Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila
Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as a suitable network perturbation and that integration of data from multiple closely related species can lead to improved reconstruction of gene regulatory networks. To test this hypothesis, we predicted networks from temporal gene expression data for 3,610 genes measured during early embryonic development in six Drosophila species and compared predicted networks to gold standard networks of ChIP-chip and ChIP-seq interactions for developmental transcription factors in five species. We found that (i) the performance of single-species networks was independent of the species where the gold standard was measured; (ii) differences between predicted networks reflected the known phylogeny and differences in biology between the species; (iii) an integrative consensus network which minimized the total number of edge gains and losses with respect to all single-species networks performed better than any individual network. Our results show that in an evolutionarily conserved system, integration of data from comparable experiments in multiple species improves the inference of gene regulatory networks. They provide a basis for future studies on the numerous multi-species gene expression datasets for other biological processes available in the literature.
Division of Developmental Biology and Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Midlothian EH25 9RG, Scotland, United Kingdom
Current address: Institute for Applied System Dynamics, Aalen University, Beethovenstrasse 1, 73430 Aalen, Germany
Corresponding author, E-mail: email@example.com
In systems biology it is hypothesized that causal regulatory influences between transcription factors (TFs) and their target genes can be reconstructed by observing changes in gene expression levels during dynamic processes or in response to perturbing the cell by gene mutations or extra-cellular signals [1, 2]. As increasing amounts of gene expression data have become available, numerous computational and statistical methods have been developed to address the gene network inference problem (reviewed in [3, 4, 5, 6, 7, 8]). Spurred by the observation that different methods applied to the same dataset can uncover complementary aspects of the underlying regulatory network [9, 10], it is now firmly established that community-based methods which integrate predictions from multiple methods perform better than individual methods . A dimension that has remained unexplored in gene regulatory network inference is evolution: Does the integration of data from multiple related species lead to improved network inference performance? Numerous comparative analyses of gene expression data from multiple species have been performed [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26], but invariably these have studied conservation and divergence of individual gene expression profiles or co-expression modules. However, it is known that (co-)expression can be conserved despite divergence of upstream cis-regulatory sequences, and although shuffling of TF-binding sites does not necessarily alter the topology of the TF–target network, cases have been documented where conserved co-expression modules are regulated by different TFs in different species (“TF switching”) (reviewed in ). It is therefore not a priori obvious if and how multi-species expression data can be harnessed for gene regulatory network inference.
To address this question we decided to focus on a regulatory model system that is well characterized and conserved across multiple species. We were therefore particularly interested in a study where gene expression was measured at several time points during early embryonic development in six Drosophila species, including the model organism D. melanogaster . Early development of the animal body plan is a highly conserved process, controlled by gene regulatory network components resistant to evolutionary change . Furthermore, the binding sites of around half of all sequence-specific regulators controlling transcription in the blastoderm in D. melanogaster have been mapped on a genome-wide scale by ChIP-chip  and for several of these factors additional binding profiles mapped by ChIP-sequencing are available in other Drosophila species [30, 31, 32]. In this study we took advantage of these unique gold standard networks of regulatory interactions across multiple species to predict and evaluate gene regulatory networks from gene expression data in six species, study their phylogeny and biology, and analyze how an integrated multi-species approach improves network inference performance.
2.1 Evolutionary and developmental dynamics have comparable effects on gene expression
We collected gene expression data for 3,610 genes in six Drosophila species measured at 9–13 time points during early embryonic development with 3–8 replicates per time point (200 samples in total) . To obtain a global view on the similarities and differences between samples, we performed multi-dimensional scaling using Sammon’s nonlinear mapping criterion on the 3,610-dimensional sample vectors (cf. Methods and Figure 1a). The first (horizontal) axis of variation corresponded to developmental time, with samples ordered along this dimension according to increasing developmental time points, while the second (vertical) axis of variation corresponded to evolutionary distance, with samples ordered along this dimension according to species. By expanding these two axes of variation into principal components, we found that the “developmental” dimension explained 34% of the total variation in the data, while the “evolutionary” dimension explained 11% (cf. Methods). This result confirms that variations in gene expression levels across Drosophila species at the same developmental time point are not greater than variations across time points within the same species. In this study we were interested whether this additional layer of inter-species expression variation can be harnessed in the reconstruction of gene regulatory networks.
