canEvolve: a web portal for integrative oncogenomics.
canEvolve: a web portal for integrative oncogenomics.
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DOI：
10.1371/journal.pone.0056228
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Shah PK
中科院分区：
文献类型：
--
作者：
Samur MK;Yan Z;Wang X;Cao Q;Munshi NC;Li C;Shah PK
使用功能基因组学平台获得的肿瘤全基因组图谱正在以天文数字的规模存入公共知识库，这是各个实验室和大型项目（如癌症基因组图谱（TCGA）和国际癌症基因组联盟）的集中努力的结果。因此，迫切需要可靠的工具，根据现有知识整合和解释这些数据，并以用户友好的方式向生物医学研究人员传播结果。我们已经建立了canEvolve门户网站来满足这一需求。canEvolve查询功能旨在满足癌症研究人员最常见的分析需求，以生成新的假设。canEvolve存储基因、microRNA（miRNA）和蛋白质表达谱、多种癌症类型的拷贝数改变以及蛋白质-蛋白质相互作用信息。canEvolve允许查询癌基因组学数据的初步分析、综合分析和网络分析的结果。初步分析的查询包括差异基因和miRNA表达以及用SNP微阵列测量的基因拷贝数的变化。canEvolve提供了基因表达谱与拷贝数改变和miRNA谱的整合分析结果，以及使用基因集富集分析的广义整合分析结果。网络分析能力包括基因共表达、推断的基因调控网络和蛋白质-蛋白质相互作用信息的存储和可视化。最后，canEvolve在单变量生存分析方面提供了基因表达与临床结局之间的相关性。目前，canEvolve提供了从90项癌症基因组学研究中提取的不同类型的信息，这些研究包括10，000多名患者。canEvolve的显著特点是存在多种数据类型、用于识别肿瘤发生调节因子的新型综合分析、网络分析和查询基因列表/途径的能力。canEvolve将促进对癌基因组学数据集的整合和荟萃分析。canEvolve门户网站位于http://www.canevolve.org/。
Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need. canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets. The canEvolve web portal is available at http://www.canevolve.org/.
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WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
14.9
作者：
Hunter S;Jones P;Mitchell A;Apweiler R;Attwood TK;Bateman A;Bernard T;Binns D;Bork P;Burge S;de Castro E;Coggill P;Corbett M;Das U;Daugherty L;Duquenne L;Finn RD;Fraser M;Gough J;Haft D;Hulo N;Kahn D;Kelly E;Letunic I;Lonsdale D;Lopez R;Madera M;Maslen J;McAnulla C;McDowall J;McMenamin C;Mi H;Mutowo-Muellenet P;Mulder N;Natale D;Orengo C;Pesseat S;Punta M;Quinn AF;Rivoire C;Sangrador-Vegas A;Selengut JD;Sigrist CJ;Scheremetjew M;Tate J;Thimmajanarthanan M;Thomas PD;Wu CH;Yeats C;Yong SY
通讯作者：
Yong SY
影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1158/1078-0432.ccr-09-2831
发表时间：
2010-03-15
期刊：
Clinical cancer research : an official journal of the American Association for Cancer Research
影响因子：
--
作者：
Dickens NJ;Walker BA;Leone PE;Johnson DC;Brito JL;Zeisig A;Jenner MW;Boyd KD;Gonzalez D;Gregory WM;Ross FM;Davies FE;Morgan GJ
通讯作者：
Morgan GJ
影响因子：
20.3
作者：
Davies, FE;Dring, AM;Anderson, KC
通讯作者：
Anderson, KC