TY - CHAP PY - 2003 DA - 2003// BT - GeneChip® Custom Express™ array design guide. Part No. 700506 Rev. 4 ID - ref1 ER - TY - CHAP PY - 2003 DA - 2003// BT - Array design and performance of the GeneChip® mouse expression set 430. Technical note. Part No. 701405 Rev. 1 ID - ref2 ER - TY - CHAP PY - 2003 DA - 2003// BT - Array design and performance of the GeneChip® rat expression set 230. Technical note. Part No. 701406 Rev. 1 ID - ref3 ER - TY - STD TI - Pontius JU, Wagner L, Schuler GD: UniGene: A unified view of the transcriptome. NCBI Handbook Chapter 21: 2003 August 13. [http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/handbook/ch21d1.pdf] 2003 August 13. UR - http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/handbook/ch21d1.pdf ID - ref4 ER - TY - CHAP PY - 2001 DA - 2001// BT - Array design for the GeneChip® human genome U133 set. Technical note. Part No. 701133 Rev. 1 ID - ref5 ER - TY - JOUR AU - Liu, G. AU - Loraine, A. E. AU - Shigeta, R. AU - Cline, M. AU - Cheng, J. AU - Valmeekam, V. AU - Sun, S. AU - Kulp, D. AU - Siani-Rose, M. A. PY - 2003 DA - 2003// TI - NetAffx: Affymetrix probesets and annotations JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg121 DO - 10.1093/nar/gkg121 ID - Liu2003 ER - TY - STD TI - Affymetrix – NetAffx analysis center[http://www.affymetrix.com/analysis/index.affx] UR - http://www.affymetrix.com/analysis/index.affx ID - ref7 ER - TY - JOUR AU - Gentleman, R. C. AU - Carey, V. J. AU - Bates, D. M. AU - Bolstad, B. AU - Dettling, M. AU - Dudoit, S. AU - Ellis, B. AU - Gautier, L. AU - Ge, Y. AU - Gentry, J. AU - Hornik, K. AU - Hothorn, T. AU - Huber, W. AU - Iacus, S. AU - Irizarry, R. AU - Leisch, F. AU - Li, C. AU - Maechler, M. AU - Rossini, A. J. AU - Sawitzki, G. AU - Smith, C. AU - Smyth, G. AU - Tierney, L. AU - Yang, J. Y. H. AU - Zhang, J. PY - 2004 DA - 2004// TI - Bioconductor: Open software development for computational biology and bioinformatics JO - Genome Biology VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r80 DO - 10.1186/gb-2004-5-10-r80 ID - Gentleman2004 ER - TY - STD TI - Bioconductor task view: AnnotationData[http://www.bioconductor.org/packages/release/AnnotationData.html] UR - http://www.bioconductor.org/packages/release/AnnotationData.html ID - ref9 ER - TY - STD TI - UCSC Genome Bioinformatics[http://genome.ucsc.edu] UR - http://genome.ucsc.edu ID - ref10 ER - TY - STD TI - Affymetrix – Technical support documentation for mouse expression set 430[http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430] UR - http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430 ID - ref11 ER - TY - JOUR AU - Huxley, C. AU - Fried, M. PY - 1990 DA - 1990// TI - The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA JO - Mol Cell Biol VL - 10 UR - https://doi.org/10.1128/MCB.10.2.605 DO - 10.1128/MCB.10.2.605 ID - Huxley1990 ER - TY - JOUR AU - Kent, W. J. AU - Sugnet, C. W. AU - Furey, T. S. AU - Roskin, K. M. AU - Pringle, T. H. AU - Zahler, A. M. AU - Haussler, D. PY - 2002 DA - 2002// TI - The Human Genome Browser at UCSC JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229102. Article published online before print in May 2002 DO - 10.1101/gr.229102. Article published online before print in May 2002 ID - Kent2002 ER - TY - JOUR AU - Karolchik, D. AU - Baertsch, R. AU - Diekhans, M. AU - Furey, T. S. AU - Hinrichs, A. AU - Lu, Y. T. AU - Roskin, K. M. AU - Schwartz, M. AU - Sugnet, C. W. AU - Thomas, D. J. AU - Weber, R. J. AU - Haussler, D. AU - Kent, W. J. PY - 2003 DA - 2003// TI - The UCSC Genome Browser Database JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg129 DO - 10.1093/nar/gkg129 ID - Karolchik2003 ER - TY - STD TI - Ensembl[http://www.ensembl.org/index.html] UR - http://www.ensembl.org/index.html ID - ref15 ER - TY - STD TI - NCBI Entrez Nucleotide[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=12836489] UR - http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=12836489 ID - ref16 ER - TY - JOUR AU - Williams, T. J. AU - Fried, M. PY - 1986 DA - 1986// TI - The MES-1 murine enhancer element is closely associated with the heterogeneous 5' ends of two divergent transcription units JO - Mol Cell Biol VL - 6 UR - https://doi.org/10.1128/MCB.6.12.4558 DO - 10.1128/MCB.6.12.4558 ID - Williams1986 ER - TY - STD TI - NCBI Entrez Nucleotide[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=5336339] UR - http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=5336339 ID - ref18 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT – The BLAST-Like Alignment Tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER - TY - STD TI - NCBI Index of . [ ]. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ Index of . []. UR - ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ ID - ref20 ER - TY - STD TI - NCBI Index of . [ ]. ftp://ftp.ncbi.nih.gov/repository/UniGene/ Index of . []. UR - ftp://ftp.ncbi.nih.gov/repository/UniGene/ ID - ref21 ER - TY - JOUR AU - Barrett, T. AU - Suzek, T. O. AU - Troup, D. B. AU - Wilhite, S. E. AU - Ngau, W. -. C. AU - Ledoux, P. AU - Rudnev, D. AU - Lash, A. E. AU - Fujibuchi, W. AU - Edgar, R. PY - 2005 DA - 2005// TI - NCBI GEO: mining millions of expression profiles – database and tools JO - Nucl Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki022 DO - 10.1093/nar/gki022 ID - Barrett2005 ER - TY - JOUR AU - Perez-Iratxeta, C. AU - Palidwor, G. AU - Porter, C. G. AU - Sanche, N. A. AU - Huska, M. R. AU - Suomela, B. P. AU - Muro, E. M. AU - Krzyzanowski, P. M. AU - Hughes, E. AU - Campbell, P. A. AU - Rudnicki, M. A. AU - Andrade, M. A. PY - 2005 DA - 2005// TI - Study of stem cell function using microarray experiments JO - FEBS Letters VL - 579 UR - https://doi.org/10.1016/j.febslet.2005.02.020 DO - 10.1016/j.febslet.2005.02.020 ID - Perez-Iratxeta2005 ER - TY - JOUR AU - Westhoff, T. H. AU - Scheid, S. AU - Tolle, M. AU - Kaynak, B. AU - Schmidt, S. AU - Zidek, W. AU - Sperling, S. AU - van der Giet, M. PY - 2005 DA - 2005// TI - A physiogenomic approach to study the regulation of blood pressure JO - Physiol Genomics VL - 23 UR - https://doi.org/10.1152/physiolgenomics.00077.2005 DO - 10.1152/physiolgenomics.00077.2005 ID - Westhoff2005 ER - TY - STD TI - Wu Z, Irizarry R: Description of gcrma. Bioconductor Vignettes 2005 May 18 [http://www.bioconductor.org/repository/devel/vignette/gcrma.pdf] 2005 May 18 UR - http://www.bioconductor.org/repository/devel/vignette/gcrma.pdf ID - ref25 ER - TY - JOUR AU - Quackenbush, J. PY - 2002 DA - 2002// TI - Microarray data normalization and transformation JO - Nature Genetics VL - 32 UR - https://doi.org/10.1038/ng1032 DO - 10.1038/ng1032 ID - Quackenbush2002 ER - TY - JOUR AU - Coleman, T. P. AU - Tran, Q. AU - Roesser, J. R. PY - 2003 DA - 2003// TI - Binding of a candidate splice regulator to a calcitonin-specific splice enhancer regulates calcitonin/CGRP pre-mRNA splicing JO - Biochimica et Biophysica Acta VL - 1625 UR - https://doi.org/10.1016/S0167-4781(02)00601-2 DO - 10.1016/S0167-4781(02)00601-2 ID - Coleman2003 ER - TY - STD TI - NCBI Entrez Nucleotide[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide] UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide ID - ref28 ER - TY - STD TI - NetAffx Probe Set Display[https://www.affymetrix.com/psd?target_id=RAE230A:1368596_AT] UR - https://www.affymetrix.com/psd?target_id=RAE230A:1368596_AT ID - ref29 ER - TY - JOUR AU - Dai, M. AU - Wang, P. AU - Boyd, A. D. AU - Kostov, G. AU - Athey, B. AU - Jones, E. G. AU - Bunney, W. E. AU - Myers, R. AU - Speed, T. P. AU - Akil, H. AU - Watson, S. J. AU - Meng, F. PY - 2005 DA - 2005// TI - Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data JO - Nucl Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gni179 DO - 10.1093/nar/gni179 ID - Dai2005 ER - TY - JOUR AU - Harbig, J. AU - Sprinkle, R. AU - Enkemann, S. A. PY - 2005 DA - 2005// TI - A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array JO - Nucl Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gni027 DO - 10.1093/nar/gni027 ID - Harbig2005 ER - TY - JOUR AU - Zhang, J. AU - Finney, R. P. AU - Clifford, R. J. AU - Derr, L. K. AU - Buetow, K. H. PY - 2005 DA - 2005// TI - Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach JO - Genomics VL - 85 UR - https://doi.org/10.1016/j.ygeno.2004.11.004 DO - 10.1016/j.ygeno.2004.11.004 ID - Zhang2005 ER - TY - JOUR AU - Gautier, L. AU - Møller, M. AU - Friis-Hansen, L. AU - Knudsen, S. PY - 2004 DA - 2004// TI - Alternative mapping of probes to genes for Affymetrix chips JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-111 DO - 10.1186/1471-2105-5-111 ID - Gautier2004 ER - TY - JOUR AU - Mignone, F. AU - Gissi, C. AU - Liuni, S. AU - Pesole, G. PY - 2002 DA - 2002// TI - Untranslated regions of mRNAs JO - Genome Biol VL - 3 UR - https://doi.org/10.1186/gb-2002-3-3-reviews0004 DO - 10.1186/gb-2002-3-3-reviews0004 ID - Mignone2002 ER - TY - JOUR AU - Akiva, P. AU - Toporik, A. AU - Edelheit, S. AU - Peretz, Y. AU - Diber, A. AU - Shemesh, R. AU - Novik, A. AU - Sorek, R. PY - 2006 DA - 2006// TI - Transcription-mediated gene fusion in the human genome JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.4137606 DO - 10.1101/gr.4137606 ID - Akiva2006 ER - TY - JOUR AU - Parra, G. AU - Reymond, A. AU - Dabbouseh, N. AU - Dermitzakis, E. AU - Castelo, R. AU - Thomson, T. AU - Antonarakis, S. AU - Guigo, R. PY - 2006 DA - 2006// TI - Tandem chimerism as a means to increase protein complexity in the human genome JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.4145906 DO - 10.1101/gr.4145906 ID - Parra2006 ER - TY - JOUR AU - Pruitt, K. D. AU - Maglott, D. R. PY - 2001 DA - 2001// TI - RefSeq and LocusLink: NCBI gene-centered resources JO - Nucl Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.1.137 DO - 10.1093/nar/29.1.137 ID - Pruitt2001 ER - TY - CHAP PY - 2004 DA - 2004// BT - Transcript assignment for Affymetrix GeneChip® probe arrays ID - ref38 ER - TY - STD TI - Zhang J: Basic functions of AnnBuilder. Bioconductor Vignettes 2004 September 14 [http://www.bioconductor.org/repository/devel/vignette/AnnBuilder.pdf] 2004 September 14 UR - http://www.bioconductor.org/repository/devel/vignette/AnnBuilder.pdf ID - ref39 ER - TY - STD TI - Zhang J: How to use AnnBuilder. Bioconductor Vignettes 2004 September 14 [http://www.bioconductor.org/repository/devel/vignette/ABPrimer.pdf] 2004 September 14 UR - http://www.bioconductor.org/repository/devel/vignette/ABPrimer.pdf ID - ref40 ER - TY - JOUR PY - 2002 DA - 2002// TI - Initial sequencing and comparative analysis of the mouse genome JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01262 DO - 10.1038/nature01262 ID - ref41 ER - TY - JOUR PY - 2004 DA - 2004// TI - Genome sequence of the Brown Norway rat yields insights into mammalian evolution JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02426 DO - 10.1038/nature02426 ID - ref42 ER - TY - STD TI - Interface AffyProbe[http://www.ensembl.org/Mus_musculus/featureview?type=OligoProbe;id=1416213_x_at] UR - http://www.ensembl.org/Mus_musculus/featureview?type=OligoProbe;id=1416213_x_at ID - ref43 ER - TY - STD TI - Affymetrix – Technical support documentation for rat expression set 230[http://www.affymetrix.com/support/technical/byproduct.affx?product=rae230] UR - http://www.affymetrix.com/support/technical/byproduct.affx?product=rae230 ID - ref44 ER - TY - JOUR AU - Ihaka, R. AU - Gentleman, R. PY - 1996 DA - 1996// TI - R: A language for data analysis and graphics JO - Journal of Computational and Graphical Statistics VL - 5 ID - Ihaka1996 ER -