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Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

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The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus

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Genome-wide Association Study Identifies Four Genetic Loci Associated with Thyroid Volume and Goiter Risk

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Genetic and Epigenetic Regulation of Human lincRNA Gene Expression

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Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

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A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

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Long Noncoding RNAs with Enhancer-like Function in Human Cells

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Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

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Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

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lincRNAs: Genomics, Evolution, and Mechanisms

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A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

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The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

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Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

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Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

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LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

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Long noncoding RNAs and human disease

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lincRNAs act in the circuitry controlling pluripotency and differentiation

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STAR: ultrafast universal RNA-seq aligner

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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Trimmomatic: a flexible trimmer for Illumina sequence data

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CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

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The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

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lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

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Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development

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The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

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Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

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Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

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Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

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Identification of Genetic Variants That Affect Histone Modifications in Human Cells

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Genome Regulation by Long Noncoding RNAs

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ViennaRNA Package 2.0

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Scikit-learn: Machine Learning in Python

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Considerations when investigating lncRNA function in vivo

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Functional Implications of Intergenic GWAS SNPs in Immune-Related LncRNAs

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cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

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Risk SNP-induced lncRNA-SLCC1 drives colorectal cancer through activating glycolysis signaling

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Bayesian nonparametric discovery of isoforms and individual specific quantification

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Joint analysis of expression levels and histological images identifies genes associated with tissue morphology

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Co-expression networks reveal the tissue-specific regulation of transcription and splicing

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Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs

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Disease-Associated SNPs in Inflammation-Related lncRNAs

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Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications

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Epigenomic and Transcriptomic Prioritization of Candidate Obesity-Risk Regulatory GWAS SNPs

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