2.2 Single-species network reconstruction recovers known transcriptional regulatory interactions in early Drosophila development
We used the context-likelihood of relatedness (CLR) algorithm  with Pearson correlation as a similarity measure to predict regulatory interactions in each species separately from the developmental gene expression data. As candidate regulators we used a set of 14 sequence-specific transcription factors (TFs) present on the expression array whose binding sites have been mapped by ChIP-chip in D. melanogaster at developmental time points relevant for the present study . A gold standard network of known transcriptional regulatory interactions in D. melanogaster development was constructed by assigning binding sites of these TFs to their closest gene (cf. Methods). The gold standard network was dense (25% of all possible edges were present) consistent with the fact that genes on the expression array were selected from genes known to be expressed during embryonic development  and that the 14 TFs comprise one-third of all sequence-specific regulators controlling transcription in the D. melanogaster blastoderm embryo .
We compared the predicted regulatory networks in all six species to the D. melanogaster gold standard network using standard recall and precision measurements . Without exception all six predicted networks showed percentages of true positives close to or in excess of 50% at a recall level of 10%, corresponding to networks with 1,300–1,400 predicted interactions (Table 1 and Figure 1b). Any differences in performance between species were found to be small (nearly identical areas under the curve (AUC), Figure 1b). The recall cut-off of 10% in Table 1 was chosen because it was closest for most species to the inflection point where precision starts to drop more rapidly with increasing recall. The levels of accuracy in network prediction obtained here have previously only been observed for bacteria [9, 8] and demonstrate the importance of using a gold standard network measured in an appropriate experimental condition. Indeed, when we used the more heterogeneous modENCODE  or Flynet  D. melanogaster reference networks, performance dropped dramatically (data not shown).
2.3 Chip-sequencing data confirms similar network reconstruction performance independent of species
Although the gold standard network reconstructed from ChIP-chip data was in D. melanogaster, perhaps surprisingly the D. melanogaster predicted network did not perform better overall than the networks predicted for the other species (Figure 1b). To get confidence in this observation, we downloaded ChIP-sequencing data for three TFs (BCD, KR, HB) in three Drosophila species (melanogaster, pseudoobscura and virilis)  and one TF (TWI) in four species (melanogaster, simulans, ananassae and pseudoobscura) , and created ChIP-seq gold standard networks for five species (cf. Methods). The recall-precision curves generated from the D. melanogaster ChIP-seq gold standard network (Supplementary Figure S1b) were in good agreement with the ChIP-chip data, demonstrating again that the D. melanogaster predicted network performed no better than other Drosophila species. We also calculated recall-precision curves using the D. ananassae, D. pseudobscura, D. simulans and D. virilis ChIP-seq gold standard networks. Again, the regulatory network in that species did not perform better compared to the other species (Supplementary Figure S1c–f).
2.4 Reconstructed regulatory networks are enriched for ubiquitous interactions
The result that network reconstruction performance is similar across species regardless of the species-origin of the gold standard network suggests that each species-specific dataset represents a different perturbation of an underlying conserved regulatory network. To better understand how the predicted networks in each species relate to each other, we analysed the reconstructed regulatory networks at the 10% recall level (Table 1) in greater detail. Taken together, these networks contained 3,329 regulatory interactions between 14 TFs and 1098 genes. About 10% of these interactions (382) were predicted in all species. To systematically evaluate if this overlap can occur by chance, we randomized independently each interaction network keeping its in- and out-degree distribution constant and calculated the frequencies of having one to six edges overlap in 100 randomized networks. The predicted networks were significantly enriched for interactions ubiquitous to all species (-score) and depleted for species-specific interactions (-score) (Figure 2a).
We then calculated if individual TFs were biased towards species-specific or ubiquitous interactions. Zygotic factors such as SNA () shared statistically significant predicted targets among all six species whereas maternal factors such as CAD did not share a single target across the six species. This together with the observation that early zygotic genes at sequence level evolved much slower  leads to the hypothesis that not only the sequences of early zygotic lineage genes but also the transcriptional program controlling their expression has evolved slower. The early zygotic genes are indeed overrepresented in the targets with conserved interactions across all species ().
