Comparison of methods for genomic coverage within tiling array applications.
Tiling arrays are a subtype of microarray chips. Like traditional microarrays, they function by hybridizing labeled DNA or RNA target molecules to probes fixed onto a solid surface.
Tiling arrays differ from traditional microarrays in the nature of the probes. Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe intensively for sequences which are known to exist in a contiguous region. This is useful for characterizing regions that are sequenced, but whose local functions are largely unknown. Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH.[1] In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. Specific probes are present in millions of copies (as opposed to only several in traditional arrays) within an array unit called a feature, with anywhere from 10,000 to more than 6,000,000 different features per array.[2] Variable mapping resolutions are obtainable by adjusting the amount of sequence overlap between probes, or the amount of known base pairs between probe sequences, as well as probe length. For smaller genomes such as Arabidopsis, whole genomes can be examined.[3] Tiling arrays are a useful tool in genome-wide association studies.
^Yazaki, J; Gregory, BD; Ecker, JR (October 2007). "Mapping the genome landscape using tiling array technology". Current Opinion in Plant Biology. 10 (5): 534–42. doi:10.1016/j.pbi.2007.07.006. PMC 2665186. PMID 17703988.
^Mockler, TC; Chan, S; Sundaresan, A; Chen, H; Jacobsen, SE; Ecker, JR (January 2005). "Applications of DNA tiling arrays for whole-genome analysis". Genomics. 85 (1): 1–15. doi:10.1016/j.ygeno.2004.10.005. PMID 15607417.
^Yamada, K; Lim, J; Dale, JM; Chen, H; Shinn, P; Palm, CJ; Southwick, AM; Wu, HC; Kim, C; Nguyen, M; Pham, P; Cheuk, R; et al. (Oct 31, 2003). "Empirical analysis of transcriptional activity in the Arabidopsis genome". Science. 302 (5646): 842–6. Bibcode:2003Sci...302..842Y. doi:10.1126/science.1088305. PMID 14593172. S2CID 7076927.
Tilingarrays are a subtype of microarray chips. Like traditional microarrays, they function by hybridizing labeled DNA or RNA target molecules to probes...
nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based...
wallpaper groups. A tiling that lacks a repeating pattern is called "non-periodic". An aperiodic tiling uses a small set of tile shapes that cannot form...
In computing, an array of structures (AoS), structure of arrays (SoA) or array of structures of arrays (AoSoA) are contrasting ways to arrange a sequence...
ARTADE (ARabidopsis TilingArray-based Detection of Exons) is a database for the annotation of genome-wide tiling-array data in Arabidopsis DNA microarray...
The techniques and tools for tiling is advanced, evidenced by the fine workmanship and close fit of the tiles. Such tiling can be seen in Ruwanwelisaya...
any kind of partitioning is tiling. Array partitioning can improve access to array subsets significantly: by adjusting tiling to the access pattern, the...
level of recursion. // Array A[] has the items to sort; array B[] is a work array. void TopDownMergeSort(A[], B[], n) { CopyArray(A, 0, n, B); // one time...
approximately 400 watts. The water-cooled Training Tile packages 25 D1 chips into a 5×5 array. Each tile supports 36 TB/sec of aggregate bandwidth via 40...
Reverse transcription PCR Higher-plex techniques: SAGE DNA microarray Tilingarray RNA-Seq Gene expression omnibus (GEO) at NCBI Expression Atlas at the...
lysis. Alternative splicing can be analysed with a splicing array or with a tilingarray (see DNA microarray). All in vivo RNA is complexed as RNPs. The...
produce this optimization is called loop tiling, also known as loop blocking or strip mine and interchange. Loop tiling partitions a loop's iteration space...
only by total DNA, but also by methylated DNA immunoprecipitation (with tilingarray), microRNA (such as with Megaplex) and total RNA (RNA-sequencing). Diagnostic...
blot analysis of this 477bp sequence yielded no results. A subsequent tilingarray analysis sequencing Hfq-binding sRNA found that the Watson strand did...
MicroTiles display. This allows resolutions to be displayed on smaller tilearrays at the native 0.57 mm pixel pitch (for up to six tiles)—larger arrays need...
Widefield Array (MWA) is a joint project between an international consortium of organisations to construct and operate a low-frequency radio array. 'Widefield'...
21°24′40″E / 30.72111°S 21.41111°E / -30.72111; 21.41111 The Square Kilometre Array (SKA) is an intergovernmental international radio telescope project being...
copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays". Proc Natl Acad Sci U S A. 103 (12): 4534–4539. Bibcode:2006PNAS...
that the tiling pattern is adjusted to the query access patterns; several tiling strategies assist in establishing a well-performing tiling. A geo index...
mid-2014 new 4K monitors such as the Asus PB287Q no longer rely on MST tiling technique to achieve 4K at 60 Hz, instead, using the standard SST (Single-Stream...
Tile processors for computer hardware, are multicore or manycore chips that contain one-dimensional, or more commonly, two-dimensional arrays of identical...
based system to find genes using heterogeneous information: RNA-seq, tilingarrays Eukaryotes MORGAN Decision tree system to find genes in vertebrate DNA...
mathematics, a Costas array can be regarded geometrically as a set of n points, each at the center of a square in an n×n square tiling such that each row...
genome that uses next-generation DNA-sequencing technologies and genomic tilingarrays, technologies able to automatically generate large amounts of data at...
mapped in several early experiments examining S. cerevisiae using a tilingarray approach, which indicated that a large amount of transcriptional activity...
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