Cited by 634Genomics and Phylogenetic StudiesGene expression and cancer classificationRNA Research and Splicing

The DOI matches its Crossref record; 19 of the 20 references it cites were found in a registry or an index.

Using the transcriptome to annotate the genome

Saha, Saurabh, Sparks, Andrew B., Rago, Carlo, Akmaev, Viatcheslav, Wang, Clarence J., Vogelstein, Bert, Kinzler, Kenneth W., Velculescu, Victor E.·2002·Nature Biotechnology

DOI 10.1038/nbt0502-508

Open this paper in CoChat — free account

Abstract

A remaining challenge for the human genome project involves the identification and annotation of expressed genes. The public and private sequencing efforts have identified approximately 15,000 sequences that meet stringent criteria for genes, such as correspondence with known genes from humans or other species, and have made another approximately 10,000-20,000 gene predictions of lower confidence, supported by various types of in silico evidence, including homology studies, domain searches, and ab initio gene predictions. These computational methods have limitations, both because they are unable to identify a significant fraction of genes and exons and because they are unable to provide definitive evidence about whether a hypothetical gene is actually expressed. As the in silico approaches identified a smaller number of genes than anticipated, we wondered whether high-throughput experimental analyses could be used to provide evidence for the expression of hypothetical genes and to reveal previously undiscovered genes. We describe here the development of such a method--called long serial analysis of gene expression (LongSAGE), an adaption of the original SAGE approach--that can be used to rapidly identify novel genes and exons.

Integrity signals

Registry

Crossref · 10.1038/nbt0502-508

Cites

19 of 19 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Prediction of complete gene structures in human genomic DNA
Burge, C., & Karlin, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0951 · Cited by 4,211
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713
Self-citation
A model for p53-induced apoptosis
Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., & Vogelstein, B. (1997) · Nature · doi:10.1038/38525 · Cited by 2,500
Self-citation
The DNA sequence of human chromosome 22
Dunham, I., Hunt, A. R., Collins, J. E., Bruskiewich, R., Beare, D. M., Clamp, M. E., Smink, L. J., Ainscough, R., Almeida, J. P., Babbage, A., et al. (1999) · Nature · doi:10.1038/990031 · Cited by 1,147
Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
Adams, Kerlavage, A. R., Fleischmann, R. D., Ra, F., Cj, B., Lee, N., Ef, K., Kg, W., Gocayne, J. D., & White, O. R. (1995) · PubMed · Cited by 793
Analysis of human transcriptomes
Velculescu, V. E., Madden, S. L., Zhang, L., Lash, A., Yu, J., Rago, C., Lal, A., Wang, C. J., Beaudry, G. A., Ciriello, K. M., et al. (1999) · Nature Genetics · doi:10.1038/70487 · Cited by 775
Self-citation
The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
Caron, H. N., van Schaik, B. D. C., van der Mee, M., Baas, F., Riggins, G. J., Sluis, P. V., Hermus, M.-C., van Asperen, R., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 730
Experimental annotation of the human genome using microarray technology
Shoemaker, D. D., Schadt, E. E., Armour, C. D., He, Y. D., Garrett-Engele, P. W., MCDONAGH, P. D., Loerch, P., Leonardson, A. S., Lum, P. Y., Cavet, G., et al. (2001) · Nature · doi:10.1038/35057141 · Cited by 440

Flagged first, then by citations

Show all 20 references

1 of the 20 references couldn’t be matched to a known paper.

