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Database Commons - CaSNP

CaSNP

Citations: 17

z-index 1.31

Short name CaSNP
Full name
Description CaSNP is a comprehensive collection of copy number alteration (CNA) from SNP arrays.
URL http://cistrome.dfci.harvard.edu/CaSNP/
Year founded 2010
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted Zhejiang University
Address Hangzhou, 310012, China
City Hangzhou
Province/State Zhejiang
Country/Region China
Contact name X. Shirley Liu
Contact email xliu@hsph.harvard.edu
Data type(s)
Major organism(s)
Keyword(s)
  • cancer
  • CNV
  • SNP
Publication(s)
  • CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. [PMID: 20972221]

    Qingyi Cao, Meng Zhou, Xujun Wang, Cliff A Meyer, Yong Zhang, Zhi Chen, Cheng Li, X Shirley Liu
    Nucleic acids research 2011:39(Database issue)
    17 Citations (Google Scholar as of 2016-05-04)

    Abstract: Cancer is known to have abundant copy number alterations (CNAs) that greatly contribute to its pathogenesis and progression. Investigation of CNA regions could potentially help identify oncogenes and tumor suppressor genes and infer cancer mechanisms. Although single-nucleotide polymorphism (SNP) arrays have strengthened our ability to identify CNAs with unprecedented resolution, a comprehensive collection of CNA information from SNP array data is still lacking. We developed a web-based CaSNP (http://cistrome.dfci.harvard.edu/CaSNP/) database for storing and interrogating quantitative CNA data, which curated ?11,500 SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. Finally, we used CaSNP to study the CNA of protein-coding genes as well as LincRNA genes across all cancer SNP arrays, and found putative regions harboring novel oncogenes and tumor suppressors. In summary, CaSNP is a useful tool for cancer CNA association studies, with the potential to facilitate both basic science and translational research on cancer.

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200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
-1 Failed2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
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200 OK2016-12-20
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200 OK2016-11-25
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200 OK2016-11-18
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200 OK2016-11-08
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200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
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200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
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200 OK2016-04-08
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200 OK2016-03-29
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200 OK2016-03-25
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200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
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200 OK2016-02-05
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200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Disease DNA
Homo sapiens
cancer CNV SNP

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2016-03-31]
    • Mengwei Li [2016-03-29]
    • Mengwei Li [2015-06-27]
Stats