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Long non-coding RNA gene regulation and trait associations across human tissues

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What this work says

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

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Genetic and Epigenetic Regulation of Human lincRNA Gene Expression

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Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

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Mapping the Mouse Cell Atlas by Microwell-Seq

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Mapping the Mouse Cell Atlas by Microwell-Seq

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Molecular Mechanisms of Long Noncoding RNAs

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MICA Engagement by Human Vγ2Vδ2 T Cells Enhances Their Antigen-Dependent Effector Function

inferredcites →https://doi.org/10.1038/349038a0openalex-snapshot

A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome

inferredcites →https://doi.org/10.1038/35047580openalex-snapshot

X-chromosome inactivation: counting, choice and initiation

inferredcites →https://doi.org/10.1038/75556openalex-snapshot

Gene Ontology: tool for the unification of biology

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Costimulation of CD8αβ T cells by NKG2D via engagement by MIC induced on virus-infected cells

inferredcites →https://doi.org/10.1038/nature11233openalex-snapshot

Landscape of transcription in human cells

inferredcites →https://doi.org/10.1038/nature21374openalex-snapshot

An atlas of human long non-coding RNAs with accurate 5′ ends

inferredcites →https://doi.org/10.1038/nbt.4283openalex-snapshot

Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

inferredcites →https://doi.org/10.1038/ncomms11889openalex-snapshot

Homeobox NKX2-3 promotes marginal-zone lymphomagenesis by activating B-cell receptor signalling and shaping lymphocyte dynamics

inferredcites →https://doi.org/10.1038/ncomms7370openalex-snapshot

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

inferredcites →https://doi.org/10.1038/ng.3192openalex-snapshot

The landscape of long noncoding RNAs in the human transcriptome

inferredcites →https://doi.org/10.1038/ng.3200openalex-snapshot

Large multiallelic copy number variations in humans

inferredcites →https://doi.org/10.1038/ng.3834openalex-snapshot

The impact of structural variation on human gene expression

inferredcites →https://doi.org/10.1038/ng.3988openalex-snapshot

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

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WASP: allele-specific software for robust molecular quantitative trait locus discovery

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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

inferredcites →https://doi.org/10.1038/nrg.2015.10openalex-snapshot

Unique features of long non-coding RNA biogenesis and function

inferredcites →https://doi.org/10.1038/nsmb.2428openalex-snapshot

Cis-acting noncoding RNAs: friends and foes

inferredcites →https://doi.org/10.1038/s41588-018-0268-8openalex-snapshot

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

inferredcites →https://doi.org/10.1038/srep03924openalex-snapshot

Contribution of NKX2-3 Polymorphisms to Inflammatory Bowel Diseases: A Meta-Analysis of 35358 subjects

inferredcites →https://doi.org/10.1073/pnas.1507125112openalex-snapshot

A survey of human brain transcriptome diversity at the single cell level

inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s96openalex-snapshot

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

inferredcites →https://doi.org/10.1093/bioinformatics/btg405openalex-snapshot

affy—analysis of Affymetrix GeneChip data at the probe level

inferredcites →https://doi.org/10.1093/bioinformatics/btm563openalex-snapshot

Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R

inferredcites →https://doi.org/10.1093/bioinformatics/bts196openalex-snapshot

RNA-SeQC: RNA-seq metrics for quality control and process optimization

inferredcites →https://doi.org/10.1093/bioinformatics/bty339openalex-snapshot

lncFunTK: a toolkit for functional annotation of long noncoding RNAs

inferredcites →https://doi.org/10.1093/emboj/19.9.2015openalex-snapshot

NKX2.3 is required for MAdCAM‐1 expression and homing of lymphocytes in spleen and mucosa‐associated lymphoid tissue

inferredcites →https://doi.org/10.1093/nar/gkq130openalex-snapshot

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells

inferredcites →https://doi.org/10.1093/nar/gku1060openalex-snapshot

An update on LNCipedia: a database for annotated human lncRNA sequences

inferredcites →https://doi.org/10.1093/nar/gku988openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkv295openalex-snapshot

An update on LNCipedia: a database for annotated human lncRNA sequences

inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

inferredcites →https://doi.org/10.1093/nar/gky1055openalex-snapshot

The Gene Ontology Resource: 20 years and still GOing strong

inferredcites →https://doi.org/10.1093/nar/gkz410openalex-snapshot

LnCompare: gene set feature analysis for human long non-coding RNAs

inferredcites →https://doi.org/10.1093/nar/gkz621openalex-snapshot

An expanded landscape of human long noncoding RNA

inferredcites →https://doi.org/10.1101/282129openalex-snapshot

Widespread transcriptional scanning in the testis modulates gene evolution rates

inferredcites →https://doi.org/10.1101/531210openalex-snapshot

The mutational constraint spectrum quantified from variation in 141,456 humans

inferredcites →https://doi.org/10.1101/gad.17446611openalex-snapshot

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

inferredcites →https://doi.org/10.1101/gr.132159.111openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.214205.116openalex-snapshot

