Genomes and Genes
Affiliation: Affymetrix Inc
- Large-scale transcriptional activity in chromosomes 21 and 22Philipp Kapranov
Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
Science 296:916-9. 2002..When compared with the sequence annotations available for these chromosomes, it is noted that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized exons...
- Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arraysPhilipp Kapranov
Affymetrix Inc, Santa Clara, California 95051, USA
Genome Res 15:987-97. 2005..These results have important implications concerning the correlation of genotypes to phenotypes, the regulation of complex interlaced transcriptional patterns, and the definition of a gene...
- Transcriptional maps of 10 human chromosomes at 5-nucleotide resolutionJill Cheng
Affymetrix Inc, Santa Clara, CA 95051, USA
Science 308:1149-54. 2005..This organization has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene...
- Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22Dione Kampa
Affymetrix, Santa Clara, California 95051, USA
Genome Res 14:331-42. 2004..These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome...
- RNA maps reveal new RNA classes and a possible function for pervasive transcriptionPhilipp Kapranov
Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
Science 316:1484-8. 2007..These data support a highly interleaved organization of the human transcriptome...
- Differential analysis for high density tiling microarray dataSrinka Ghosh
Affymetrix Inc, Santa Clara, CA 95051, USA
BMC Bioinformatics 8:359. 2007....
- Biological function of unannotated transcription during the early development of Drosophila melanogasterJ Robert Manak
Affymetrix, Inc, Santa Clara, California, 95051, USA
Nat Genet 38:1151-8. 2006..Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome...
- Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAsSimon Cawley
Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
Cell 116:499-509. 2004..Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals...
- Beyond expression profiling: next generation uses of high density oligonucleotide arraysPhilipp Kapranov
Affymetrix, Inc, Santa Clara, CA 95051, USA
Brief Funct Genomic Proteomic 2:47-56. 2003..Integrating all this information will provide novel global views of the locations of RNA transcription, DNA replication and the protein nucleic acid interactions that regulate these processes...
- Genome-wide transcription and the implications for genomic organizationPhilipp Kapranov
Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
Nat Rev Genet 8:413-23. 2007..What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?..
- Efficient targeted transcript discovery via array-based normalization of RACE librariesSarah Djebali
Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
Nat Methods 5:629-35. 2008....
- Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targetsDavid S Johnson
Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
Genome Res 18:393-403. 2008..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
- Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disordersAlvaro Rada-Iglesias
Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
Genome Res 18:380-92. 2008..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders...
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
- Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regionsFrance Denoeud
Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
Genome Res 17:746-59. 2007....
- Microarray-based DNA methylation profiling: technology and applicationsAxel Schumacher
The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, Canada M5T 1R8
Nucleic Acids Res 34:528-42. 2006..The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure...
- Structured RNAs in the ENCODE selected regions of the human genomeStefan Washietl
Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
Genome Res 17:852-64. 2007..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%)...
- Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolutionDeyou Zheng
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
Genome Res 17:839-51. 2007..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
- Temporal profile of replication of human chromosomesYesu Jeon
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
Proc Natl Acad Sci U S A 102:6419-24. 2005..Thus, at least for aneuploid cancer cells, a typical discrete time of replication in S phase is not seen for large segments of the chromosomes...
- Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cellsAnnie Yang
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
Mol Cell 24:593-602. 2006..Many p63 binding regions are evolutionarily conserved and/or associated with sequence motifs for other transcription factors, suggesting that a substantial portion of p63 sites is biologically relevant...