The observation that prediction performance is independent of species (Figure S1) could be explained if only ubiquitous interactions (predicted in all species) were true positives. Although more true positives are found among interactions shared by three or more species than expected based on the total distribution of predicted interactions (Figure 2b), and with precision increasing by the number of species (Figure 2c), ubiquitous interactions account for only 18% of all true positives. Another possible explanation for the species-independent performance could be that binding events are highly conserved across species. Although it has been noted that more than 90% of TF binding sites overlapped between D. melanogaster and the closely related D. yakuba , less than 30% of those binding sites were also conserved in the more distant D. pseudoobscura . Furthermore it is also not true that conserved gold standard interactions for these TFs (BCD, HB and KR) are more likely to be inferred. Indeed, the recall for species-specific gold standard interactions or those conserved in two or three species for these factors in the 10% recall networks did not differ from the overall recall value (Figure 2d). In contrast, for the factor TWI, gold standard interactions conserved in three or four species were more likely to be included in the 10% recall networks (recall values resp. 19% and 36%, Figure 2d). This is consistent with a higher degree of binding site conservation for this factor with up to 60% conserved binding sites across six species .
2.5 Differences between predicted transcriptional regulatory networks reflect known phylogeny and biology
Since conservation of predicted or known gold standard interactions across species does not fully explain the observed species-independent network reconstruction performance, we hypothesized that the differences between these networks are not solely due to random variations in the expression data. To analyse these differences, we constructed a phylogenetic tree between the species based on the gain or loss of predicted interactions using the principle of maximum parsimony. This method minimises the number of state changes in all transitions in a tree and has been used previously to reconstruct the evolutionary history of species based on gene content  and to reconstruct and predict transition states of developmental lineage trees based on gene expression data . Using a binary matrix representing the presence or absence of all 3,329 predicted TF-target interactions in each of the 10% recall networks, a rooted tree was reconstructed which split the species in three groups: melanogaster (top), obscura (middle), virilis (bottom) (cf. Methods and Figure 2d). This tree is in full agreement with the tree reconstructed based on gene content . To ensure the robustness of the tree, we applied a standard bootstrap procedure which predicted 100% bootstrap confidence on all branches of the tree (Figure 2d). The parsimony tree, moreover, predicts the network state transitions at each branch in terms of interactions gained or lost at a given transition. The transitions show a bias towards gain of interactions at most branch points over the loss. This is probably due to the presence of a large number of species-specific interactions (Figure 2a).
We further explored whether the nine branch points (numbered 1–9 in Figure 2d) reflect the biology behind the evolution of the Drosophila species. We created gene lists at each branch point containing target genes which gained or lost transcriptional interactions at that branch point. The maximum number of genes (361) gained interactions from branch point ‘A’ to D. virilis and were enriched for neuron differentiation () and embryonic morphogenesis (). Genes gaining interactions from branch point ‘D’ to D. simulans were enriched for response to organic substances (), in line with the fact that D. simulans, unlike D. melanogaster, lives on diverse rotting, non-sweet substrates throughout the year . Gene ontology analysis of all target sets revealed that many gene sets were enriched for transcription regulation (Supplementary Table S1), i.e. transcriptional regulators were more likely to gain or lose interactions in the network rewiring. At each branch point, we found TFs losing or gaining interactions more than expected by chance (Supplementary Table S2). For instance, SLP1 is predicted to lose its interactions with genes involved in wing disc formation only in D. ananassae while Dorsal (DL) is predicted to regulate mitochondrial genes only in the melanogaster subgroup. Taken together, a biologically relevant evolutionary network history can be reconstructed using the individual predicted regulatory networks in six Drosophila species.
