BioProfiling.de: analytical web portal for high-throughput cell biology

被引：98
作者：
Antonov, Alexey V. [1 ]
机构：
[1] German Res Ctr Environm Hlth GmbH, Helmholtz Zentrum Munchen, Inst Bioinformat & Syst Biol, D-85764 Neuherberg, Germany
来源：
NUCLEIC ACIDS RESEARCH | 2011年 / 39卷
关键词：
GENE ONTOLOGY; LISTS; PROTEIN; TOOL; SPIDER; KEGG; PATHWAYS; REACTOME; DATABASE; CONTEXT;
D O I：
10.1093/nar/gkr372
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
BioProfiling.de provides a comprehensive analytical toolkit for the interpretation gene/protein lists. As input, BioProfiling.de accepts a gene/protein list. As output, in one submission, the gene list is analyzed by a collection of tools which employs advanced enrichment or network-based statistical frameworks. The gene list is profiled with respect to the most information available regarding gene function, protein interactions, pathway relationships, in silico predicted microRNA to gene associations, as well as, information collected by text mining. BioProfiling.de provides a user friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. The web portal is freely available at http://www.BioProfiling.de/gene_list.
引用
收藏
页码：W323 / W327
页数：5
相关论文
共 27 条
[1]   ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data [J].
Antonov, Alexey V. ;
Schmidt, Thorsten ;
Wang, Yu ;
Mewes, Hans W. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :W347-W351
[2]   R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases [J].
Antonov, Alexey V. ;
Schmidt, Esther E. ;
Dietmann, Sabine ;
Krestyaninova, Maria ;
Hermjakob, Henning .
NUCLEIC ACIDS RESEARCH, 2010, 38 :W78-W83
[3]   PPI spider: A tool for the interpretation of proteomics data in the context of protein-protein interaction networks [J].
Antonov, Alexey V. ;
Dietmann, Sabine ;
Rodchenkov, Igor ;
Mewes, Hans W. .
PROTEOMICS, 2009, 9 (10) :2740-2749
[4]   KEGG spider: interpretation of genomics data in the context of the global gene metabolic network [J].
Antonov, Alexey V. ;
Dietmann, Sabine ;
Mewes, Hans W. .
GENOME BIOLOGY, 2008, 9 (12)
[5]   GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists [J].
Antonov, Alexey V. ;
Dietmann, Sabine ;
Wong, Philip ;
Lutter, Dominik ;
Mewes, Hans W. .
NUCLEIC ACIDS RESEARCH, 2009, 37 :W323-W328
[6]   TICL - a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics [J].
Antonov, Alexey V. ;
Dietmann, Sabine ;
Wong, Philip ;
Mewes, Hans W. .
FEBS JOURNAL, 2009, 276 (07) :2084-2094
[7]   PLIPS, an Automatically Collected Database of Protein Lists Reported by Proteomics Studies [J].
Antonov, Alexey V. ;
Dietmann, Sabine ;
Wong, Philip ;
Igor, Rodchenkov ;
Mewes, Hans W. .
JOURNAL OF PROTEOME RESEARCH, 2009, 8 (03) :1193-1197
[8]   The IntAct molecular interaction database in 2010 [J].
Aranda, B. ;
Achuthan, P. ;
Alam-Faruque, Y. ;
Armean, I. ;
Bridge, A. ;
Derow, C. ;
Feuermann, M. ;
Ghanbarian, A. T. ;
Kerrien, S. ;
Khadake, J. ;
Kerssemakers, J. ;
Leroy, C. ;
Menden, M. ;
Michaut, M. ;
Montecchi-Palazzi, L. ;
Neuhauser, S. N. ;
Orchard, S. ;
Perreau, V. ;
Roechert, B. ;
van Eijk, K. ;
Hermjakob, H. .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D525-D531
[9]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[10]   MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets [J].
Baron, Daniel ;
Bihouee, Audrey ;
Teusan, Raluca ;
Dubois, Emeric ;
Savagner, Frederique ;
Steenman, Marja ;
Houlgatte, Remi ;
Ramstein, Gerard .
BIOINFORMATICS, 2011, 27 (05) :725-726
123