Sorted by citations

Items 201–300 of 634

Expression of Extracellular Matrix Proteins in Ovarian Serous Tumors
Salani, R., Neuberger, I., Kurman, R. J., Bristow, R. E., Chang, H., Wang, T., & Shih, I. (2007) · International Journal of Gynecological Pathology · doi:10.1097/01.pgp.0000229994.02815.f9 · Cited by 40
A comparative analysis of transcript abundance using SAGE and Affymetrix arrays
Ibrahim, A. F. M., Hedley, P. E., Cardle, L., Kruger, W. M., Marshall, D., Muehlbauer, G. J., & Waugh, R. (2005) · Functional & Integrative Genomics · doi:10.1007/s10142-005-0135-4 · Cited by 40
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
Khattra, J., Delaney, A. D., Zhao, Y., Siddiqui, A., Asano, J., McDonald, H., Pandoh, P., Dhalla, N., Prabhu, A.-L., Ma, K., et al. (2007) · Genome Research · doi:10.1101/gr.5488207 · Cited by 40
Towards unambiguous transcript mapping in the allotetraploid Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.
Parkin, I. A. P., Clarke, W. E., Sidebottom, C. H. D., Zhang, W., Robinson, S. J., Links, M. G., Karcz, S. R., Higgins, E. E., Fobert, P. R., & Sharpe, A. (2010) · Genome · doi:10.1139/g10-053 · Cited by 39
Serial Analysis of Gene Expression Identifies Connective Tissue Growth Factor Expression as a Prognostic Biomarker in Gallbladder Cancer
Alvarez, H., Corvalán, A. H., Roa, J. C., Argani, P., Murillo, F., Edwards, J. B., Beaty, R. M., Feldmann, G., Hong, S., Mullendore, M. E., et al. (2008) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-07-1991 · Cited by 38
Serial analysis of gene expression
Hu, M., & Polyák, K. (2006) · Nature Protocols · doi:10.1038/nprot.2006.269 · Cited by 39
DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Zhernakova, D. V., de Klerk, E., Westra, H.-J., Mastrokolias, A., Amini, S., Ariyürek, Y., Jansen, R., Penninx, B. W. J. H., Hottenga, J., Willemsen, G. A. H. M., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003594 · Cited by 38
Differential microRNA Expression and Regulation in the Rat Model of Post-Infarction Heart Failure
Liu, X., Meng, H., Jiang, C., Yang, S., Cui, F., & Yang, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160920 · Cited by 36
Noncoding RNAs
Makarova, J. A., & Kramerov, D. A. (2007) · Biochemistry (Moscow) · doi:10.1134/s0006297907110016 · Cited by 36
Biomarkers of Oxidative Stress
Lowe, F. (2014) · Springer eBooks · doi:10.1007/978-3-642-30018-9_4 · Cited by 37
Detecting novel low-abundant transcripts in Drosophila
Lee, S., Bao, J., Zhou, G., Shapiro, J. A., Xu, J., Shi, R., Lu, X., Clark, T., Johnson, D. S., Kim, Y. C., et al. (2005) · RNA · doi:10.1261/rna.7239605 · Cited by 36
Transcriptomic and Metabolomic Approaches to the Analysis of Plant Freezing Tolerance and Cold Acclimation
Hincha, D. K., Espinoza, C., & Zuther, E. (2012) · Wiley eBooks · doi:10.1002/9783527632930.ch11 · Cited by 34
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Rallapalli, G., Kemen, E. M., Robert‐Seilaniantz, A., Segonzac, C., Etherington, G., Sohn, K. H., MacLean, D., & Jones, J. D. G. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-341 · Cited by 34
Next Generation Genome Sequencing
Janitz, M. (2008) · Wiley eBooks · doi:10.1002/9783527625130 · Cited by 35
Comparative transcriptomic characterization of the eyestalk in Pacific white shrimp (Litopenaeus vannamei) during ovarian maturation
Wang, Z., Luan, S., Meng, X., Cao, B., Luo, K., & Kong, J. (2019) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2019.01.002 · Cited by 34
Functional genomic methodologies
Ginsberg, S. D., & Mirnics, K. (2006) · Progress in brain research · doi:10.1016/s0079-6123(06)58002-1 · Cited by 34
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome
Hanriot, L., Keime, C., Gay, N., Faure, C., Dossat, C., Wincker, P., Scoté-Blachon, C., Peyron, C., & Gandrillon, O. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-418 · Cited by 34
Lipopolysaccharide-inducible Gene Expression Profile in Human Monocytes
Hashimoto, S., Morohoshi, K., Suzuki, T., & Matsushima, K. (2003) · Scandinavian Journal of Infectious Diseases · doi:10.1080/00365540310015926 · Cited by 34
Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)
Taft, A. S., Vermeire, J. J., Bernier‐Latmani, J., Birkeland, S., Cipriano, M. J., Papa, A. R., McArthur, A. G., & Yoshino, T. P. (2009) · Parasitology · doi:10.1017/s0031182009005733 · Cited by 34
Expression profiling using a hexamer-based universal microarray
Roth, M. E., Feng, L., McConnell, K. J., Schaffer, P. J., Guerra, C. E., Affourtit, J. P., Piper, K. R., Guccione, L., Hariharan, J., Ford, M. J., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt948 · Cited by 34
aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells
Heidenblut, A. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh130 · Cited by 34
Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights
Khudyakov, J. I., Preeyanon, L., Champagne, C. D., Ortiz, R. M., & Crocker, D. E. (2015) · BMC Genomics · doi:10.1186/s12864-015-1253-6 · Cited by 33
Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults
Ruzanov, P., Riddle, D. L., Marra, M. A., McKay, S., & Jones, S. M. (2007) · Experimental Gerontology · doi:10.1016/j.exger.2007.04.002 · Cited by 33
Genomic Signature Tags (GSTs): A System for Profiling Genomic DNAPreprint
Dunn, J. J., McCorkle, S., Praissman, L. A., Hínd, G., van der Lelie, D., Bahou, W. F., Gnatenko, D. V., & Krause, M. K. (2002) · Genome Research · doi:10.1101/gr.306102 · Cited by 33
Global Expression Analysis Revealed Novel Gender-Specific Gene Expression Features in the Blood Fluke Parasite Schistosoma japonicum
Piao, X., Cai, P., Liu, S., Hou, N., Hao, L., Yang, F., Wang, H., Wang, J., Jin, Q., & Chen, Q. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018267 · Cited by 31
Immunoproteasome Overexpression Underlies the Pathogenesis of Thyroid Oncocytes and Primary Hypothyroidism: Studies in Humans and Mice
Kimura, H. J., Chen, C. Y., Tzou, S.-C., Rocchi, R., Landek‐Salgado, M. A., Suzuki, K., Kimura, M., Rose, N. R., & Caturegli, P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007857 · Cited by 31
Reverse Serial Analysis of Gene Expression (SAGE) Characterization of Orphan SAGE Tags from Human Embryonic Stem Cells Identifies the Presence of Novel Transcripts and Antisense Transcription of Key Pluripotency Genes
Richards, M., Tan, S., Chan, W., & Bongso, A. (2006) · Stem Cells · doi:10.1634/stemcells.2005-0304 · Cited by 31
Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: evidence for nonrandom gene order
Divina, P., Vlček, Č., Strnad, P., Pačes, V., & Forejt, J. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-29 · Cited by 31
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
Chiu, K. P., Wong, C., Chen, Q., Ariyaratne, P. N., Ooi, H., Wei, C., Sung, W.-K. K., & Ruan, Y. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-390 · Cited by 31
Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictionsPreprint
Naval-Sánchez, M., Potier, D., Haagen, L., Sánchez, M., Munck, S., de Sande, B. V., Casares, F., Christiaens, V., & Aerts, S. (2012) · Genome Research · doi:10.1101/gr.140426.112 · Cited by 31
Toxicity and Safety Evaluation of Nanoclays
Brandelli, A. (2018) · Springer eBooks · doi:10.1007/978-3-030-05144-0_4 · Cited by 30
Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.
Liu, Y., Munro, D., Layfield, D., Dellinger, A. E., Walter, J. W., Peterson, K. M., Rickman, C. B., Allingham, R. R., & Hauser, M. A. (2011) · Europe PMC (PubMed Central) · Cited by 30
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
Philippe, N., Boureux, A., Bréhélin, L., Tarhio, J., Commes, T., & Rivals, É. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp492 · Cited by 30
Magnaporthe griseaInfection Triggers RNA Variation and Antisense Transcript Expression in Rice
Gowda, M., Venu, R. C., Li, H., Jantasuriyarat, C., Chen, S., Bellizzi, M. D. R., Pampanwar, V., Kim, H., Dean, R. A., Stahlberg, E. A., et al. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.095653 · Cited by 30
Molecular approaches to diagnosing nutritional physiology in harmful algae: Implications for studying the effects of eutrophication
Dyhrman, S. T. (2008) · Harmful Algae · doi:10.1016/j.hal.2008.08.016 · Cited by 29
Primer on Medical Genomics Part II: Background Principles and Methods in Molecular Genetics
Tefferi, A., Wieben, E. D., Dewald, G. W., Whiteman, D. A. H., Bernard, M., & Spelsberg, T. C. (2002) · Mayo Clinic Proceedings · doi:10.4065/77.8.785 · Cited by 29
Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development
Yang, Y., Wang, J., Han, T., Liu, T., Wang, C., Xiao, J., Mu, C., Li, R., Yu, F., & Shi, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138862 · Cited by 29
Self-citation
Biomarkers and Effects
Hampel, M., Blasco, J., & Díaz, M. L. M. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-803371-5.00005-9 · Cited by 32
Fungal transcriptomics
Bhadauria, V., Popescu, L., Zhao, W., & Peng, Y. (2007) · Microbiological Research · doi:10.1016/j.micres.2007.06.006 · Cited by 28
Transcriptional analysis and functional genomics in wheat