2.6 Multi-species analysis improves network reconstruction
It has been observed that different network inference algorithms applied to the same data uncover complementary aspects of the true underlying regulatory network [9, 10] and this has formed the basis for integrative approaches which combine the predictions from multiple algorithms . In our case, since the networks predicted from different species equally well recover known transcriptional interactions while their differences reflect known phylogeny and biology, we reasoned that a multi-species analysis which combines predictions across species should also lead to a better network reconstruction. To test this hypothesis we considered several integrative approaches. Firstly, we combined the expression data from all species into one dataset to which we again applied the CLR algorithm (“merged data” method). Secondly, we kept CLR scores from the individual species and applied rank-aggregation methods to derive an “intersection”, “union” and “average” consensus ranking of predicted interactions (cf. Methods). Finally, motivated by the phylogenetic tree reconstruction, we also constructed a consensus ranking as the centroid of the six species-specific rankings for the cityblock distance, which for discrete networks corresponds to counting total number of edge gains and losses between two networks (“centroid” method, see Methods for details).
To quantitatively compare different methods across different gold standard networks we considered the area under the recall–precision curve (AUC) and the precision at 10% recall (PREC10) as performance measures and converted them to -values by comparison to AUCs and PREC10s of networks generated by randomly assigning ranks to all possible edges in the corresponding gold standard network (cf. Methods and Figure S2 for the recall vs. precision curves). While the AUC assesses the overall performance of a predicted network, PREC10 measures the quality of the top-ranked predictions, a property that may be of greater practical relevance. This analysis showed that no predicted network performs best for either measure across all gold standards (Figure 3a-f). The single-species virilis networks performed best for 5 out of 12 AUC and PREC10 scores, albeit not for the ChIP-seq network measured in its own species. This overall good performance is consistent with virilis having the highest number of measured time points in the data (Supplementary Table S3). D. melanogaster also had more data points available than the other four species, but its time series were less complete (Supplementary Table S3). Among the integrative methods, the centroid and union methods both performed best for 5 out of 12 AUC and PREC10 scores (Figure 3a-f). Both also had higher average AUC score than the best single-species network, but only the centroid method had higher average PREC10 score than the best single-species network (Figure 3g). The most important result however is the fact that the single-species network for the species were the gold standard network was measured never has the highest single-species AUC and only twice has the highest PREC10. In contrast, the centroid method always performs as good, and in most cases better, than the single-species network for the reference species (Figure 3a-f). We conclude that the centroid method is the most robust network integration method achieving consistently high AUC and PREC10 scores, at least on this dataset.
Here we predicted and evaluated developmental gene regulatory networks from temporal gene expression data in six Drosophila species, studied their phylogeny and biology, and analyzed how an integrated multi-species analysis improved network inference performance using gold standard networks of regulatory interactions measured by ChIP-chip and ChIP-seq in five species.
We unexpectedly found that network prediction performance of the single-species networks was independent of the species where the gold standard was measured. With precision values around or greater than 50% at a recall level of 10% for all predicted networks, this result was clearly not due to poor overall prediction performance. Although there was a trend that interactions predicted in all species had higher precision than interactions predicted in only one species and that conserved interactions in the gold standard networks for at least one of the TFs had higher chance to be correctly predicted, neither trend was sufficiently strong to account for the observed performance similarities. An alternative or additional explanation could be that the “true” gene expression and binding profiles are highly conserved between these six species but the observed profiles show species-dependent variation due to the inherent noisyness of high-throughput data. Because such random fluctuations in gene expression and binding data would be unrelated, one would then indeed expect similar performance independent of species. This explanation however conflicts with the published findings that binding divergence for these TFs increases with evolutionary distance and our observation that the differences between the predicted regulatory networks are consistent with the known phylogeny and differences in biology between these six Drosophila species. Future work in other species will have to elucidate if the observed species-independent performance is an artefact of this particular dataset, a consequence of the highly conserved nature of the underlying biological process or a more general feature of this type of analysis.
