Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features

A Long Noncoding RNA Activated by TGF-β Promotes the Invasion-Metastasis Cascade in Hepatocellular Carcinoma

(2014) Ji-hang Yuan et al.   CANCER CELL

Identification and analysis of large intergenic non-coding RNAs regulated by p53 family members through a genome-wide analysis of p53-binding sites

(2014) Masashi Idogawa et al.   HUMAN MOLECULAR GENETICS

Inferring novel lncRNA–disease associations based on a random walk model of a lncRNA functional similarity network

(2014) Jie Sun et al.   Molecular BioSystems

Novel human lncRNA–disease association inference based on lncRNA expression profiles

(2013) Xing Chen et al.   BIOINFORMATICS

The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer

(2013) Xiang-hua Liu et al.   BMC CANCER

Long non-coding RNAs: A new frontier in the study of human diseases

(2013) Xuefei Shi et al.   CANCER LETTERS

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway

(2013) Guohui Wan et al.   CELLULAR SIGNALLING

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: A case study of glioblastoma

(2013) Y. Xiao et al.   NEURO-ONCOLOGY

HMDD v2.0: a database for experimentally supported human microRNA and disease associations

(2013) Yang Li et al.   NUCLEIC ACIDS RESEARCH

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

The Noncoding RNA Expression Profile and the Effect of lncRNA AK126698 on Cisplatin Resistance in Non-Small-Cell Lung Cancer Cell

(2013) Yong Yang et al.   PLoS One

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

(2013) Alayne L Brunner et al.   GENOME BIOLOGY

Active Immunization Against Tumor Necrosis Factor-alpha Decreases Proinflammatory Cytokines, Oxidative Stress Mediators and Adhesion Molecules Risk Factors in Streptozotocin-induced Diabetic Rats

(2013) Muobarak Tuorkey et al.   Endocrine Metabolic & Immune Disorders-Drug Targets

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

(2012) Femke Simmer et al.   Epigenetics

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark 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

miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer

(2012) Katarzyna Augoff et al.   Molecular Cancer

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

(2012) Markus Kretz et al.   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

(2012) Andrew Keniry et al.   NATURE CELL BIOLOGY

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

Cis-acting noncoding RNAs: friends and foes

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long non-coding RNA expression profiles predict clinical phenotypes in glioma

(2012) Xiaoqin Zhang et al.   NEUROBIOLOGY OF DISEASE

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Prioritizing cancer-related key miRNA–target interactions by integrative genomics

(2012) Yun Xiao et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks

(2012) Xingli Guo et al.   NUCLEIC ACIDS RESEARCH

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

Noncoder: a web interface for exon array-based detection of long non-coding RNAs

(2012) Pascal Gellert et al.   NUCLEIC ACIDS RESEARCH

Prostate Cancer Cell Surface-Associated Keratin 8 and Its Implications for Enhanced Plasmin Activity

(2012) Melissa Hirsch Kuchma et al.   PROTEIN JOURNAL

Macro lncRNAs

(2012) Philipp M. Guenzl et al.   RNA Biology

Non-coding RNAs: key regulators of mammalian transcription

(2012) Jennifer F. Kugel et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome-wide DNA methylation profiling of non-small cell lung carcinomas

(2012) Rejane Carvalho et al.   Epigenetics & Chromatin

Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

(2011) Guangfu Jin et al.   CARCINOGENESIS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

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

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

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(2011) A. Feber et al.   GENOME RESEARCH

Differential expression pattern-based prioritization of candidate genes through integrating disease-specific expression data

(2011) Yun Xiao et al.   GENOMICS

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

(2011) Ci Chu et al.   MOLECULAR CELL

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

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

Human Cancer Long Non-Coding RNA Transcriptomes

(2011) Ewan A. Gibb et al.   PLoS One

Exploring long non-coding RNAs through sequencing

(2011) Sophie R. Atkinson et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

E3 ubiquitin protein ligase, E6-associated protein (E6-AP) regulates PI3K-Akt signaling and prostate cell growth

(2010) Sathish Srinivasan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2010) Maite Huarte et al.   CELL

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

(2010) Jing Zhao et al.   MOLECULAR CELL

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim 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

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs

(2010) Amit N. Khachane et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

TGFβ in Cancer

(2008) Joan Massagué   CELL