publication . Article . 2015

ReactionFlow: an interactive visualization tool for causality analysis in biological pathways.

Dang, Tuan Nhon; Murray, Paul; Aurisano, Jillian; Forbes, Angus Graeme;
Open Access English
  • Published: 01 Aug 2015 Journal: BMC Proceedings, volume 9, issue Suppl 6, page S6 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
Background Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins. Results We...
Subjects
free text keywords: Research, Pathway visualization, Biological networks, Causality analysis, Topological ordering
28 references, page 1 of 2

Hanahan, D, Weinberg, RA. Hallmarks of cancer: the next generation. Cell. 2011; 144 (5): 646-674 [OpenAIRE] [PubMed] [DOI]

Cairns, RA, Harris, IS, Mak, TW. Regulation of cancer cell metabolism. Nature Reviews Cancer. 2011; 11 (2): 85-95 [PubMed] [DOI]

Luo, J, Manning, BD, Cantley, LC. Targeting the pi3k-akt pathway in human cancer-rationale and promise. Cancer Cell. 2003; 4 (4): 257-262 [OpenAIRE] [PubMed] [DOI]

Reya, T, Morrison, SJ, Clarke, MF, Weissman, IL. Stem cells, cancer, and cancer stem cells. Nature. 2011; 414 (6859): 105-111 [PubMed]

Albrecht, M, Kerren, A, Klein, K, Kohlbacher, O, Mutzel, P, Paul, W, Schreiber, F, Wybrow, M. On open problems in biological network visualization. Graph Drawing Lecture Notes in Computer Science. 2010; 5849: 256-267 [OpenAIRE] [DOI]

Kerren, A, Schreiber, F. Network visualization for integrative bioinformatics. Approaches in Integrative Bioinformatics. 2014: 173-202

Kitano, H. Systems biology: a brief overview. Science. 2002; 295 (5560): 1662-1664 [OpenAIRE] [PubMed] [DOI]

Saraiya, P, North, C, Duca, K. Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Information Visualization. 2005; 4 (3): 191-205 [OpenAIRE] [DOI]

Dubitzky, W, Wolkenhauer, O, Cho, KH, Yokota, H. Encyclopedia of Systems Biology. 2013

Croft, D, Mundo, AF, Haw, R, Milacic, M, Weiser, J, Wu, G. The reactome pathway knowledgebase. Nucleic Acids Research. 2014; 42 (D1): D472-D477 [PubMed] [DOI]

Lex, A, Partl, C, Kalkofen, D, Streit, M, Gratzl, S, Wassermann, AM. Entourage: Visualizing relationships between biological pathways using contextual subsets. Visualization and Computer Graphics, IEEE Transactions. 2013; 19 (12): 2536-2545 [OpenAIRE]

Shannon, P, Markiel, A, Ozier, O, Baliga, NS, Wang, JT, Ramage, D. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003; 13 (11): 2498-2504 [OpenAIRE] [PubMed] [DOI]

Babur, O, Dogrusoz, U, Demir, E, Sander, C. Chibe: interactive visualization and manipulation of biopax pathway models. Bioinformatics. 2010; 26 (3): 429-431 [OpenAIRE] [PubMed] [DOI]

Junker, B, Klukas, C, Schreiber, F. Vanted: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006; 7 (1): 109 [OpenAIRE] [PubMed] [DOI]

Demir, E, Cary, MP, Paley, S, Fukuda, K, Lemer, C, Vastrik, I. The biopax community standard for pathway data sharing. Nature Biotechnology. 2010; 28 (9): 935-942 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
Abstract
Background Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins. Results We...
Subjects
free text keywords: Research, Pathway visualization, Biological networks, Causality analysis, Topological ordering
28 references, page 1 of 2

Hanahan, D, Weinberg, RA. Hallmarks of cancer: the next generation. Cell. 2011; 144 (5): 646-674 [OpenAIRE] [PubMed] [DOI]

Cairns, RA, Harris, IS, Mak, TW. Regulation of cancer cell metabolism. Nature Reviews Cancer. 2011; 11 (2): 85-95 [PubMed] [DOI]

Luo, J, Manning, BD, Cantley, LC. Targeting the pi3k-akt pathway in human cancer-rationale and promise. Cancer Cell. 2003; 4 (4): 257-262 [OpenAIRE] [PubMed] [DOI]

Reya, T, Morrison, SJ, Clarke, MF, Weissman, IL. Stem cells, cancer, and cancer stem cells. Nature. 2011; 414 (6859): 105-111 [PubMed]

Albrecht, M, Kerren, A, Klein, K, Kohlbacher, O, Mutzel, P, Paul, W, Schreiber, F, Wybrow, M. On open problems in biological network visualization. Graph Drawing Lecture Notes in Computer Science. 2010; 5849: 256-267 [OpenAIRE] [DOI]

Kerren, A, Schreiber, F. Network visualization for integrative bioinformatics. Approaches in Integrative Bioinformatics. 2014: 173-202

Kitano, H. Systems biology: a brief overview. Science. 2002; 295 (5560): 1662-1664 [OpenAIRE] [PubMed] [DOI]

Saraiya, P, North, C, Duca, K. Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Information Visualization. 2005; 4 (3): 191-205 [OpenAIRE] [DOI]

Dubitzky, W, Wolkenhauer, O, Cho, KH, Yokota, H. Encyclopedia of Systems Biology. 2013

Croft, D, Mundo, AF, Haw, R, Milacic, M, Weiser, J, Wu, G. The reactome pathway knowledgebase. Nucleic Acids Research. 2014; 42 (D1): D472-D477 [PubMed] [DOI]

Lex, A, Partl, C, Kalkofen, D, Streit, M, Gratzl, S, Wassermann, AM. Entourage: Visualizing relationships between biological pathways using contextual subsets. Visualization and Computer Graphics, IEEE Transactions. 2013; 19 (12): 2536-2545 [OpenAIRE]

Shannon, P, Markiel, A, Ozier, O, Baliga, NS, Wang, JT, Ramage, D. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003; 13 (11): 2498-2504 [OpenAIRE] [PubMed] [DOI]

Babur, O, Dogrusoz, U, Demir, E, Sander, C. Chibe: interactive visualization and manipulation of biopax pathway models. Bioinformatics. 2010; 26 (3): 429-431 [OpenAIRE] [PubMed] [DOI]

Junker, B, Klukas, C, Schreiber, F. Vanted: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006; 7 (1): 109 [OpenAIRE] [PubMed] [DOI]

Demir, E, Cary, MP, Paley, S, Fukuda, K, Lemer, C, Vastrik, I. The biopax community standard for pathway data sharing. Nature Biotechnology. 2010; 28 (9): 935-942 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
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