Leader, D. J. (2005) · Journal of Cereal Science · doi:10.1016/j.jcs.2004.10.006 · Cited by 28
Norepinephrine transport-mediated gene expression in noradrenergic neurogenesis
Hu, Y. F., Caron, M. G., & Sieber‐Blum, M. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-151 · Cited by 28
Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE
Dong, H. F., Ge, X., Shen, Y., Chen, L., Kong, Y., Zhang, H., Man, X., Tang, L. V., Yuan, H., Wang, H., et al. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-5 · Cited by 28
Digital Transcript Profile Analysis with aRNA-LongSAGE Validates FERMT1 As a Potential Novel Prognostic Marker for Colon Cancer
Fan, J., Yan, D., Teng, M., Tang, H., Zhou, C., Wang, X., Li, D., Qiu, G., & Peng, Z. (2011) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-10-2552 · Cited by 28
Transcriptional Profiling of γδ T Cells
Hedges, J. F., Graff, J. C., & Jutila, M. A. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.171.10.4959 · Cited by 28
LongSAGE profiling of nine human embryonic stem cell lines
Hirst, M., Delaney, A. D., Rogers, S. A., Schnerch, A., Persaud, D. R., O’Connor, M. D., Zeng, T., Moksa, M., Fichter, K., Mah, D. G., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r113 · Cited by 28
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human
Zhang, Z., Pang, A. W. C., & Gerstein, M. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s14 · Cited by 28
LongSAGE analysis of the early response to cold stress in Arabidopsis leaf
Byun, Y., Kim, H., & Lee, D.-H. (2009) · Planta · doi:10.1007/s00425-009-0903-9 · Cited by 27
Differential gene expression analysis in ageing muscle and drug discovery perspectives
Melouane, A., Ghanemi, A., Aubé, S., Yoshioka, M., & St‐Amand, J. (2017) · Ageing Research Reviews · doi:10.1016/j.arr.2017.10.006 · Cited by 28
Multiple Facets of Marine Invertebrate Conservation Genomics
Lopez, J. V., Kamel, B., Medina, M., Collins, T. M., & Baums, I. B. (2018) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115034 · Cited by 29
Development of a DNA Barcode Tagging Method for Monitoring Dynamic Changes in Gene Expression by using an Ultra High-Throughput Sequencer
Maeda, N., Nishiyori, H., Nakamura, M., Kawazu, C., Murata, M., Sano, H., Hayashida, K., Fukuda, S., Tagami, M., Hasegawa, A., et al. (2008) · BioTechniques · doi:10.2144/000112814 · Cited by 27
Identification of microbial DNA in human cancer
Duncan, C. G., Leary, R. J., Lin, J., Cummins, J. M., Di, C., Schaefer, C. F., Wang, T., Riggins, G. J., Edwards, J. B., Bigner, D. D., et al. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-22 · Cited by 28
Self-citation
Methods for quantitation of gene expression
Nygaard, V. (2009) · Frontiers in bioscience · doi:10.2741/3262 · Cited by 27
p53 Is a Direct Transcriptional Repressor of Keratin 17: Lessons from a Rat Model of Radiation Dermatitis
Liao, C., Xie, G., Zhu, L., Chen, X., Li, X., Lu, H., Xu, B., Ramot, Y., Paus, R., & Yue, Z. (2015) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2015.12.021 · Cited by 27
Tag-based approaches for deep transcriptome analysis in plants
Vega‐Sánchez, M. E., Gowda, M., & Wang, G. (2007) · Plant Science · doi:10.1016/j.plantsci.2007.07.005 · Cited by 27
Transcriptome annotation using tandem SAGE tags
Rivals, É., Boureux, A., Lejeune, M., Ottonès, F., Pérez, O. P., Tarhio, J., Pierrat, F., Rufflé, F., Commes, T., & Marti, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm495 · Cited by 27
SAGE and related approaches for cancer target identification
PORTER, D. A., Yao, J., & Polyák, K. (2006) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03694-9 · Cited by 27
Detecting and Comparing Non-Coding RNAs in the High-Throughput Era
Bussotti, G., Notredame, C., & Enright, A. J. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms140815423 · Cited by 26
Yellow pages to the transcriptome
Scheel, J., von Brevern, M., Hörlein, A., Fischer, A., Schneider, A., & Bach, A. (2002) · Pharmacogenomics · doi:10.1517/14622416.3.6.791 · Cited by 26
Overview of single‐cell RNA sequencing analysis and its application to spermatogenesis research
Suzuki, T. (2023) · Reproductive Medicine and Biology · doi:10.1002/rmb2.12502 · Cited by 24
Identification of a set of genes showing regionally enriched expression in the mouse brain
D’Souza, C. A., Chopra, V. S., Varhol, R., Xie, Y., Bohacec, S., Zhao, Y., Lee, L. L. C., Bilenky, M., Portales-Casamar, É., He, A., et al. (2008) · BMC Neuroscience · doi:10.1186/1471-2202-9-66 · Cited by 25
Locating and parsing bibliographic references in HTML medical articles