Motivated by the result that all species-specific networks showed good inference performance and that their differences reflected true phylogenetic relations, we pursued integrative approaches whereby predicted networks from all species were combined into consensus networks. In addition to established aggregation methods such as taking the intersection, union or rank average of individual predictions, we also considered a novel centroid method which minimizes the total sum of edge gains and losses with respect to all individual networks. Multi-species methods showed better overall performance than the single-species networks, consistent with the observation that correct predictions are not restricted to interactions predicted in all species. Of note, the single-species network matching the gold standard species was almost never the best performing single-species network. Because in real-world applications the aim of network inference is usually to reconstruct a TF-target network for a species of interest in the absence of gold standard ChIP-seq/chip data, our results suggest that by combining predicted networks from multiple closely related species, a better network will be inferred than by using data for the species of interest only, and that the combined network is likely to perform better, or at least as good as, the best single-species network. A novel multi-species network integration method which reconstructs an “ancestral” network minimizing the number of edge gains and losses to each single-species network appeared to be particularly promising in this regard.
Our work has shown that in an evolutionarily conserved system such as early embryonic development, integration of data from comparable experiments in multiple species improves the inference of gene regulatory networks. Although the data for the present study came from a well-controlled experiment in a model organism, with matching time-course data adjusted for differences in developmental time between species, our approach is based solely on comparing expression profiles of different genes within the same species, and expression levels in different species were never directly compared. We therefore expect that our results should also hold for other biological processes, when more heterogeneous data are used or when data from more distantly related species are combined, in order to cover the entire spectrum of available multi-species gene expression datasets.
4.1 Gene expression data
Embryonic developmental time-course expression data in 6 Drosophila species (D. melanogaster (“amel”), D. ananassae (“ana”), D. persimilis (“per”), D. pseudoobscura (“pse”), D. simulans (“sim”) and D. virilis (“vir”)) was obtained from  (ArrayExpress accession code E-MTAB-404). The data consists of 10 (amel), 13 (vir) or 9 (ana, per, pse, sim) developmental time points with several replicates per time point resulting in a total of 56 (amel), 36 (vir) or 27 (ana, per, pse, sim) arrays per species (Supplementary Table S3). The downloaded data was processed by averaging absolute expression levels over all reporters for a gene followed by taking the transform.
4.2 Multi-dimensional scaling and variance explained
We used two-dimensional scaling using the Eucledian distance and Sammon’s nonlinear mapping criterion on the 3,610-dimensional sample vectors using the built-in “mdscale” function of Matlab. To estimate the variance explained by each of the two dimensions, we first calculated the principal components of the data matrix. These are a set of 200 mutually orthogonal -dimensional vectors, each explaining a proportion of the total variance, i.e. . Each dimension in Figure 1 also corresponds to a vector and the proportion of variance explained by is found by expansion into principal components, , where it is assumed that and all have unit norm. To correct for systematic biases in the data, genes were standardized to have mean zero and standard deviation one over all 200 samples.
4.3 ChIP-chip data
ChIP-chip data for 21 sequence-specific Drosophila transcription factors (TFs) measured in D. melanogaster embryos was obtained from . We considered the 1% FDR bound regions and defined target genes for each TF by assigning to each bound region its closest gene, if the distance between the region and the gene was less than 5,000 base pairs. For TFs with repeat measurements, target lists were defined by taking the union over replicates. Fourteen of the TFs were present on the array and used to construct a gold standard regulatory network.
4.4 ChIP-sequencing data
The peaks for three transcription factors present on the array (BCD, HB and KR) for three species (D. melanogaster, D. pseudoobscura and D. virilis) were obtained from . Genes with normalized peak height greater than 0 were selected as the gold standard targets of a given transcription factor. The peaks for one factor (TWI) for four species (D. melanogaster, D. ananassae, D. pseudoobscura and D. simulans) were obtained from . Peaks were mapped to the nearest transcription start site of genes by using the gene annotation from FlyBase (FB2013_03). Genes with peak height greater than 10 were selected as the gold standard targets for each species.
4.5 Transcriptional regulatory network reconstruction
We used the CLR (Context Likelihood of Relatedness) algorithm  using Pearson correlation as a similarity measure to predict transcriptional regulatory networks in each species, using the aforementioned 14 TFs as candidate regulators. Because the CLR algorithm only considers the right-hand tail of similarity values for every TF–gene combination, in theory the absolute values of the Pearson correlations should be provided to the CLR software. However, we observed improved performance with respect to all gold standard networks when the Pearson correlations were not transformed to absolute values before calling the CLR algorithm (effectively ignoring negative correlations) and therefore used this approach for all reported results. Pearson correlation followed by CLR also performed better than the default mutual information similarity measure followed by CLR as well as using Pearson correlation or mutual information without CLR (data not shown).
