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Improved rat genome gene prediction by integration of ESTs with RNA-Seq information

Liping Li, Enguo Chen, Chun Yang, Jun Zhu, Pushkala Jayaraman, Jeffrey De Pons, Catherine C. Kaczorowski, Howard J. Jacob, Andrew S. Greene, Matthew R. Hodges, Allen W. Cowley, Mingyu Liang (+3 others)
2014 Computer applications in the biosciences : CABIOS  
In this study, we incorporated deep RNA-Seq data from three rat tissues-bone marrow, brain and kidney-with EST data to improve the annotation of the rat genome.  ...  Comparisons of our predicted protein-coding gene sets with those in public datasets suggest that RNA-Seq significantly improves genome annotation and identifies novel genes and isoforms in the rat.  ...  Universities of China.  ... 
doi:10.1093/bioinformatics/btu608 pmid:25217576 pmcid:PMC4296142 fatcat:66zmikhnpbchnjp64yc66v3rhe

Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics

Xiaojing Wang, Bing Zhang
2014 Journal of Proteome Research  
In addition to database searching and protein assembly algorithms, computational approaches have been developed to integrate genomic, transcriptomic, and interactome information to improve peptide and  ...  More recently, with the increasing affordability of the Next Generation Sequencing (NGS) technologies, personalized protein databases derived from sample-specific genomic and transcriptomic data have emerged  ...  from RNA-Seq data can enable the detection of known and novel peptide variants. 49 In an integrated genomics and proteomics analysis of rat liver, variants derived from genome and transcriptome variation  ... 
doi:10.1021/pr500194t pmid:24792918 pmcid:PMC4059263 fatcat:cyd4cxeh6rfpvkb7mptrnw7wby

Forty-Four Novel Protein-Coding Loci Discovered Using a Proteomics Informed by Transcriptomics (PIT) Approach in Rat Male Germ Cells1

Sophie Chocu, Bertrand Evrard, Régis Lavigne, Antoine D. Rolland, Florence Aubry, Bernard Jégou, Frédéric Chalmel, Charles Pineau
2014 Biology of Reproduction  
Sequencing was performed by the IGBMC Microarray and Sequencing platform, member of the France Génomique program.  ...  We thank all members of the SEQanswers forums for helpful advice; Steven Salzberg and Cole Trapnell for continuous support with the Tuxedo suite; and Emmanuelle Com and the PRIDE team for the submission  ...  Nevertheless, the validation of gene products at the peptide level demonstrates the robustness of our integrative strategy and clearly establishes its relevance for the improvement of rat genome annotation  ... 
doi:10.1095/biolreprod.114.122416 pmid:25210130 fatcat:rojyhn4ibzcj7bjiadfoszudyu

Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues

Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu, Dan Xie
2018 BMC Genomics  
Current comparative study of gene regulation between the two species are limited by low quality of gene annotation and lack of regulatory element data on M. fascicularis genome.  ...  Results: In this study, we improved the M. fascicularis gene annotation with 57 gene expression data from multiple tissues and, more importantly, a manual curation procedure.  ...  Availability of data and materials The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive [52] in BIG Data Center [53] , Beijing Institute of Genomics (BIG),  ... 
doi:10.1186/s12864-018-5183-y fatcat:yx6ozted5fatjfohq73ckuecya

The Ensembl gene annotation system

Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri (+12 others)
2016 Database: The Journal of Biological Databases and Curation  
The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models.  ...  The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects.  ...  We also thank the members of the many genome-sequencing consortia that we have worked with for providing genome sequences and supporting data in advance of publication.  ... 
doi:10.1093/database/baw093 pmid:27337980 pmcid:PMC4919035 fatcat:jsnympsq4rczzhh5nupzv5b4ha

Ensembl 2013

Paul Flicek, Ikhlak Ahmed, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil (+43 others)
2012 Nucleic Acids Research  
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat.  ...  Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates  ...  They acknowledge those researchers, organizations and large-scale projects that have provided data to Ensembl before publication under the understandings of the Fort Lauderdale meeting discussing Community  ... 
doi:10.1093/nar/gks1236 pmid:23203987 pmcid:PMC3531136 fatcat:5hwmkwmozbcpbk3bzrzuhwdqhe

Transcriptomics technologies

Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
2017 PLoS Computational Biology  
The information content of an organism is recorded in the DNA of its genome and expressed through transcription.  ...  An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.  ...  Integration of RNA-Seq datasets across different tissues has been used to improve annotation of gene functions in commercially important organisms (e.g., cucumber) [133] or threatened species (e.g.,  ... 
doi:10.1371/journal.pcbi.1005457 pmid:28545146 pmcid:PMC5436640 fatcat:24tzxx6abjdxlgj3vq3ykzbwdy

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

Gloria M. Sheynkman, Michael R. Shortreed, Anthony J. Cesnik, Lloyd M. Smith
2016 Annual Review of Analytical Chemistry  
, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations.  ...  We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.  ...  A.J.C. was supported by National Library of Medicine Training Grant 5T15LM007359, and G.M.S. was supported by National Institutes of Health Training Grant T32CA009361. Literature Cited  ... 
doi:10.1146/annurev-anchem-071015-041722 pmid:27049631 pmcid:PMC4991544 fatcat:pebtnvfkenaktec4jxbdgs635i

