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Wanderer，一款用于探索人类癌症中DNA甲基化和基因表达数据的交互式查看器。

Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer.

作者信息

Díez-Villanueva Anna, Mallona Izaskun, Peinado Miguel A

机构信息

Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Ctra. de Can Ruti, camí de les Escoles, s/n, 08916 Badalona, Spain.

Health Research Institute Germans Trias i Pujol (IGTP), Can Ruti Campus, Ctra. de Can Ruti, camí de les Escoles, s/n, 08916 Badalona, Spain.

出版信息

Epigenetics Chromatin. 2015 Jun 23;8:22. doi: 10.1186/s13072-015-0014-8. eCollection 2015.

DOI:10.1186/s13072-015-0014-8
PMID:26113876
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4480445/
Abstract

BACKGROUND: The Cancer Genome Atlas (TCGA) offers a multilayered view of genomics and epigenomics data of many human cancer types. However, the retrieval of expression and methylation data from TCGA is a cumbersome and time-consuming task. RESULTS: Wanderer is an intuitive Web tool allowing real time access and visualization of gene expression and DNA methylation profiles from TCGA. Given a gene query and selection of a TCGA dataset (e.g., colon adenocarcinomas), the Web resource provides the expression profile, at the single exon level, and the DNA methylation levels of HumanMethylation450 BeadChip loci inside or in the vicinity of the queried gene. Graphic and table outputs include individual and summary data as well as statistical tests, allowing the comparison of tumor and normal profiles and the exploration along the genomic locus and across tumor collections. CONCLUSIONS: Wanderer offers a simple interface to straightforward access to TCGA data, amenable to experimentalists and clinicians without bioinformatics expertise. Wanderer may be accessed at http://maplab.cat/wanderer.

摘要

背景：癌症基因组图谱（TCGA）提供了多种人类癌症类型的基因组学和表观基因组学数据的多层次视图。然而，从TCGA检索表达和甲基化数据是一项繁琐且耗时的任务。 结果：Wanderer是一个直观的网络工具，允许实时访问和可视化来自TCGA的基因表达和DNA甲基化谱。给定一个基因查询并选择一个TCGA数据集（例如，结肠腺癌），该网络资源可提供单个外显子水平的表达谱以及查询基因内部或附近的HumanMethylation450 BeadChip位点的DNA甲基化水平。图形和表格输出包括个体数据和汇总数据以及统计测试，允许比较肿瘤和正常谱，并沿着基因组位点和跨肿瘤集合进行探索。 结论：Wanderer提供了一个简单的界面，可直接访问TCGA数据，适合没有生物信息学专业知识的实验人员和临床医生使用。可通过http://maplab.cat/wanderer访问Wanderer。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/2f87a15dd55e/13072_2015_14_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/b271754b2ffa/13072_2015_14_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/a472a63c49a5/13072_2015_14_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/a139a7525af5/13072_2015_14_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/2f87a15dd55e/13072_2015_14_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/b271754b2ffa/13072_2015_14_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/a472a63c49a5/13072_2015_14_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/a139a7525af5/13072_2015_14_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/96c5/4480445/2f87a15dd55e/13072_2015_14_Fig4_HTML.jpg

相似文献

[1]
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本文引用的文献

[1]
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Nucleic Acids Res. 2015-1

[2]
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Nat Methods. 2014-6

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Nat Rev Genet. 2013-10-9

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Sci Rep. 2013-10-2

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Nat Genet. 2013-10

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PLoS One. 2013-8-20

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Nat Methods. 2013-8

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Gene. 2012-12-7

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