2024-03-29T09:18:02Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/123102019-08-30T11:37:00Zcom_10033_6822com_10033_6821com_10033_6820col_10033_6895
He, Feng
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Zeng, An-Ping
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2007-06-08T14:30:36Z
2007-06-08T14:30:36Z
2006
BMC Bioinformatics 2006, 7:69
1471-2105
16478547
10.1186/1471-2105-7-69
http://hdl.handle.net/10033/12310
BACKGROUND: The increasing availability of time-series expression data opens up new possibilities to study functional linkages of genes. Present methods used to infer functional linkages between genes from expression data are mainly based on a point-to-point comparison. Change trends between consecutive time points in time-series data have been so far not well explored. RESULTS: In this work we present a new method based on extracting main features of the change trend and level of gene expression between consecutive time points. The method, termed as trend correlation (TC), includes two major steps: 1, calculating a maximal local alignment of change trend score by dynamic programming and a change trend correlation coefficient between the maximal matched change levels of each gene pair; 2, inferring relationships of gene pairs based on two statistical extraction procedures. The new method considers time shifts and inverted relationships in a similar way as the local clustering (LC) method but the latter is merely based on a point-to-point comparison. The TC method is demonstrated with data from yeast cell cycle and compared with the LC method and the widely used Pearson correlation coefficient (PCC) based clustering method. The biological significance of the gene pairs is examined with several large-scale yeast databases. Although the TC method predicts an overall lower number of gene pairs than the other two methods at a same p-value threshold, the additional number of gene pairs inferred by the TC method is considerable: e.g. 20.5% compared with the LC method and 49.6% with the PCC method for a p-value threshold of 2.7E-3. Moreover, the percentage of the inferred gene pairs consistent with databases by our method is generally higher than the LC method and similar to the PCC method. A significant number of the gene pairs only inferred by the TC method are process-identity or function-similarity pairs or have well-documented biological interactions, including 443 known protein interactions and some known cell cycle related regulatory interactions. It should be emphasized that the overlapping of gene pairs detected by the three methods is normally not very high, indicating a necessity of combining the different methods in search of functional association of genes from time-series data. For a p-value threshold of 1E-5 the percentage of process-identity and function-similarity gene pairs among the shared part of the three methods reaches 60.2% and 55.6% respectively, building a good basis for further experimental and functional study. Furthermore, the combined use of methods is important to infer more complete regulatory circuits and network as exemplified in this study. CONCLUSION: The TC method can significantly augment the current major methods to infer functional linkages and biological network and is well suitable for exploring temporal relationships of gene expression in time-series data.
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In search of functional association from time-series microarray data based on the change trend and level of gene expression.
Article
2018-06-13T05:37:18Z
BACKGROUND: The increasing availability of time-series expression data opens up new possibilities to study functional linkages of genes. Present methods used to infer functional linkages between genes from expression data are mainly based on a point-to-point comparison. Change trends between consecutive time points in time-series data have been so far not well explored. RESULTS: In this work we present a new method based on extracting main features of the change trend and level of gene expression between consecutive time points. The method, termed as trend correlation (TC), includes two major steps: 1, calculating a maximal local alignment of change trend score by dynamic programming and a change trend correlation coefficient between the maximal matched change levels of each gene pair; 2, inferring relationships of gene pairs based on two statistical extraction procedures. The new method considers time shifts and inverted relationships in a similar way as the local clustering (LC) method but the latter is merely based on a point-to-point comparison. The TC method is demonstrated with data from yeast cell cycle and compared with the LC method and the widely used Pearson correlation coefficient (PCC) based clustering method. The biological significance of the gene pairs is examined with several large-scale yeast databases. Although the TC method predicts an overall lower number of gene pairs than the other two methods at a same p-value threshold, the additional number of gene pairs inferred by the TC method is considerable: e.g. 20.5% compared with the LC method and 49.6% with the PCC method for a p-value threshold of 2.7E-3. Moreover, the percentage of the inferred gene pairs consistent with databases by our method is generally higher than the LC method and similar to the PCC method. A significant number of the gene pairs only inferred by the TC method are process-identity or function-similarity pairs or have well-documented biological interactions, including 443 known protein interactions and some known cell cycle related regulatory interactions. It should be emphasized that the overlapping of gene pairs detected by the three methods is normally not very high, indicating a necessity of combining the different methods in search of functional association of genes from time-series data. For a p-value threshold of 1E-5 the percentage of process-identity and function-similarity gene pairs among the shared part of the three methods reaches 60.2% and 55.6% respectively, building a good basis for further experimental and functional study. Furthermore, the combined use of methods is important to infer more complete regulatory circuits and network as exemplified in this study. CONCLUSION: The TC method can significantly augment the current major methods to infer functional linkages and biological network and is well suitable for exploring temporal relationships of gene expression in time-series data.
