Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

A novel antisense long noncoding RNA regulates the expression of MDC1 in bladder cancer

(2015) Yao Xue et al.   Oncotarget

The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression

(2014) Iwona Pawlikowska et al.   BIOINFORMATICS

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

(2014) V. R. Paralkar et al.   BLOOD

Novel insights into G protein and G protein-coupled receptor signaling in cancer

(2014) Morgan O’Hayre et al.   CURRENT OPINION IN CELL BIOLOGY

LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma

(2014) Jiagen Li et al.   GUT

A Long Noncoding RNA Transcriptional Regulatory Circuit Drives Thermogenic Adipocyte Differentiation

(2014) Xu-Yun Zhao et al.   MOLECULAR CELL

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5

(2014) T. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of a Novel Long Noncoding RNA, SCAL1, Induced by Cigarette Smoke and Elevated in Lung Cancer Cell Lines

(2013) Philip Thai et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer

(2013) Wang He et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Long non-coding RNA MEG3 inhibits NSCLC cells proliferation and induces apoptosis by affecting p53 expression

(2013) Kai-hua Lu et al.   BMC CANCER

Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer

(2013) Ken-ichi Takayama et al.   EMBO JOURNAL

Emerging Roles of Competing Endogenous RNAs in Cancer: Insights from the Regulation of PTEN

(2013) A. de Giorgio et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

(2013) Zhou Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Analysis of long non-coding RNA expression profiles in gastric cancer

(2013) Wei-Jun Cao   WORLD JOURNAL OF GASTROENTEROLOGY

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Genes responsible for the characteristics of primary cultured invasive phenotype hepatocellular carcinoma cells

(2012) Zu-Yau Lin et al.   BIOMEDICINE & PHARMACOTHERAPY

Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder

(2012) P. Szafranski et al.   GENOME RESEARCH

BRAFV600Eremodels the melanocyte transcriptome and inducesBANCRto regulate melanoma cell migration

(2012) Ross J. Flockhart et al.   GENOME RESEARCH

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

(2012) T. Derrien et al.   GENOME RESEARCH

MEG3 noncoding RNA: a tumor suppressor

(2012) Yunli Zhou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

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

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Colon cancer associated transcript-1: A novel RNA expressed in malignant and pre-malignant human tissues

(2011) Aviram Nissan et al.   INTERNATIONAL JOURNAL OF CANCER

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

Ubiquitin-conjugating enzyme UBE2C: molecular biology, role in tumorigenesis, and potential as a biomarker

(2011) Zhonglin Hao et al.   TUMOR BIOLOGY

Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human

(2011) Patrick Schorderet et al.   PLoS Genetics

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Maite Huarte et al.   CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

(2010) Deepti Malhotra et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

HJURP Is a Cell-Cycle-Dependent Maintenance and Deposition Factor of CENP-A at Centromeres

(2009) Elaine M. Dunleavy et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA