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Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
2006
BMC Bioinformatics
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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
2003
Genome Research
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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
2007
Nucleic Acids Research
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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
2003
Current Opinion in Oncology
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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
2015
BMC Plant Biology
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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
2011
Chinese Science Bulletin
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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
2004
Genomics
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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
2004
BMC Genomics
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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
2008
Genome Biology
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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
2010
Physiological Genomics
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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
2009
PLoS ONE
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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
2009
Genome Biology
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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
2011
Nature Precedings
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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
2011
Nature Precedings
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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
2007
Genome Research
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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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