Zou, J., Le, D. X., & Thoma, G. R. (2010) · International Journal on Document Analysis and Recognition (IJDAR) · doi:10.1007/s10032-009-0105-9 · Cited by 25
Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long‐SAGE)
Krupp, D. R., Xu, P., Thomas, S., Dellinger, A. E., Etchevers, H., Vekemans, M. J. J., Gilbert, J. R., Speer, M. C., Ashley‐Koch, A. E., & Gregory, S. G. (2012) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.23040 · Cited by 25
Transcript profiling reveals expression differences in wild-type and glabrous soybean lines
Hunt, M., Kaur, N., Strömvik, M. V., & Vodkin, L. O. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-145 · Cited by 25
Comparison of the gene expression profiles of resistant and non‐resistant Japanese black pine inoculated with pine wood nematode using a modified LongSAGE technique
Nose, M., & Shiraishi, S. (2010) · Forest Pathology · doi:10.1111/j.1439-0329.2010.00646.x · Cited by 25
MGOS: A Resource for Studying Magnaporthe grisea and Oryza sativa Interactions
Soderlund, C. A., Haller, K., Pampanwar, V., Ebbole, D. J., FARMAN, M. L., Orbach, M. J., Wang, G., Wing, R. A., Xu, J., Brown, D., et al. (2006) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-19-1055 · Cited by 25
Global transcript profiling of potato tuber using LongSAGE
Nielsen, K. L., Grønkjær, K., Welinder, K. G., & Emmersen, J. (2005) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2005.00115.x · Cited by 25
Genome annotation by high-throughput 5′ RNA end determination
Hwang, B. J., Müller, H.-M., & Sternberg, P. W. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308384100 · Cited by 25
Understanding Vegetative Desiccation Tolerance Using Integrated Functional Genomics Approaches Within a Comparative Evolutionary Framework
Cushman, J. C., & Oliver, M. J. (2011) · Ecological studies · doi:10.1007/978-3-642-19106-0_15 · Cited by 24
mpscan: Fast Localisation of Multiple Reads in Genomes
Rivals, É., Salmela, L., Kiiskinen, P., Kalsi, P., & Tarhio, J. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-04241-6_21 · Cited by 24
Application of serial analysis of gene expression to the study of human genetic disease
Horan, M. P. (2009) · Human Genetics · doi:10.1007/s00439-009-0719-5 · Cited by 23
Whole-genome expression profiling through fragment display and combinatorial gene identification
Metsis, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh126 · Cited by 24
Comparison of the expression profiles of promastigotes and axenic amastigotes in Leishmania donovani using serial analysis of gene expression
Li, Q., Zhao, Y., Ni, B., Yao, C., Zhou, Y., Xu, W., Wang, Z., & Qiao, Z. (2008) · Parasitology Research · doi:10.1007/s00436-008-1048-7 · Cited by 24
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh120 · Cited by 24
Tissue-specific alternative polyadenylation at the imprinted gene Mest regulates allelic usage at Copg2
MacIsaac, J. L., Bogutz, A., Morrissy, A. S., & Lefebvre, L. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr871 · Cited by 24
StemBase
Porter, C. J., Palidwor, G., Sandie, R., Krzyzanowski, P. M., Muro, E. M., Perez‐Iratxeta, C., & Andrade-Navarro, M. A. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-536-7_11 · Cited by 24
Regulation of a Virus-Induced Lethal Disease in Tomato Revealed by LongSAGE Analysis
Irian, S., Xu, P., Dai, X., Zhao, P. X., & Roossinck, M. J. (2007) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-20-12-1477 · Cited by 24
Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis
Wang, X. V., Verhaak, R. G. W., Purdom, E. A., Spellman, P. T., & Speed, T. P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017691 · Cited by 22
AMIGO2 as a novel indicator of liver metastasis in patients with colorectal cancer
Tanio, A., Saito, H., Amisaki, M., Hara, K., Sugezawa, K., Uejima, C., Tada, Y., Kihara, K., Yamamoto, M., Nosaka, K., et al. (2021) · Oncology Letters · doi:10.3892/ol.2021.12539 · Cited by 23
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea
Rodríguez-Esteban, G., González-Sastre, A., Rojo-Laguna, J. I., Saló, E., & Abril, J. F. (2015) · BMC Genomics · doi:10.1186/s12864-015-1533-1 · Cited by 23
Comprehensive serial analysis of gene expression of the cervical transcriptome
Shadeo, A., Chari, R., Vatcher, G. P., Campbell, J. M., Lonergan, K. M., Matisic, J. P., van Niekerk, D., Ehlen, T. G., Miller, D., Follen, M. M., et al. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-142 · Cited by 23
Digital karyotyping