ORIGINAL
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oai:repository.helmholtz-hzi.de:10033/231552019-08-30T11:30:58Zcom_10033_6822com_10033_6821com_10033_6820col_10033_6895
Liu, YH
7dab6cdbe8fd005d8fb10dd5d435757c
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Bi, JX
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Zeng, An-Ping
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Yuan, JQ
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Department of Automation, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, People’s Republic of China.
2008-04-14T09:17:54Z
2008-04-14T09:17:54Z
2008-02-06
A simple kinetic model for myeloma cell culture with consideration of lysine limitation. 2008:notBioprocess Biosyst Eng
1615-7591
18253755
10.1007/s00449-008-0204-x
http://hdl.handle.net/10033/23155
Bioprocess and biosystems engineering
A simple kinetic model is developed to describe the dynamic behavior of myeloma cell growth and cell metabolism. Glucose, glutamine as well as lysine are considered as growth limiting substrates. The cell growth was restricted as soon as the extracellular lysine is exhausted and then intracellular lysine becomes a growth limiting substrate. In addition, a metabolic regulator model together with the Monod model is used to deal with the growth lag phase after inoculation or feeding. By using these models, concentrations of substrates and metabolites, as well as densities of viable and dead cells are quantitatively described. One batch cultivation and two fed-batch cultivations with pulse feeding of nutrients are used to validate the model.
ENG
null
A simple kinetic model for myeloma cell culture with consideration of lysine limitation.
Article
2018-06-13T03:48:20Z
A simple kinetic model is developed to describe the dynamic behavior of myeloma cell growth and cell metabolism. Glucose, glutamine as well as lysine are considered as growth limiting substrates. The cell growth was restricted as soon as the extracellular lysine is exhausted and then intracellular lysine becomes a growth limiting substrate. In addition, a metabolic regulator model together with the Monod model is used to deal with the growth lag phase after inoculation or feeding. By using these models, concentrations of substrates and metabolites, as well as densities of viable and dead cells are quantitatively described. One batch cultivation and two fed-batch cultivations with pulse feeding of nutrients are used to validate the model.
ORIGINAL
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original manuscript
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oai:repository.helmholtz-hzi.de:10033/3243302019-08-30T11:30:58Zcom_10033_6822com_10033_6821com_10033_6820col_10033_6895
He, Feng
8fc023c0b668c40162f280163e029d14
500
Buer, Jan
0bc7f6a1fc536d7a99daf43ff0b3c37f
500
Zeng, An-Ping
7cf60e8eb5943f375521d6c0c84b33af
500
Balling, Rudi
7a10c90e297f2fc48dc2944e22e8e57a
500
Helmholtz Centre of infection research, Inhoffenstr. 7, D38124 Braunschweig, Germany
2014-08-06T14:02:12Z
2014-08-06T14:02:12Z
2007
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. 2007, 8 (9):R181 Genome Biol.
1465-6914
17784952
10.1186/gb-2007-8-9-r181
http://hdl.handle.net/10033/324330
Genome biology
The regulation of genes in multicellular organisms is generally achieved through the combinatorial activity of different transcription factors. However, the quantitative mechanisms of how a combination of transcription factors controls the expression of their target genes remain unknown.
en
Archived with thanks to Genome biology
Algorithms
Amino Acid Motifs
Binding Sites
Biotechnology
Cell Cycle
False Positive Reactions
Fungal Proteins
Gene Expression Regulation, Fungal
Genes, Fungal
Models, Genetic
Models, Theoretical
Saccharomyces cerevisiae
Transcription Factors
Transcription, Genetic
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation.
Article
2018-06-12T22:09:32Z
The regulation of genes in multicellular organisms is generally achieved through the combinatorial activity of different transcription factors. However, the quantitative mechanisms of how a combination of transcription factors controls the expression of their target genes remain unknown.
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Helmholtz Zentrum für Infektionsforschung Repository
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oai:repository.helmholtz-hzi.de:10033/3248022019-08-30T11:30:32Zcom_10033_6822com_10033_6821com_10033_6820col_10033_6895
Stelzer, Michael
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Sun, Jibin
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Kamphans, Tom
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Fekete, Sándor P
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Zeng, An-Ping
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2014-08-14T12:52:18Z
2014-08-14T12:52:18Z
2011-11
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. 2011, 3 (11):1071-86 Integr Biol (Camb)
1757-9708
21952610
10.1039/c1ib00008j
http://hdl.handle.net/10033/324802
Integrative biology : quantitative biosciences from nano to macro
The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270-277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.
en
Archived with thanks to Integrative biology : quantitative biosciences from nano to macro
Algorithms
Aspergillus niger
Computational Biology
Databases, Factual
Databases, Genetic
Escherichia coli
Genome
Glucose
Humans
Metabolic Networks and Pathways
Models, Biological
Software
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.
Article
2018-06-13T04:22:27Z
The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270-277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.
ORIGINAL
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oai:hzi.openrepository.com:10033/324802
2019-08-30 11:30:32.238
Helmholtz Zentrum für Infektionsforschung Repository
hzi@openrepository.com
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