CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine

Keywords

Biology, ENCODE, Computational biology, Support vector machine, Coding region

References

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• RNA regulation: a new genetics?John S. Mattick — 2004
• Non–coding RNA genes and the modern RNA worldSean R. Eddy — 2001
• Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural propertiesН. В. Петрова, Cathy Wu — 2006
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• An SVM-based system for predicting protein subnuclear localizationsZhengdeng Lei, Yang Dai — 2005
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• A Guide to the Mammalian GenomeYasushi Okazaki, David Hume — 2003
• Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNAMartin C. Frith, Timothy L. Bailey, Takeya Kasukawa — 2006
• Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector MachinesJinfeng Liu, Julian Gough, Burkhard Rost — 2006
• Rfam: annotating non-coding RNAs in complete genomesSam Griffiths‐Jones — 2004
• CDS annotation in full-length cDNA sequence.Masaaki Furuno, Takeya Kasukawa, Rintaro Saito — 2003
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• Support vector machine classification and validation of cancer tissue samples using microarray expression dataTerrence S. Furey, Nello Cristianini, Nigel Duffy — 2000
• A hitchhiker's guide to expressed sequence tag (EST) analysisShivashankar H. Nagaraj, Robin B. Gasser, Shoba Ranganathan — 2006
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• Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.Piero Carninci, Kazunori Waki, Toshiyuki Shiraki — 2003

Cited by

• Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse実也 濱本 — 2010
• Human long non‐coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factorsLuis Ángel Ortiz de Pinedo Salazar — 2011
• Discovery and functional characterization of cardiovascular long noncoding RNAs.Brent N. Reed — 2015
• De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.瑠美子 野口 — 2015
• Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomesİsmet Baran, Cem C. Tutum, Jesper Henri Hattel — 2016
• Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxinДашиева Соелма Цырен-Дашиевна — 2017
• A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory NeuropathiesMiguel Rodríguez-Piñero y Bravo-Ferrer — 2016
• Transcriptome analysis of Callery pear (Pyrus calleryana) reveals a comprehensive signalling network in response to Alternaria alternataMartín Enrique Durán-García, Emilse Durán-Aponte — 2017
• Expression status and clinical significance of lncRNA APPAT in the progression of atherosclerosisAngosto Vélez, Pedro Luís — 2018
• Genome sequence of the progenitor of wheat A subgenome Triticum urartuMiguel Ángel Caamaño Anido — 2018
• Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infectionFélix Cariñanos San Millán — 2018
• Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle ‘degradome’ of rainbow troutГ. Н. Лищина — 2018
• Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stressPatrick Toumba Haman — 2018
• Hybrid sequencing-based personal full-length transcriptomic analysis implicates proteostatic stress in metastatic ovarian cancerMark Rodgers, Miqdad Asaria, Scott E. Walker — 2019
• Genome-wide analysis of long noncoding RNA and mRNA profiles in PRRSV-infected porcine alveolar macrophages.小泉直彦, 河村豊 — 2020
• Long non-coding RNA and circular RNA and coding RNA profiling of plasma exosomes of osteosarcoma by RNA seqDaniel J. Luchins — 2023
• Identification of a long non-coding RNA gene, growth hormone secretagogue receptor opposite strand, which stimulates cell migration in non-small cell lung cancer cell lines.Eliza Whiteside, Inge Seim, JANA P. PAULI — 2013
• Long non-coding RNAs in innate and adaptive immunityThomas M. Aune, Charles F. Spurlock — 2015
• Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencingM. Muthusamy, S. Uma, S. Backiyarani — 2015
• Study strategies for long non-coding RNAs and their roles in regulating gene expressionDan Qin, Cunshuan Xu — 2015

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