G-quadruplexes and gene expression in Arabidopsis thaliana
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"G-quadruplexes and gene expression ..." refers methods in this paper
...Receiver Operator Characteristic (ROC, false positive rate plotted against true positive rate) and Precision Recall (PR, precision plotted against recall) curves were generated using scikit-learn and plotted with matplotlib (Hunter, 2007; Pedregosa et al., 2011)....
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"G-quadruplexes and gene expression ..." refers background in this paper
...1 (Love et al., 2014) and log2 transformed to get log counts per million (logCPM)....
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"G-quadruplexes and gene expression ..." refers background or methods in this paper
...228 13 Acronyms and Abbreviations Acronym Definition AGI Arabidopsis genome initiative AID Activation-induced cytidine deaminase AS Alternative splicing ATAC-seq Assay for transposase-accessible chromatin using sequencing ATP Adenosine triphosphate ATR-X/ATRX Alpha-thalassemia mental retardation syndrome/protein AUC Area under the curve BAM Binary alignment map format BED Browser extensible data format BG4 G-Quadruplex binding antibody BLAT BLAT CD Circular dichroism cDNA Complementary DNA CDS Coding sequence ChIP-seq Chromatin immunoprecipitation with sequencing CHX Cyclohexamide CPM Counts per million CSR Class switch recombination CTD Carboxy-terminal domain DMS Dimethyl sulphate DMSO Dimethyl sulphoxide DNA Deoxyribonucleic Acid DNase Deoxyribonuclease DPE Downstream promoter element DSB Double strand break dsDNA Double stranded DNA 14 EMSA Electrophoretic mobility shift assay ENA European nucleotide archive ENCODE Encyclopedia of DNA elements EXT Extensin FDR False discovery rate FISH Fluorescent in situ hybridisation FPR False positive rate FRET Förster resonance energy transfer FTP File transfer protocol G4 G-Quadruplex GC content/skew Guanine and cytosine content/skew GEM Genome multitool GEO Gene expression omnibus GO Gene ontology GRO-seq Global Run On Sequencing GTF/GFF Gene transfer format/General feature format gtRNAdb Genomic tRNA database HDAC Histone deacetylase HDF5 Hierarchical data format 5 HEK Human embryonic kidney hnRNP Heterogeneous ribonucleoprotein particle IgH Immunoglobulin Heavy Chain IGV Intergrative genome viewer IRES Internal ribosome entry site lncRNA Long non-coding RNA logCPM Log counts per million logFC Log fold change LRX Leucine rich repeat extensin LSTM Long Short Term Memory 15 LTR Long terminal repeat MA plot Mean average plot miRNA MicroRNA MLP Multi-layer perceptron mRNA Messenger RNA MS Murashige & Skoog media MWU Mann Whitney U Test ncRNA Non-coding RNA NER Nucleotide excision repair NHEIII Nuclease hypersensitive element III NMM N-Methyl Mesoporphyrin IX NMR Nuclear magnetic resonance NOESY Nuclear Overhauser effect spectroscopy PAS Polyadenylation site PCR Polymerase chain reaction PCS Potential coding sequence PDB Protein data bank PDS Pyridostatin PG4 Putative G-Quadruplex PIC Preinitiation complex Pol II RNA polymerase II PPLR Probability of positive log ratio PR Precision recall pre-mRNA Precursor mRNA qPCR Quantitative polymerase chain reaction RMA Robust multichip average RMA Robust Multi-chip Averaging RNA Ribonucleic acid RNase Ribonuclease 16 RNA-seq RNA sequencing ROC Receiver operator characteristic RT Reverse transcriptase SCE Sister chromatid exchange SELEX Systematic evolution of ligands by exponential enrichment SHAPE Selective 2’-hydroxyl acylation analyzed by primer extension smFRET Single molecule Förster resonance energy transfer snRNA Small nuclear RNA SOM Self organising map SP3/4/5 Serine proline 3/4/5 motif ssDNA Single stranded DNA STAR Spliced transcript alignment to a reference SWI/SNF Switch/Sucrose non-fermentable tAI tRNA adaptation index TAIR The Arabidopsis information resource TE Transposable element TFIIH Transcription initiation factor complex TPR True positive rate tRNA transfer RNA TSS Transcriptional start site TTS Transcriptional termination site UMAP Uniform manifold approximation and projection UTR Untranslated region UV Ultraviolet 17 Chapter 1 Introduction...
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...Since the RNAseq dataset is unstranded, Cufflinks requires the upstream mapping tool (here, STAR (Dobin et al., 2013)) to annotate the orientation of spliced reads using the intron motif (i....
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...Mapping parameters for STAR (Dobin et al., 2013) were made more stringent than defaults in an attempt to increase the precision of mapping over Extensin genes without attenuating recall of splice junctions too strongly....
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...2a (Dobin et al., 2013) with default parameters, and generated BAM files were sorted...
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...These in frame splice junctions could therefore simply be the result of mapping errors from the spliced aligner STAR (Dobin et al., 2013), which utilises heuristics which may result in some reads from contiguous parts of the genome being mapped as spliced....
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