Leary, R. J., Cummins, J. M., Wang, T., & Velculescu, V. E. (2007) · Nature Protocols · doi:10.1038/nprot.2007.276 · Cited by 23
Self-citation
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries
Keime, C., Damiola, F., Mouchiroud, D., Duret, L., & Gandrillon, O. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-143 · Cited by 23
Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS
Hene, L., Sreenu, V. B., Vuong, M. T., Abidi, S. H. I., Sutton, J., Rowland‐Jones, S., Davis, S. J., & Evans, E. J. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-333 · Cited by 23
Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling
Girma, G., Natsume, S., Carluccio, A. V., Takagi, H., Matsumura, H., Uemura, A., Muranaka, S., Takagi, H., Stavolone, L., Gedil, M. A., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0216912 · Cited by 22
SuperSAGE: Powerful Serial Analysis of Gene Expression
Matsumura, H., Urasaki, N., Yoshida, K., Krüger, D. H., Kahl, G., & Terauchi, R. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-839-9_1 · Cited by 22
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Jiang, S., Christoffels, A. G., Ramamoorthy, R., & Ramachandran, S. (2009) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.139402 · Cited by 22
Transcriptome analysis reveals season‐specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.)
Sathish, P., Withana, N. P., Biswas, M., Bryant, C., Templeton, K., Al‐Wahb, M., Smith‐Espinoza, C., Roche, J. R., Elborough, K. M., & Phillips, J. (2006) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2006.00228.x · Cited by 22
Paired‐End diTagging for Transcriptome and Genome Analysis
Ng, P., Wei, C., & Ruan, Y. (2007) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2112s79 · Cited by 22
PVALB, a New Hürthle Adenoma Diagnostic Marker Identified through Gene Expression
Cerutti, J. M., Oler, G., Delcelo, R., Gerardt, R., Michaluart, P., SOUZA, S. J. D., Galante, P. A. F., Huang, P., & Riggins, G. J. (2010) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2010-1318 · Cited by 21
Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus
Obermeier, C., Hosseini, B., Friedt, W., & Snowdon, R. J. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-295 · Cited by 21
Modeling Transcriptome Based on Transcript-Sampling Data
Zhu, J., He, F., Wang, J., & Yu, J. M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001659 · Cited by 21
Size-selection of cDNA libraries for the cloning of cDNAs after suppression subtractive hybridization
Lévesque, V., Fayad, T., Ndiaye, K., Diouf, M. N., & Lussier, J. G. (2003) · BioTechniques · doi:10.2144/03351st02 · Cited by 21
Gene Expression Profiling of Neospora caninum in Bovine Macrophages Reveals Differences Between Isolates Associated With Key Parasite Functions
García-Sánchez, M., Jiménez-Pelayo, L., Horcajo, P., Regidor‐Cerrillo, J., Collantes-Fernández, E., & Ortega‐Mora, L. M. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00354 · Cited by 20
The Future of Cancer Management: Translating the Genome, Transcriptome, and Proteome
Yeatman, T. J. (2003) · Annals of Surgical Oncology · doi:10.1245/aso.2003.05.031 · Cited by 20
LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse
Wahl, M. B., Heinzmann, U., & Imai, K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti207 · Cited by 29
Insights from Large-Scale Cancer Genome Sequencing
Mardis, E. R. (2018) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-050216-122035 · Cited by 20
Digital Gene Expression by Tag Sequencing on the Illumina Genome Analyzer
Morrissy, A. S., Zhao, Y., Delaney, A. D., Asano, J. K., Dhalla, N., Li, I., McDonald, H., Pandoh, P. K., Prabhu, A., Tam, A., et al. (2010) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1111s65 · Cited by 19
Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium
Minami, M., Kureha, O., Mori, M., Kamitsuji, H., Suzuki, K., & Irie, T. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-007-0850-y · Cited by 19
Transcriptional profile of the human peripheral nervous system by serial analysis of gene expression
de Jonge, R. R., Vreijling, J. P., Meintjes, A., Kwa, M. S. G., van Kampen, A. H. C., van Schaik, I. N., & Baas, F. (2003) · Genomics · doi:10.1016/s0888-7543(03)00124-1 · Cited by 19
Transcriptional Landscape of the Human and Fly Genomes: Nonlinear and Multifunctional Modular Model of TranscriptomesPreprint
Willingham, A. T., Dike, S., Cheng, J., Manak, J. R., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Duttagupta, R., Ganesh, M., et al. (2006) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2006.71.068 · Cited by 19

