Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

(2018) Hua-Sheng Chiu et al.   Cell Reports

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis

(2016) Massimiliano Mellone et al.   Aging-US

lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes

(2016) Yining Liu et al.   BIOINFORMATICS

Cancer-associated fibroblasts promote hepatocellular carcinoma metastasis through chemokine-activated hedgehog and TGF-β pathways

(2016) Jiao Liu et al.   CANCER LETTERS

Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer

(2016) Youyou Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Secretome profiling of oral squamous cell carcinoma-associated fibroblasts reveals organization and disassembly of extracellular matrix and collagen metabolic process signatures

(2016) Elizabete Bagordakis et al.   TUMOR BIOLOGY

Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

(2016) Arghavan Ashouri et al.   Nature Communications

Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer

(2016) Youyou Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers

(2016) James R. Bradford et al.   Oncotarget

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

(2016) Chan Zhou et al.   Genome Medicine

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer

(2015) Jun Li et al.   CANCER RESEARCH

The landscape of antisense gene expression in human cancers

(2015) O. Alejandro Balbin et al.   GENOME RESEARCH

Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology

(2015) Zhouwei Zhang et al.   JOURNAL OF CLINICAL PATHOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Christopher R Cabanski et al.   RNA Biology

Fra-1/AP-1 induces EMT in mammary epithelial cells by modulating Zeb1/2 and TGFβ expression

(2014) L Bakiri et al.   CELL DEATH AND DIFFERENTIATION

Molecular mechanisms of epithelial–mesenchymal transition

(2014) Samy Lamouille et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptional regulatory functions of nuclear long noncoding RNAs

(2014) Keith W. Vance et al.   TRENDS IN GENETICS

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

(2014) C. Wilks et al.   Database-The Journal of Biological Databases and Curation

Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cancer

(2013) Kristina P. Sørensen et al.   BREAST CANCER RESEARCH AND TREATMENT

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Cancer-Associated Fibroblasts from Hepatocellular Carcinoma Promote Malignant Cell Proliferation by HGF Secretion

(2013) Chang-Chang Jia et al.   PLoS One

RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib

(2013) James R. Bradford et al.   PLoS One

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

MEG3 noncoding RNA: a tumor suppressor

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

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers

(2011) R. Kogo et al.   CANCER RESEARCH

Interactions between cancer stem cells and their niche govern metastatic colonization

(2011) Ilaria Malanchi 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

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

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

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

(2010) Sabine Loewer et al.   NATURE GENETICS

Recurrent intrathoracic thymomas: Potential prognostic importance of cell-cycle protein expression

(2009) Tommaso C. Mineo et al.   JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY

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

(2009) Mitchell Guttman et al.   NATURE

A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer

(2009) Pierre Farmer et al.   NATURE MEDICINE

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Cancer associated fibroblasts in cancer pathogenesis

(2009) Omar E. Franco et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Chromatin Immunoprecipitation on Microarray Analysis of Smad2/3 Binding Sites Reveals Roles of ETS1 and TFAP2A in Transforming Growth Factor   Signaling

(2008) D. Koinuma et al.   MOLECULAR AND CELLULAR BIOLOGY