NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data

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NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1093/NAR/GKW799
P932PMC publication ID5175344
P698PubMed publication ID27471031

P50authorHeidi WeissQ39193905
P2093author name stringHong Wang
Hao Wu
Chi Wang
Arnold J Stromberg
Craig Horbinski
Jinpeng Liu
Shaoyi Sheng
Yinxing Liu
P2860cites workDifferential expression analysis for sequence count dataQ21184103
A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domainsQ22254191
Pin1 and WWP2 regulate GluR2 Q/R site RNA editing by ADAR2 with opposing effectsQ24323023
Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancerQ24338421
Substrate recognition by ADAR1 and ADAR2Q24540028
RNA editing by adenosine deaminases that act on RNAQ24679593
To edit or not to edit: regulation of ADAR editing specificity and efficiencyQ26776422
The Epitranscriptome and Innate ImmunityQ26776423
edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataQ27860819
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cellsQ27937615
Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylomeQ28115015
Screening of stable G-protein-coupled receptor variants in Saccharomyces cerevisiaeQ50443274
Structural Requirements for RNA Editing in Glutamate Receptor Pre-mRNAs by Recombinant Double-stranded RNA Adenosine DeaminaseQ57204480
Screening miRNAs related to different subtypes of breast cancer with miRNAs microarrayQ85844305
A mammalian RNA editing enzymeQ28273153
Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signatureQ28275605
MiR-15b and miR-152 reduce glioma cell invasion and angiogenesis via NRP-2 and MMP-3Q28564217
RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulationQ28575209
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Q29547403
Direct multiplexed measurement of gene expression with color-coded probe pairsQ29614417
High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG methodQ29615751
Small-sample estimation of negative binomial dispersion, with applications to SAGE dataQ33295482
Moderated statistical tests for assessing differences in tag abundanceQ33299648
Matching active site and substrate structures for an RNA editing reactionQ33488651
Green fluorescent protein as a reporter of transcription and protein localization in fungiQ33538659
MicroRNA profiling implies new markers of chemoresistance of triple-negative breast cancerQ33560283
Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in DrosophilaQ33598445
baySeq: empirical Bayesian methods for identifying differential expression in sequence count dataQ33653650
mRNA transcript quantification in archival samples using multiplexed, color-coded probesQ33891675
Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditariaQ33906416
Prognostic value of miR-221-3p, miR-342-3p and miR-491-5p expression in colon cancerQ33961980
NanoStriDE: normalization and differential expression analysis of NanoString nCounter dataQ34104092
Hypoxic signature of microRNAs in glioblastoma: insights from small RNA deep sequencing.Q34107629
High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase.Q34115490
A-to-I RNA editing and human diseaseQ34162058
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA dataQ34238131
High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch.Q34255120
dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editingQ34362817
RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1Q34376081
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq dataQ34419135
MiR-374b-5p suppresses RECK expression and promotes gastric cancer cell invasion and metastasisQ34696685
Effect of miR-142-3p on the M2 macrophage and therapeutic efficacy against murine glioblastomaQ34736639
Rapid neurogenesis through transcriptional activation in human stem cells.Q34987004
New and old roles of the double-stranded RNA-binding domainQ35029554
Predicting sites of ADAR editing in double-stranded RNAQ35039886
Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2Q35098008
MicroRNA expression differences in human hematopoietic cell lineages enable regulated transgene expressionQ35207667
An evaluation and replication of miRNAs with disease stage and colorectal cancer-specific mortalityQ35598290
A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1.Q35776242
High level of miR-221/222 confers increased cell invasion and poor prognosis in gliomaQ36112656
Mechanistic insights into editing-site specificity of ADARsQ36438418
Large-scale overexpression and purification of ADARs from Saccharomyces cerevisiae for biophysical and biochemical studiesQ36647877
Nucleic Acid Modifications in Regulation of Gene ExpressionQ36654186
Binding properties of newly identified Xenopus proteins containing dsRNA-binding motifsQ36722970
Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivityQ37032837
Isocitrate dehydrogenase 1 (IDH1) mutation-specific microRNA signature predicts favorable prognosis in glioblastoma patients with IDH1 wild typeQ37358051
RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiaeQ37375826
Mutational spectrum of the ADAR1 gene in dyschromatosis symmetrica hereditariaQ37698988
MiR-221/222 promote human glioma cell invasion and angiogenesis by targeting TIMP2.Q38904607
A high-throughput screen to identify enhancers of ADAR-mediated RNA-editingQ41295215
Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.Q41877792
Seven novel mutations of the ADAR gene in Chinese families and sporadic patients with dyschromatosis symmetrica hereditaria (DSH).Q44898248
RED2, a brain-specific member of the RNA-specific adenosine deaminase familyQ45345704
Hsa-miR-181a-5p Expression and Effects on Cell Proliferation in Gastric CancerQ46255555
Knockdown of long non-coding RNA XIST exerts tumor-suppressive functions in human glioblastoma stem cells by up-regulating miR-152.Q48380068
MiR-152 functions as a tumor suppressor in glioblastoma stem cells by targeting Krüppel-like factor 4.Q48545857
P275copyright licenseCreative Commons Attribution-NonCommercial 4.0 InternationalQ34179348
P6216copyright statuscopyrightedQ50423863
P433issue20
P407language of work or nameEnglishQ1860
P921main subjectstatisticsQ12483
P304page(s)e151
P577publication date2016-07-28
P1433published inNucleic Acids ResearchQ135122
P1476titleNanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data
P478volume44

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