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Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

Rodrigo Malig, Cristian Varela, Eduardo Agosin, Francisco Melo
2006 BMC Bioinformatics  
In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE).  ...  We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments.  ...  Acknowledgements We acknowledge José Tomás Eterovic and Alejandro Panjkovich for the writing of some computer scripts to parse data. We are also grateful to M.S.  ... 
doi:10.1186/1471-2105-7-487 pmid:17083742 pmcid:PMC1637119 fatcat:sehi2xspdzdhhb4owkgwcm5mkm

Assessment of SAGE in Transcript Identification

E. D. Pleasance
2003 Genome Research  
An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag.  ...  This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing tag-to-gene mappings for two model organisms.  ...  We gratefully acknowledge the support of the BC Cancer Agency and the BC Cancer Foundation. The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.873003 pmid:12743019 pmcid:PMC403648 fatcat:xnbew47zqrg2jng3grpcp3hkhe

SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation

T. Norambuena, R. Malig, F. Melo
2007 Nucleic Acids Research  
We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE).  ...  of gene expression and gene discovery.  ...  ACKNOWLEDGEMENTS This work was funded by grants 1050688, 1070357 and 1051112 from FONDECYT.  ... 
doi:10.1093/nar/gkm429 pmid:17626053 pmcid:PMC1933165 fatcat:mgrudicf6bd2nklx75jd5psp74

Serial analysis of gene expression and cancer

Heiko Hermeking
2003 Current Opinion in Oncology  
The author apologizes to colleagues whose articles were not cited because of space limitations. References and recommended reading  ...  Acknowledgments The author thanks Kornelia Polyak, Victor Velculescu, Greg Riggins, and the members of the Molecular Oncology laboratory at the Max-Planck-Institute of Biochemistry for comments and critical  ...  A 14-bp to 15-bp tag can unambiguously identify cDNAs, whereas it is not sufficient to map a gene in the genome precisely.  ... 
doi:10.1097/00001622-200301000-00006 pmid:12490760 fatcat:qzwonj4wovam3m27rxeddxhbqe

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids

Jinjin Jiang, Yue Wang, Bao Zhu, Tingting Fang, Yujie Fang, Youping Wang
2015 BMC Plant Biology  
The unambiguous tag-mapped genes in the libraries were compared.  ...  In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome.  ...  14KJB210008), the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Innovation Team of Yangzhou University, China.  ... 
doi:10.1186/s12870-015-0417-5 pmid:25623840 pmcid:PMC4312607 fatcat:yvkbwt4ofvhpjf6adcom5guifi

Comparative profiling of the transcriptional response to soybean cyst nematode infection of soybean roots by deep sequencing

XiaoYan Li, Xue Wang, ShaoPeng Zhang, DaWei Liu, YuXi Duan, Wei Dong
2011 Chinese Science Bulletin  
To gain insight into the changes in the transcriptome of soybean roots during soybean cyst nematode (SCN) infection, we conducted genome-wide gene expression profiling using serial analysis of gene expression  ...  Approximately 7% of tags mapped to the antisense strand of genes, indicating widespread antisense transcription.  ...  This work was supported by the National Natural Science Foundation of China (30392100).  ... 
doi:10.1007/s11434-011-4510-3 fatcat:tsuyntn7ircqtdewjrxf3r6l6u

A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips

Jun Lu, Anita Lal, Barry Merriman, Stan Nelson, Gregory Riggins
2004 Genomics  
Although SAGE and Affymetrix chip expression levels showed a significant correlation using the set of genes for which there was reliable and unambiguous mapping from tag-to-gene identification, correlation  ...  A quantitative analysis comparing the use of 10-bp SAGE tags to 17-bp SAGE tags indicated that the short SAGE technology was more efficient at identifying differentially expressed tags.  ...  Sherman Research Professorship in Neurosurgery (to G.J.R.).  ... 
doi:10.1016/j.ygeno.2004.06.014 pmid:15475240 fatcat:ne2h3ov7wncatky5qgdyy2xlfi

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

Matthias B Wahl, Randolph B Caldwell, Andrzej M Kierzek, Hiroshi Arakawa, Eduardo Eyras, Nina Hubner, Christian Jung, Manuel Soeldenwagner, Manuela Cervelli, Yan-Dong Wang, Volkmar Liebscher, Jean-Marie Buerstedde
2004 BMC Genomics  
We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000  ...  The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software  ...  Acknowledgments This work was supported by the EU grants 'Genetics in a cell line' and 'Mechanisms of gene integration'. We would like to thank Kenji Imai for stimulating discussion.  ... 
doi:10.1186/1471-2164-5-98 pmid:15610564 pmcid:PMC543457 fatcat:n6kxthrvwrdmfi662bnwz3wtqu

Identification of transcripts with enriched expression in the developing and adult pancreas

Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven JM Jones, Marco A Marra, Cheryl D Helgason
2008 Genome Biology  
We validated the clusters first using quantitative real time PCR and then by analyzing the Theiler stage 22 pancreas in situ hybridization staining patterns of over 600 of the identified genes using the  ...  Results: We used a specificity metric to identify 2,536 tags with pancreas-enriched expression compared to 195 other mouse SAGE libraries.  ...  We would also like to thank Genome BC for their assistance in project management and the staff of the Animal Resource Center at the BBCRC.  ... 
doi:10.1186/gb-2008-9-6-r99 pmid:18554416 pmcid:PMC2481431 fatcat:f5ltas7xlnayboqaji7usje2zy

Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal

Pavle Vrljicak, Alex C. Y. Chang, Olena Morozova, Elizabeth D. Wederell, Kyle Niessen, Marco A. Marra, Aly Karsan, Pamela A. Hoodless
2010 Physiological Genomics  
Four Serial Analysis of Gene Expression libraries were generated and analyzed from the mouse atrio-ventricular canal (AVC) at embryonic days 9.5-12.5, covering the stages from initiation of endothelial  ...  These results identify molecular signatures that distinguish different phases of early heart valve formation allowing gene expression and function to be further investigated.  ...  ACKNOWLEDGMENTS The authors are grateful to Li Cai (Rutgers University) for providing the Java implementation of the PoissonC k-means clustering algorithm and to Drs.  ... 
doi:10.1152/physiolgenomics.00142.2009 pmid:19952280 pmcid:PMC2825764 fatcat:pxaiizmim5aypb2yemqgrpl6xq

Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling

Nicola Palmieri, Christian Schlötterer, Rodolfo Aramayo
2009 PLoS ONE  
Methodology/Principal Findings: We performed an in silico analysis to evaluate whether incorrect mapping of the sequence reads results in a biased expression pattern.  ...  In humans, about 10% of the genes had fewer than 50% of the sequence reads correctly mapped. Sequence polymorphism up to 9% had almost no effect on the mapping accuracy of 100 bp reads.  ...  Acknowledgments We are thankful to the members of the Institute of Population Genetics for helpful discussion and comments on the manuscript.  ... 
doi:10.1371/journal.pone.0006323 pmid:19636379 pmcid:PMC2712089 fatcat:bosypmxe3na2zjz7afjfukczpe

Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

Fernando Faunes, Natalia Sánchez, Javier Castellanos, Ismael A Vergara, Francisco Melo, Juan Larraín
2009 Genome Biology  
In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression  ...  Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods.  ...  Acknowledgements We thank R Gutiérrez, GH Olivares, E Contreras, P Astudillo and C Iturriaga for critical reading of the manuscript.  ... 
doi:10.1186/gb-2009-10-2-r15 pmid:19210784 pmcid:PMC2688288 fatcat:yfygrkltlng6pcc4gg6ivawn2m

Advancing transcriptome platforms

Shuobo Shi, Shuobo Shi
2011 Nature Precedings  
Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome.  ...  Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently  ...  Serial analysis of gene expression (SAGE) is a method that could both qualitatively and quantitatively evaluate the expression of thousands of genes simultaneously by sequencing the tagged cDNA fragments  ... 
doi:10.1038/npre.2011.5894 fatcat:3fyzpnkd5rhqrf4jjq5eufe6ey

Advancing transcriptome platforms

Shuobo Shi, Shuobo Shi
2011 Nature Precedings  
Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome.  ...  Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently  ...  Serial analysis of gene expression (SAGE) is a method that could both qualitatively and quantitatively evaluate the expression of thousands of genes simultaneously by sequencing the tagged cDNA fragments  ... 
doi:10.1038/npre.2011.5894.1 fatcat:bvqyg346mnbwdmcxsqnqfxbg54

Gene expression profiling by massively parallel sequencing

T. T. Torres, M. Metta, B. Ottenwalder, C. Schlotterer
2007 Genome Research  
Gene expression measurements generated by restriction analysis and nebulization for fragments within the 80-to 300-bp range showed correlations similar to those reported for replicated microarray experiments  ...  (0.83-0.91); 97% of the cDNA fragments could be unambiguously mapped to the genomic DNA, demonstrating the advantage of longer sequence reads.  ...  This work was supported by Fonds zur Förderung der wissenschaftlichen Forschung grants to C.S. and a fellowship of the Brazilian National Council for Scientific and Technological Development (CNPq) to  ... 
doi:10.1101/gr.6984908 pmid:18032722 pmcid:PMC2134766 fatcat:xt5qsjmjpjfwtbypk77gkybubq
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