region. J Biol Chem (2011) 0.83

Gene expression analysis reveals evidence for inactivation of the TGF-beta signaling cascade in autonomously functioning thyroid nodules. Oncogene (2004) 0.83

Relative quantification of indium-111 pentetreotide and gallium-68 DOTATOC uptake in the thyroid gland and association with thyroid pathologies. Thyroid (2009) 0.83

Cases of borderline in vitro constitutive thyrotropin receptor activity: how to decide whether a thyrotropin receptor mutation is constitutively active or not? Thyroid (2009) 0.83

Detection of PAX8/PPARG and RET/PTC rearrangements is feasible in routine air-dried fine needle aspiration smears. Thyroid (2012) 0.82

Novel thyrotropin receptor germline mutation (Ile568Val) in a Saxonian family with hereditary nonautoimmune hyperthyroidism. Thyroid (2005) 0.82

Therapeutic perspectives of adipocytokines. Expert Opin Pharmacother (2005) 0.82

Calciphylaxis in chronic, non-dialysis-dependent renal disease. BMC Nephrol (2003) 0.82