Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

The genome-wide transcriptome profiling of cancerous and normal tissue samples can provide insights into the molecular mechanisms of cancer initiation and progression. RNA Sequencing (RNA-Seq) is a revolutionary tool that has been used extensively in cancer research. However, no existing RNA-Seq database provides all of the following features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential expression and regulatory networks. We have constructed the first public database that meets these criteria, the Cancer RNA-Seq Nexus (CRN, http://syslab4.nchu.edu.tw/CRN). CRN has a user-friendly web interface designed to facilitate cancer research and personalized medicine. It is an open resource for intuitive data exploration, providing coding-transcript/lncRNA expression profiles to support researchers generating new hypotheses in cancer research and personalized medicine.

[1]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[2]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[3]  J. Pietenpol,et al.  p63: Molecular complexity in development and cancer. , 2004, Carcinogenesis.

[4]  Pei-Chun Chang,et al.  CRSD: a comprehensive web server for composite regulatory signature discovery , 2006, Nucleic Acids Res..

[5]  Christopher E Barbieri,et al.  Loss of p63 leads to increased cell migration and up-regulation of genes involved in invasion and metastasis. , 2006, Cancer research.

[6]  Debojyoti Dutta,et al.  Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors , 2006, Bioinform..

[7]  L. Ellisen,et al.  p63 and p73: Life and Death in Squamous Cell Carcinoma , 2006, Cell cycle.

[8]  T. Barrette,et al.  Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. , 2007, Neoplasia.

[9]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[10]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[11]  Graziano Pesole,et al.  Identification and functional characterization of two new transcriptional variants of the human p63 gene , 2009, Nucleic acids research.

[12]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[13]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[14]  John Quackenbush,et al.  GCOD - GeneChip Oncology Database , 2011, BMC Bioinformatics.

[15]  M. Ronaghi,et al.  Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data , 2010, PloS one.

[16]  Takeshi Toyoshima,et al.  Increased ΔNp63 expression is predictive of malignant transformation in oral epithelial dysplasia and poor prognosis in oral squamous cell carcinoma. , 2011, International journal of oncology.

[17]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[18]  Feng Yang,et al.  Long noncoding RNA CCAT1, which could be activated by c-Myc, promotes the progression of gastric carcinoma , 2013, Journal of Cancer Research and Clinical Oncology.

[19]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[20]  Gerd Ritter,et al.  Colon cancer associated transcript‐1: A novel RNA expressed in malignant and pre‐malignant human tissues , 2012, International journal of cancer.

[21]  Ugur Sahin,et al.  RNA-Seq Atlas - a reference database for gene expression profiling in normal tissue by next-generation sequencing , 2012, Bioinform..

[22]  F. Schmitt,et al.  p40: A p63 Isoform Useful for Lung Cancer Diagnosis – A Review of the Physiological and Pathological Role of p63 , 2012, Acta Cytologica.

[23]  Alexander Stojadinovic,et al.  Differential expression of colon cancer associated transcript1 (CCAT1) along the colonic adenoma-carcinoma sequence , 2013, BMC Cancer.

[24]  Giuseppe Pelosi,et al.  p40 (ΔNp63) is superior to p63 for the diagnosis of pulmonary squamous cell carcinoma , 2012, Modern Pathology.

[25]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[26]  L. Pachter,et al.  Streaming fragment assignment for real-time analysis of sequencing experiments , 2012, Nature Methods.

[27]  David C. Rice,et al.  Frequent Coamplification and Cooperation between C-MYC and PVT1 Oncogenes Promote Malignant Pleural Mesothelioma , 2014, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[28]  D. Largaespada,et al.  PVT1 dependence in cancer with MYC copy-number increase , 2014, Nature.

[29]  Yan Liu,et al.  High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method , 2013, Nucleic acids research.

[30]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[31]  Taku Tsukamoto,et al.  8q24 amplified segments involve novel fusion genes between NSMCE2 and long noncoding RNAs in acute myelogenous leukemia , 2014, Journal of Hematology & Oncology.

[32]  Shi-Hua Zhang,et al.  IIIDB: a database for isoform-isoform interactions and isoform network modules , 2015, BMC Genomics.

[33]  Alexander Stojadinovic,et al.  Colon Cancer Associated Transcript-1 (CCAT1) Expression in Adenocarcinoma of the Stomach , 2015, Journal of Cancer.

[34]  D. Karolchik,et al.  The UCSC Genome Browser database: 2016 update , 2015, bioRxiv.

[35]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..