Proteogenomics: concepts, applications and computational strategies

Alexey I Nesvizhskii
2014 Nature Methods  
In recent years, owing to the emergence of next generation sequencing technologies such as RNA-Seq and dramatic improvements in the depths and throughput of mass spectrometry-based proteomics, the pace  ...  Proteogenomics is an area of research at the interface of proteomics and genomics.  ...  Acknowledgments This work has been funded in part with US National Institute of Health grant R01-GM-094231.  ... 
doi:10.1038/nmeth.3144 pmid:25357241 pmcid:PMC4392723 fatcat:ldychwshp5fuzoxdlemiydcxda

A comprehensive rat transcriptome built from large scale RNA-seq-based annotation

Xiangjun Ji, Peng Li, James C Fuscoe, Geng Chen, Wenzhong Xiao, Leming Shi, Baitang Ning, Zhichao Liu, Huixiao Hong, Jun Wu, Jinghua Liu, Lei Guo (+9 others)
2020 Nucleic Acids Research  
We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium.  ...  Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively.  ...  Data analysis and interpretation were performed by X.J. and P.L. The RTR online database was designed and constructed by T.S. and X.J.  ... 
doi:10.1093/nar/gkaa638 pmid:32749457 fatcat:t76wuam5srcifh4j3w62y5dzzi

Systems biology approaches in the study of Chinese herbal formulae

Fei-Fei Cai, Wen-Jun Zhou, Rong Wu, Shi-Bing Su
2018 Chinese Medicine  
Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function.  ...  To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and  ...  Acknowledgements The authors extend their appreciation for financial support by the Macao Foundation and International Society of Chinese Medicine.  ... 
doi:10.1186/s13020-018-0221-x pmid:30619503 pmcid:PMC6311004 fatcat:z664ct2tkndthowcekmassense

Exploiting advances in transcriptomics to improve on human-relevant toxicology

Thomas A. DARDE, Frédéric CHALMEL, Terje SVINGEN
2019 Current Opinion in Toxicology  
For instance, single-cell Digital Gene Expression-(DGE-) and single-cell RNA (scRNA-) sequencing techniques hold great promise for not only enabling the analyses of large sample sizes at low cost, but  ...  In turn, lack of mechanistic insight stalls the development of more cost-efficient and highthroughput alternative assays, which is a prerequisite if we are to deal with the large number of untested compounds  ...  This work was partially funded by the French agency for food and safety [ANSES n °EST-13-081 to F.C], the French National Research Agency [ANR n° 16-CE14-0017-02 to F.C], and the Fondation pour la recherche  ... 
doi:10.1016/j.cotox.2019.02.001 fatcat:p6g3hfg7araanafh3w7lnhfzci

From genotype to phenotype in bovine functional genomics

C. S. Pareek, R. Smoczynski, M. Pierzchala, U. Czarnik, A. Tretyn
2011 Briefings in Functional Genomics  
genes are likely to be involved, and improved integrated interactive database.  ...  With the availability of full bovine genomic sequence, yet we still have a lot of daunting tasks on 'genotype-to-phenotype problem' particularly about the phenotypic variations and trying to predict what  ...  Genome annotation is the process of attaching biological information to sequence identifying elements on the genome (gene prediction) and attaching biological information to these elements.  ... 
doi:10.1093/bfgp/elr019 pmid:21628315 fatcat:edfsc3fdozeo3lo4b3fqahxnsa

Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus

Xi Wang, Xintian You, Julian D. Langer, Jingyi Hou, Fiona Rupprecht, Irena Vlatkovic, Claudia Quedenau, Georgi Tushev, Irina Epstein, Bernhard Schaefke, Wei Sun, Liang Fang (+4 others)
2019 Nature Communications  
Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons.  ...  Gene annotation is a critical resource in genomics research.  ...  This work was also partially supported by Center for Computational Science and Engineering of Southern University of Science and Technology for providing the high-performance computational infrastructure  ... 
doi:10.1038/s41467-019-13037-0 pmid:31676752 pmcid:PMC6825209 fatcat:zdejjv4cabgqhpiw3t3ofsssbe

Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

Yuming Zhao, Fang Wang, Su Chen, Jun Wan, Guohua Wang
2017 BioMed Research International  
MicroRNAs (miRNAs) are short (~22 nucleotides) noncoding RNAs and disseminated throughout the genome, either in the intergenic regions or in the intronic sequences of protein-coding genes.  ...  This review summarized several most popular miRNA promoter prediction models which used genome sequence features, or other features, for example, histone markers, RNA Pol II binding sites, and nucleosome-free  ...  Acknowledgments This work was supported by the State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University) (201207), the Fundamental Research Funds for the Central Universities (  ... 
doi:10.1155/2017/7049406 pmid:28656148 pmcid:PMC5474535 fatcat:scxls2ntcjdeppcpznygucwnrm
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