Figure 2 - uploaded by Jürgen Zanghellini
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Comparison between iCHO3K and its predecessors: (A) Comparison of 275 iCHO3K with previous CHO metabolic reconstructions (iCHO1766, iCHO2101, and 276 iCHO2291) in terms of the number of reactions, metabolites and genes. (B) The 277 proportion of reactions in iCHO3K with comprehensive gene-protein-reaction (GPR) 278 annotations, covering 7,920 reactions (72% of the total), which considerably enhances 279 transcriptomic and proteomic data integration from CHO cell lines. (C) Comparison of the 280 number of reactions per system in each reconstruction, highlighting the expanded 281 metabolic pathways in iCHO3K. (D) Experimentally validated essential genes included in 282 each CHO reconstruction. (E) Correlation between experimentally validated essential 283
Source publication
Genome-scale metabolic models (GEMs) are indispensable for studying and engineering cellular metabolism. Here, we present i CHO3K, a community-consensus, manually-curated reconstruction of the Chinese Hamster metabolic network. In addition to accounting for 11004 reactions associated with 3597 genes, i CHO3K includes 3489 protein structures and str...
Contexts in source publication
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... demonstrates a considerable expansion of the metabolic network, 224 incorporating between 3500 -4700 more reactions than earlier models. Moreover, it 225 includes 1216 additional genes compared to the most extensive prior CHO 226 reconstruction, iCHO2291 (Figure 2A). 227 A standout feature of iCHO3K is its comprehensive GPR annotation. ...
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... A standout feature of iCHO3K is its comprehensive GPR annotation. The model 228 includes 3,597 genes with detailed associations to 7,920 reactions, accounting for 72% 229 of the total reactions in the reconstruction ( Figure 2B). was not certified by peer review) is the author/funder. ...
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... alignment allowed us to directly compare the 245 number of reactions present in each system between iCHO3K and its predecessors. Our 246 analysis revealed that iCHO3K surpasses previous reconstructions in the number of 247 reactions within every principal system, indicating a comprehensive expansion rather than 248 isolated additions in specific pathways ( Figure 2C). Notably, in the system of "Lipid 249 ...
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... that 257 these genes are involved in diverse biological processes, it is expected that not all of them 258 will be linked to metabolic reactions 40 . However, a comparison across all metabolic 259 reconstructions revealed that iCHO3K contains the largest number of genes overlapping 260 with this dataset (Figure 2D), which indicates that this reconstruction includes more 261 genes fundamental for cell growth. was not certified by peer review) is the author/funder. ...
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... while iCHO3K showed the broadest coverage of essential genes, iCHO2291 268 performed better in accurately predicting essential genes that were experimentally 269 validated ( Figure 2E). This discrepancy may be attributed to the additional reactions in 270 iCHO3K, which could render some previously essential reactions non-essential due to 271 the presence of alternative pathways capable of producing essential metabolites required 272 for growth. ...
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... demonstrates a considerable expansion of the metabolic network, 224 incorporating between 3500 -4700 more reactions than earlier models. Moreover, it 225 includes 1216 additional genes compared to the most extensive prior CHO 226 reconstruction, iCHO2291 (Figure 2A). 227 A standout feature of iCHO3K is its comprehensive GPR annotation. ...
Context 7
... A standout feature of iCHO3K is its comprehensive GPR annotation. The model 228 includes 3,597 genes with detailed associations to 7,920 reactions, accounting for 72% 229 of the total reactions in the reconstruction ( Figure 2B). was not certified by peer review) is the author/funder. ...
Context 8
... alignment allowed us to directly compare the 245 number of reactions present in each system between iCHO3K and its predecessors. Our 246 analysis revealed that iCHO3K surpasses previous reconstructions in the number of 247 reactions within every principal system, indicating a comprehensive expansion rather than 248 isolated additions in specific pathways ( Figure 2C). Notably, in the system of "Lipid 249 ...
Context 9
... that 257 these genes are involved in diverse biological processes, it is expected that not all of them 258 will be linked to metabolic reactions 40 . However, a comparison across all metabolic 259 reconstructions revealed that iCHO3K contains the largest number of genes overlapping 260 with this dataset (Figure 2D), which indicates that this reconstruction includes more 261 genes fundamental for cell growth. was not certified by peer review) is the author/funder. ...
Context 10
... while iCHO3K showed the broadest coverage of essential genes, iCHO2291 268 performed better in accurately predicting essential genes that were experimentally 269 validated ( Figure 2E). This discrepancy may be attributed to the additional reactions in 270 iCHO3K, which could render some previously essential reactions non-essential due to 271 the presence of alternative pathways capable of producing essential metabolites required 272 for growth. ...
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