TumorFusions: an integrative resource for cancer-associated transcript fusions.
TumorFusions: an integrative resource for cancer-associated transcript fusions.
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DOI：
10.1093/nar/gkx1018
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Verhaak RGW
中科院分区：
文献类型：
--
作者：
Hu X;Wang Q;Tang M;Barthel F;Amin S;Yoshihara K;Lang FM;Martinez-Ledesma E;Lee SH;Zheng S;Verhaak RGW
基因融合代表了癌症中的一类分子畸变，并已被用于治疗目的。在本文中，我们描述了 TumorFusions，这是一个数据门户，它对来自癌症基因组图谱 (TCGA) 的 9966 个经过充分表征的癌症样本和 648 个正常样本中检测到的 20 731 个基因融合进行了分类。该门户涵盖 TCGA 中的 33 种癌症类型。融合转录本通过统一的流程进行鉴定，包括对在 648 个非肿瘤样本中检测到的 3838 个转录本融合列表进行过滤。融合被映射到使用 561 个癌症样本的全基因组测序数据作为验证手段确定的体细胞 DNA 重排。我们观察到 65% 的转录融合与染色体改变相关，这在门户中进行了注释。该门户的其他功能包括基于 SNP 阵列的拷贝数水平和突变模式的链接、伙伴基因的外显子和转录本水平表达，以及用于优先考虑功能融合的基于网络的中心性评分。我们的门户网站旨在成为癌症基因注释的广泛适用且用户友好的资源，并可在 http://www.tumorfusions.org 上公开获取。
Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as a means of validation. We observed that 65% of transcript fusions were associated with a chromosomal alteration, which is annotated in the portal. Other features of the portal include links to SNP array-based copy number levels and mutational patterns, exon and transcript level expressions of the partner genes, and a network-based centrality score for prioritizing functional fusions. Our portal aims to be a broadly applicable and user friendly resource for cancer gene annotation and is publicly available at http://www.tumorfusions.org.
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31种癌症类型的端粒长度和躯体改变的系统分析。
影响因子：
30.8
作者：
Barthel FP;Wei W;Tang M;Martinez-Ledesma E;Hu X;Amin SB;Akdemir KC;Seth S;Song X;Wang Q;Lichtenberg T;Hu J;Zhang J;Zheng S;Verhaak RG
通讯作者：
Verhaak RG
影响因子：
50.3
作者：
Fishbein L;Leshchiner I;Walter V;Danilova L;Robertson AG;Johnson AR;Lichtenberg TM;Murray BA;Ghayee HK;Else T;Ling S;Jefferys SR;de Cubas AA;Wenz B;Korpershoek E;Amelio AL;Makowski L;Rathmell WK;Gimenez-Roqueplo AP;Giordano TJ;Asa SL;Tischler AS;Cancer Genome Atlas Research Network;Pacak K;Nathanson KL;Wilkerson MD
通讯作者：
Wilkerson MD
影响因子：
14.9
作者：
Keshava Prasad TS;Goel R;Kandasamy K;Keerthikumar S;Kumar S;Mathivanan S;Telikicherla D;Raju R;Shafreen B;Venugopal A;Balakrishnan L;Marimuthu A;Banerjee S;Somanathan DS;Sebastian A;Rani S;Ray S;Harrys Kishore CJ;Kanth S;Ahmed M;Kashyap MK;Mohmood R;Ramachandra YL;Krishna V;Rahiman BA;Mohan S;Ranganathan P;Ramabadran S;Chaerkady R;Pandey A
通讯作者：
Pandey A
影响因子：
64.5
作者：
Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu;Cancer Genome Atlas Research Network
通讯作者：
Cancer Genome Atlas Research Network
影响因子：
14.9
作者：
Lee M;Lee K;Yu N;Jang I;Choi I;Kim P;Jang YE;Kim B;Kim S;Lee B;Kang J;Lee S
通讯作者：
Lee S