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

inferredcites →https://doi.org/10.1101/gr.216747.116openalex-snapshot

Quantifying the regulatory effect size of cis -acting genetic variation using allelic fold change

inferredcites →https://doi.org/10.1101/gr.218032.116openalex-snapshot

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

inferredcites →https://doi.org/10.1101/gr.242222.118openalex-snapshot

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

inferredcites →https://doi.org/10.1126/science.aaa0355openalex-snapshot

The human transcriptome across tissues and individuals

inferredcites →https://doi.org/10.1126/science.aaz1776openalex-snapshot

The GTEx Consortium atlas of genetic regulatory effects across human tissues

inferredcites →https://doi.org/10.1126/science.aaz5900openalex-snapshot

Transcriptomic signatures across human tissues identify functional rare genetic variation

inferredcites →https://doi.org/10.1177/1177271918757480openalex-snapshot

Nkx2-3—A Slippery Slope From Development Through Inflammation Toward Hematopoietic Malignancies

inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot

WGCNA: an R package for weighted correlation network analysis

inferredcites →https://doi.org/10.1186/1471-2164-15-675openalex-snapshot

Influence of RNA extraction methods and library selection schemes on RNA-seq data

inferredcites →https://doi.org/10.1186/s12859-017-1535-xopenalex-snapshot

In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression

inferredcites →https://doi.org/10.1186/s12864-019-5497-4openalex-snapshot

PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities

inferredcites →https://doi.org/10.1186/s13059-014-0467-2openalex-snapshot

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

inferredcites →https://doi.org/10.1186/s13059-015-0762-6openalex-snapshot

Tools and best practices for data processing in allelic expression analysis

inferredcites →https://doi.org/10.1186/s13059-016-0873-8openalex-snapshot

Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans

inferredcites →https://doi.org/10.1186/s13059-020-02122-zopenalex-snapshot

A vast resource of allelic expression data spanning human tissues

inferredcites →https://doi.org/10.1198/106186006x137047openalex-snapshot

Optimal Full Matching and Related Designs via Network Flows

inferredcites →https://doi.org/10.1242/dev.126.10.2215openalex-snapshot

Targeted disruption of the homeobox transcription factor Nkx2-3 in mice results in postnatal lethality and abnormal development of small intestine and spleen

inferredcites →https://doi.org/10.12688/f1000research.17145.1openalex-snapshot

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors

inferredcites →https://doi.org/10.12688/f1000research.17145.2openalex-snapshot

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors

inferredcites →https://doi.org/10.1523/jneurosci.4488-13.2014openalex-snapshot

Cell Type-Specific Expression Analysis to Identify Putative Cellular Mechanisms for Neurogenetic Disorders

inferredcites →https://doi.org/10.3389/fimmu.2015.00097openalex-snapshot

NKG2D Ligands in Tumor Immunity: Two Sides of a Coin

inferredcites →https://doi.org/10.4049/jimmunol.170.8.4002openalex-snapshot

Architectural Defects in the Spleens of Nkx2-3-Deficient Mice Are Intrinsic and Associated with Defects in Both B Cell Maturation and T Cell-Dependent Immune Responses

What points at this work

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

inferred← citeshttps://doi.org/10.1002/jbmr.4622openalex-snapshot

Identification of Known and Novel Long Noncoding RNAs Potentially Responsible for the Effects of Bone Mineral Density (BMD) Genomewide Association Study (GWAS) Loci

inferred← citeshttps://doi.org/10.1007/s00011-026-02257-yopenalex-snapshot

Multivariable genome-wide analysis elucidates the shared genetic architecture, immunosenescence features, and gut-origin therapeutic targets of ulcerative colitis-associated multisystem inflammation

inferred← citeshttps://doi.org/10.1016/b978-0-323-90406-3.00002-6openalex-snapshot

History and definitions of ncRNAs

inferred← citeshttps://doi.org/10.1021/acsanm.2c01944openalex-snapshot

Single-Stranded Deoxyribonucleic Acid Bonded to Sub-Percolated Gold Films on Monolayer Graphene Field-Effect Transistors as Coronavirus Ribonucleic Acid Sensors

inferred← citeshttps://doi.org/10.1038/s10038-022-01012-5openalex-snapshot

Cis-regulated expression of non-conserved lincRNAs associates with cardiometabolic related traits

inferred← citeshttps://doi.org/10.1038/s41598-020-77586-xopenalex-snapshot

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

inferred← citeshttps://doi.org/10.1038/s41598-024-82393-9openalex-snapshot

High tissue specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA

inferred← citeshttps://doi.org/10.1101/787903openalex-snapshot

The GTEx Consortium atlas of genetic regulatory effects across human tissues

inferred← citeshttps://doi.org/10.1126/science.aaz1776openalex-snapshot

The GTEx Consortium atlas of genetic regulatory effects across human tissues

inferred← citeshttps://doi.org/10.1161/atvbaha.120.315045openalex-snapshot

Nonconserved Long Intergenic Noncoding RNAs Associate With Complex Cardiometabolic Disease Traits

inferred← citeshttps://doi.org/10.1186/s13059-020-02122-zopenalex-snapshot

A vast resource of allelic expression data spanning human tissues

inferred← citeshttps://doi.org/10.59717/j.xinn-life.2026.100196openalex-snapshot

A comprehensive survey on artificial intelligence for biomolecule design

inferred← citeshttps://doi.org/10.70675/bf8d6d28z4d9az4745z9b52zabde958139fbopenalex-snapshot

Study of the genetic component of feed efficiency (FE) in layer lines divergent for FE using the RNA-seq technology

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