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Methods: ECgene: Genome-based EST clustering and gene modeling for alternative splicing
- Namshin Kim,
- Seokmin Shin,
- and Sanghyuk Lee
Genome Res. April 2005 15: 566-576; doi:10.1101/gr.3030405
...experiments, conserved regions across species, repeat sequences, and so on. The UCSC browser database is an excellent example of integrating genomic resources from the public sector ( Karolchik et al. 2003 ). For example, even if an EST cluster represents only part of a gene due to insufficient data coverage...
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LETTER: Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes
- Sven Nelander,
- Petter Mostad,
- and Per Lindahl
Genome Res. August 2003 13: 1838-1854; Published in Advance July 17, 2003, doi:10.1101/gr.1197303
...in a nonambiguous manner at success rates that can be estimated in advance. RESULTS Quantitative Expression Profiles Generated From Public EST Data Discriminate SMC-Specific Genes The mouse UniGene data contain 2.7 million ESTs from 639 different libraries ( Fig. 1 ), and thus constitute an enormous source...
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LETTER: A Comparative Molecular Analysis of Developing Mouse Forelimbs and Hindlimbs Using Serial Analysis of Gene Expression (SAGE)
- Elliott H. Margulies,
- Sharon L.R. Kardia,
- and Jeffrey W. Innis
Genome Res. October 1, 2001 11: 1686-1698; Published in Advance September 20, 2001, doi:10.1101/gr.192601
..., University of Michigan Medical School, 2Epidemiology, University of Michigan School of Public Health, and 3Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Abstract The analysis of differentially expressed genes is a powerful approach...
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Methods: Assessment of SAGE in Transcript Identification
- Erin D. Pleasance,
- Marco A. Marra,
- and Steven J.M. Jones
Genome Res. June 2003 13: 1203-1215; Published in Advance May 12, 2003, doi:10.1101/gr.873003
...) for tag mapping is NCBI's SAGEmap ( http://www.ncbi.nlm.nih.gov/SAGE/ ). As described in their most recent publication ( Lash et al. 2000 ), this tag mapping is done on the basis of matching SAGE data to tags extracted from Expressed Sequence Tag (EST) and cDNA sequences found in the NCBI UniGene clusters...
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METHODS: In Silico Cloning of Novel Endothelial-Specific Genes
- Lukasz Huminiecki and
- Roy Bicknell
Genome Res. November 1, 2000 10: 1796-1806; doi:10.1101/gr.150700
...deemed optimal after a series of test BLAST searches. SAGE Data and SAGEmap xProfiler Differential Analysis Internet-based SAGE library subtraction (SAGEmap xProfiler ) was used as the second datamining strategy for the identification of novel endothelial-specific or preferentially endothelial genes. Two...
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RESOURCE: The Human Genome Browser at UCSC
- W. James Kent,
- Charles W. Sugnet,
- Terrence S. Furey,
- Krishna M. Roskin,
- Tom H. Pringle,
- Alan M. Zahler,
- and and David Haussler
Genome Res. June 1, 2002 12: 996-1006; Published in Advance May 16, 2002, doi:10.1101/gr.229102
.... A page with links to NCBI's human -specific resources is at http://www.ncbi.nlm.nih.gov//guide/human/ . These resources include the RefSeq set of nonredundant mRNA sequences ( Maglott et al. 2000 ; Pruitt and Maglott 2001 ). Functional descriptions of many of the RefSeq genes are available...
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LETTER: Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
- W. Troy Loging,
- Anita Lal,
- I-Mei Siu,
- Tania L. Loney,
- Carol J. Wikstrand,
- Marco A. Marra,
- Christa Prange,
- Darell D. Bigner,
- Robert L. Strausberg,
- and Gregory J. Riggins
Genome Res. September 1, 2000 10: 1393-1402; doi:10.1101/gr.138000
...mined a public database for candidate genes (see our previous report on this database; Lal et al. 1999 ) and used fluorescent-PCR expression comparison (F-PEC) to assess their expression on a panel of tumor and normal samples. The F-PEC method is based on continuous fluorescent monitoring of PCR...
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ARTICLE: Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile
- Martin J. Lercher,
- Jean-Vincent Chamary,
- and Laurence D. Hurst
Genome Res. June 2004 14: 1002-1013; doi:10.1101/gr.1597404
...Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile Martin J. Lercher , Jean-Vincent Chamary , and Laurence D. Hurst 1 Department of Biology and Biochemistry, University of Bath, Bath...
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METHODS: The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach
- Stefania Bortoluzzi,
- Fabio d'Alessi,
- Chiara Romualdi,
- and Gian Antonio Danieli
Genome Res. March 1, 2000 10: 344-349; doi:10.1101/gr.10.3.344
...a general catalog (http://telethon.bio.unipd.it/ GETProfiles/Skeletal_Muscle) in which each gene has a description, UniGene ID, and link for access to specific information (LocusLink, OMIM, SAGEMap). Moreover, this approach simplifies the statistical analysis and the comparison with other catalogs obtained...
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Methods: Global Survey of Chromatin Accessibility Using DNA Microarrays
- M. Ryan Weil,
- Piotr Widlak,
- John D. Minna,
- and Harold R. Garner
Genome Res. July 2004 14: 1374-1381; doi:10.1101/gr.1396104
...., Schuler, G.D., Strausberg, R.L., Riggins, G.J., and Altschul, S.F. 2000 . SAGEmap: A public gene expression resource. Genome Res. 10 : 1051 –1060. ↵ Orphanides, G. and Reinberg, D. 2002 . A unified theory of gene expression. Cell 108 : 439 –451. ↵ Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M...

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