Identifying biological themes within lists of genes with EASE
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* Corresponding author: Richard A Lempicki rlempicki@niaid.nih.gov
Genome Biology 2003, 4:R70 doi:10.1186/gb-2003-4-10-r70
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Research
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Software
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Research article
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Research
Promoter features related to tissue specificity as measured by Shannon entropy Jonathan Schug, Winfried-Paul Schuller, Claudia Kappen, J Michael Salbaum, Maja Bucan, Christian J Stoeckert Genome Biology 2005, 6:R33 (29 March 2005) A genome-wide analysis of promoters was carried out in the context of gene expression patterns in tissue surveys using human microarray and EST-based expression data. The study revealed that most genes show statistically significant tissue-dependent variations of expression level and identified components of promoters that distinguish tissue-specific from ubiquitous genes. |
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Research article
Gene expression signature of estrogen receptor α status in breast cancer Martín C Abba, Yuhui Hu, Hongxia Sun, Jeffrey A Drake, Sally Gaddis, Keith Baggerly, Aysegul Sahin, C Marcelo Aldaz BMC Genomics 2005, 6:37 (11 March 2005) |
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Method
Genomic analysis of early murine mammary gland development using novel probe-level algorithms Stephen R Master, Alexander J Stoddard, L Charles Bailey, Tien-Chi Pan, Katherine D Dugan, Lewis A Chodosh Genome Biology 2005, 6:R20 (1 February 2005) A novel algorithm (ChipStat) is presented for detecting gene-expression changes from Affymetrix microarray data. The method is used to identify changes in murine mammary development. |
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Software
GECKO: a complete large-scale gene expression analysis platform Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell BMC Bioinformatics 2004, 5:195 (10 December 2004) The Unix based software, GECKO, provides a well structured user interface for the large-scale management and analysis of microarray gene expression data
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Methodology article
Comparing functional annotation analyses with Catmap Thomas Breslin, Patrik Edén, Morten Krogh BMC Bioinformatics 2004, 5:193 (9 December 2004) |
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Research
Gene expression profiling of epithelial ovarian tumours correlated with malignant potential Susanne Warrenfeltz, Stephen Pavlik, Susmita Datta, Eileen T Kraemer, Benedict Benigno, John F McDonald Molecular Cancer 2004, 3:27 (7 October 2004) |
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Methodology article
Graph-based iterative Group Analysis enhances microarray interpretation Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:100 (23 July 2004) Graph-based iterative Group Analysis (GiGA), a graph-based approach to identify biologically relevant changes in expression data, visually enhances microarray interpretation.
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Methodology article
Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:34 (29 March 2004) |
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Software
PubMatrix: a tool for multiplex literature mining Kevin G Becker, Douglas A Hosack, Glynn Dennis, Richard A Lempicki, Tiffani J Bright, Chris Cheadle, Jim Engel BMC Bioinformatics 2003, 4:61 (10 December 2003) |