Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data.
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热*SEQ：用于与公共数据的高通量测序实验比较的交互式Web工具。
DOI：
10.1093/bioinformatics/btw407
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发表时间：
2016-11-01
期刊：
影响因子：
--
通讯作者：
Joshi A
中科院分区：
文献类型：
--
作者：
Devailly G;Mantsoki A;Joshi A
总结：更好的方案和降低的成本使得高通量测序实验现在甚至对小型实验室也是可行的。然而，由于缺乏生物信息学专业知识，将单个实验室生成的一个或几个实验与公共领域中免费提供的大量相关数据进行比较可能会受到限制。尽管包括基因组浏览器在内的一些工具允许在单个基因水平上进行这种比较，但它们并不能提供全基因组的视角。我们开发了Heat*seq，这是一种网络工具，允许将用户提供的高通量实验（染色质免疫沉淀，随后测序，RNA测序和基因表达的Cap分析）的基因组规模与公共领域的数据进行比较。Heat*seq目前包含超过12，000个实验，涉及人类、小鼠和果蝇的不同组织和细胞类型。Heat*seq显示交互式相关热图，能够动态地子集化数据集以使用户实验情境化。高质量的数字和表格可以以多种格式下载。可用性和实施：Web应用程序：http://www.heatstarseq.roslin.ed.ac.uk/。源代码：https://github.com/gdevailly。联系人：Guillaume. roslin.ed.ac.uk或Anagha. roslin.ed.ac.uk补充信息：补充数据可在生物信息学在线获得。
Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats. Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/. Source code: https://github.com/gdevailly. Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Sánchez-Castillo M;Ruau D;Wilkinson AC;Ng FS;Hannah R;Diamanti E;Lombard P;Wilson NK;Gottgens B
通讯作者：
Gottgens B
影响因子：
14.9
作者：
Karolchik, D;Hinrichs, AS;Kent, WJ
通讯作者：
Kent, WJ
影响因子：
64.8
作者：
Roadmap Epigenomics Consortium;Kundaje A;Meuleman W;Ernst J;Bilenky M;Yen A;Heravi-Moussavi A;Kheradpour P;Zhang Z;Wang J;Ziller MJ;Amin V;Whitaker JW;Schultz MD;Ward LD;Sarkar A;Quon G;Sandstrom RS;Eaton ML;Wu YC;Pfenning AR;Wang X;Claussnitzer M;Liu Y;Coarfa C;Harris RA;Shoresh N;Epstein CB;Gjoneska E;Leung D;Xie W;Hawkins RD;Lister R;Hong C;Gascard P;Mungall AJ;Moore R;Chuah E;Tam A;Canfield TK;Hansen RS;Kaul R;Sabo PJ;Bansal MS;Carles A;Dixon JR;Farh KH;Feizi S;Karlic R;Kim AR;Kulkarni A;Li D;Lowdon R;Elliott G;Mercer TR;Neph SJ;Onuchic V;Polak P;Rajagopal N;Ray P;Sallari RC;Siebenthall KT;Sinnott-Armstrong NA;Stevens M;Thurman RE;Wu J;Zhang B;Zhou X;Beaudet AE;Boyer LA;De Jager PL;Farnham PJ;Fisher SJ;Haussler D;Jones SJ;Li W;Marra MA;McManus MT;Sunyaev S;Thomson JA;Tlsty TD;Tsai LH;Wang W;Waterland RA;Zhang MQ;Chadwick LH;Bernstein BE;Costello JF;Ecker JR;Hirst M;Meissner A;Milosavljevic A;Ren B;Stamatoyannopoulos JA;Wang T;Kellis M
通讯作者：
Kellis M
影响因子：
14.9
作者：
Attrill H;Falls K;Goodman JL;Millburn GH;Antonazzo G;Rey AJ;Marygold SJ;FlyBase Consortium
通讯作者：
FlyBase Consortium
影响因子：
30.8
作者：
Lonsdale, John;Thomas, Jeffrey;Salvatore, Mike;Phillips, Rebecca;Lo, Edmund;Shad, Saboor;Hasz, Richard;Walters, Gary;Garcia, Fernando;Young, Nancy;Foster, Barbara;Moser, Mike;Karasik, Ellen;Gillard, Bryan;Ramsey, Kimberley;Sullivan, Susan;Bridge, Jason;Magazine, Harold;Syron, John;Fleming, Johnelle;Siminoff, Laura;Traino, Heather;Mosavel, Maghboeba;Barker, Laura;Jewell, Scott;Rohrer, Dan;Maxim, Dan;Filkins, Dana;Harbach, Philip;Cortadillo, Eddie;Berghuis, Bree;Turner, Lisa;Hudson, Eric;Feenstra, Kristin;Sobin, Leslie;Robb, James;Branton, Phillip;Korzeniewski, Greg;Shive, Charles;Tabor, David;Qi, Liqun;Groch, Kevin;Nampally, Sreenath;Buia, Steve;Zimmerman, Angela;Smith, Anna;Burges, Robin;Robinson, Karna;Valentino, Kim;Bradbury, Deborah;Cosentino, Mark;Diaz-Mayoral, Norma;Kennedy, Mary;Engel, Theresa;Williams, Penelope;Erickson, Kenyon;Ardlie, Kristin;Winckler, Wendy;Getz, Gad;DeLuca, David;MacArthur, Daniel;Kellis, Manolis;Thomson, Alexander;Young, Taylor;Gelfand, Ellen;Donovan, Molly;Meng, Yan;Grant, George;Mash, Deborah;Marcus, Yvonne;Basile, Margaret;Liu, Jun;Zhu, Jun;Tu, Zhidong;Cox, Nancy J.;Nicolae, Dan L.;Gamazon, Eric R.;Im, Hae Kyung;Konkashbaev, Anuar;Pritchard, Jonathan;Stevens, Matthew;Flutre, Timothee;Wen, Xiaoquan;Dermitzakis, Emmanouil T.;Lappalainen, Tuuli;Guigo, Roderic;Monlong, Jean;Sammeth, Michael;Koller, Daphne;Battle, Alexis;Mostafavi, Sara;McCarthy, Mark;Rivas, Manual;Maller, Julian;Rusyn, Ivan;Nobel, Andrew;Wright, Fred;Shabalin, Andrey;Feolo, Mike;Sharopova, Nataliya;Sturcke, Anne;Paschal, Justin;Anderson, James M.;Wilder, Elizabeth L.;Derr, Leslie K.;Green, Eric D.;Struewing, Jeffery P.;Temple, Gary;Volpi, Simona;Boyer, Joy T.;Thomson, Elizabeth J.;Guyer, Mark S.;Cathy Ng;Abdallah, Assya;Colantuoni, Deborah;Insel, Thomas R.;Koester, Susan E.;Little, A. Roger;Bender, Patrick K.;Lehner, Thomas;Yao, Yin;Compton, Carolyn C.;Vaught, Jimmie B.;Sawyer, Sherilyn;Lockhart, Nicole C.;Demchok, Joanne;Moore, Helen F.
通讯作者：
Moore, Helen F.