Authors: Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E.
Affiliations: Howard Hughes Medical Institute (US)
Corresponding author: Kinzler, Kenneth W.
Velculescu, Victor E.
ORCID: Saha, Saurabh
Akmaev, Viatcheslav
Vogelstein, Bert
Kinzler, Kenneth W.
Velculescu, Victor E.
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2002-05
Volume: 20
Issue: 5
Pages: 508-512
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt0502-508
OpenAlex: W2002982210
Cited by: 630
References: 20
Citations by year: 2026: 2 · 2025: 1 · 2024: 3 · 2023: 6 · 2022: 6 · 2021: 4 · 2020: 7 · 2019: 14 · 2018: 18 · 2017: 6 · 2016: 8 · 2015: 15 · 2014: 14 · 2013: 15 · 2012: 24
FWCI: 19.47
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature Biotechnology (publishedVersion)
PubMed (publishedVersion)
Funders: National Cancer Institute (CA 57345)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords: LongSAGE, serial analysis of gene expression, transcriptome, genome annotation, gene discovery, exon identification, expressed genes, human genome annotation, sage
MeSH terms: Genetic Techniques, Humans, Models, Genetic, RNA, Messenger, Software, Human Genome Project, Genome, DNA, Complementary, Reverse Transcriptase Polymerase Chain Reaction

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Using the transcriptome to annotate the genome

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks