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arrayMap 2014: an updated cancer genome resource.

Cai H, Gupta S, Rath P, Ai N, Baudis M - Nucleic Acids Res. (2014)

Bottom Line: Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines.Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets.Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China haoyang.cai@gmail.com.

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Distribution of arrays archived in arrayMap according to platform types and resolution. The usage of higher resolution platforms increased dramatically in recent years, with a concomitant decrease of especially low resolution BAC/P1 platforms.
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Figure 1: Distribution of arrays archived in arrayMap according to platform types and resolution. The usage of higher resolution platforms increased dramatically in recent years, with a concomitant decrease of especially low resolution BAC/P1 platforms.

Mentions: At the time of its launch, the original arrayMap edition contained about 40 000 arrays from 260 different platforms, representing 224 cancer diagnoses as defined in the International Classification of Diseases in Oncology (ICD-O 3) (22). For the 2014 edition, the absolute number of data sets has been increased to 64 814 genomic copy number arrays from 985 experimental series, involving 343 array platforms. The primary data had been published in more than 700 original publications, and now represents 252 ICD-O cancer entities (Table 1). Over time, relatively low resolution array platforms are replaced by higher resolution or multi-function platforms. At the moment, the platform with the highest probe numbers in arrayMap contains about 2.2 million individual probes. In line with this trend, ∼60% of the added arrays contain more than 250K probes. Since the data generated by high resolution arrays increased rapidly in recent years, we anticipate that this growth trend will continue (Figure 1) with special impact on the detection of focal genomic imbalances.


arrayMap 2014: an updated cancer genome resource.

Cai H, Gupta S, Rath P, Ai N, Baudis M - Nucleic Acids Res. (2014)

Distribution of arrays archived in arrayMap according to platform types and resolution. The usage of higher resolution platforms increased dramatically in recent years, with a concomitant decrease of especially low resolution BAC/P1 platforms.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383937&req=5

Figure 1: Distribution of arrays archived in arrayMap according to platform types and resolution. The usage of higher resolution platforms increased dramatically in recent years, with a concomitant decrease of especially low resolution BAC/P1 platforms.
Mentions: At the time of its launch, the original arrayMap edition contained about 40 000 arrays from 260 different platforms, representing 224 cancer diagnoses as defined in the International Classification of Diseases in Oncology (ICD-O 3) (22). For the 2014 edition, the absolute number of data sets has been increased to 64 814 genomic copy number arrays from 985 experimental series, involving 343 array platforms. The primary data had been published in more than 700 original publications, and now represents 252 ICD-O cancer entities (Table 1). Over time, relatively low resolution array platforms are replaced by higher resolution or multi-function platforms. At the moment, the platform with the highest probe numbers in arrayMap contains about 2.2 million individual probes. In line with this trend, ∼60% of the added arrays contain more than 250K probes. Since the data generated by high resolution arrays increased rapidly in recent years, we anticipate that this growth trend will continue (Figure 1) with special impact on the detection of focal genomic imbalances.

Bottom Line: Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines.Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets.Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China haoyang.cai@gmail.com.

Show MeSH
Related in: MedlinePlus