This track shows the locations of the 25 bp probes on the Affymetrix ENCODE tiling array, which are spaced every 22 bp on average. The chip, which was produced using Affymetrix GeneChip technology, has 737,680 probes representing all the non-repetitive DNA sequence of the ENCODE regions. This chip was designed for high throughput experiments to explore the human transcriptome at high resolution. The probes represent all the transcribed regions, including mRNAs as well as non-coding RNAs that are used both structurally and in the regulation of gene expression. Disruption of these structures or changes in the levels of transcription or translation may play a role in disease pathogenesis; therefore, this array is a valuable tool for the discovery and elucidation of disease processes.
Probe locations are indicated by solid blocks in the graphical display.
Probe positions were provided by Affymetrix, and the sequence was verified upon mapping to the genome. The array can be utilized to study transcribed regions (see Affy RNA Signal and Affy Transfrags tracks), transcription factor binding sites (Affy pVal and Affy Sites tracks), sites of chromatin modification, sites for DNA methylation and chromosomal origins of replication.
This chip was generated and analyzed by the Gingeras/Struhl collaboration with the Tom Gingeras group at Affymetrix and the Kevin Struhl group at Harvard Medical School.
Please see the Affymetrix Transcriptome site for a project overview and additional references to Affymetrix tiling array publications.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2), 185-193 (2003).
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4), 499-509 (2004).
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P., and Gingeras, T. R. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296(5569), 916-919 (2002).