4.6 Phylogenetic tree construction
We created a binary matrix of 3,329 rows and 6 columns representing predicted TF–target interactions in each species at a CLR -score cutoff corresponding to 10% recall with respect to the D. melanogaster ChIP-chip network. In this matrix, the element denotes whether the interaction is present in the species or not. Network states and state changes were mapped onto the branches of inferred phylogenetic trees using the PARS program from the PHYLIP package  by defining D. virilis as the root of the tree. Bootstrapping was performed using the SEQBOOT program from the PHYLIP package where 100 datasets were generated by randomly replacing a given six species network matrix. A consensus tree with a bootstrap confidence on each branch of the tree was reconstructed using the CONSENSE program from the PHYLIP package.
4.7 Enrichment analyses
Gene set enrichment for each phylogenetic tree state change was calculated using the DAVID suite of programs . For each transcription factor, enrichment of overlap of the candidate target gene set with each transition state gene set was calculated using a hypergeometric test. Early zygotic, late zygotic, maternal and adult gene lists were downloaded from  and enrichment was calculated using a hypergeometric test.
4.8 Prediction aggregation methods
To combine predicted networks from multiple-species, we considered five prediction aggregation methods. The first method combined expression data from all species into one dataset to which we again applied the CLR method (“merged data” method). For the four other methods, predictions from each species were first ranked by their respective CLR-scores, such that the highest score received the highest rank value and tied values were given their average rank value, using Matlab’s “tiedrank” function. Three methods used standard functions to combine the edge ranks of the six single-species predicted networks, namely the minimum (“intersection” method), maximum (“union” method) and average (“average” method) rank value. The intersection and union methods are named such because if a threshold is used to convert a fixed number of top-ranked predictions to a binary graph, these would result precisely in the intersection and union of the binary graphs over all species. Conversely, on binary graphs, the phylogenetic tree construction infers ancestral networks by minimizing the number of edge gains and losses between single-species networks. This corresponds to minimizing their “cityblock” distance, defined for two -dimensional vectors and as . As the final prediction aggregation method we therefore considered the centroid network for the six single-species networks for the cityblock distance, defined by the edge weights which minimize
where is the matrix of edge rank values for species . The matrix is easily computed using Matlab’s “kmeans” function, by specifying the cityblock distance and grouping species into one cluster.
4.9 Network reconstruction performance
To compare the network reconstruction performance of several predicted networks across multiple gold standard networks, we used the area under the precision-recall curve (AUC) and the precision at 10% recall (PREC10) as scoring measures. Absolute scores were converted to -values following established protocols of the DREAM project . Briefly, 100,000 random predictions were generated for each gold standard network by assigning a random rank to each possible TF-target interaction. Next, an asymmetric stretched exponential function of the form
was fitted to each histogram (1000 bins) of random AUCs and random PREC10s, using the “fit” function in Matlab’s Curve Fitting Toolbox. Finally, -values for real AUCs and PREC10s were calculated by integrating the right tail of the corresponding fitted and normalized stretched exponential distribution function using Matlab’s “trapz” function.
Appendix A Supplementary figures
Appendix B Supplementary tables
|A B loss||post-embyonic organ development|
|regulation of transcription|
|A B gain||cell fate commitment|
|regulation of transcription|
|A C loss||cell–cell adhesion|
|exocrine system development|
|A C gain||cell fate commitment|
|regulation of transcription|
|A vir loss||regulation of transcription|
|A vir gain||neuron differentiation|
|B per loss||positive regulation of apoptosis|
|B per gain||translation factor activity|
|regulation of transcription|
|B pse loss||sensory organ development|
|transcription factor activity|
|B pse gain||intracellular organelle lumen|
|C ana loss||appendage development|
|C ana gain||regulation of transcription|
|C D loss||gastrulation|
|C D gain||mitochondrion|
|D amel loss||positive regulation of apoptosis|
|D amel gain||tissue morphogenesis|
|D sim loss||rRNA processing|
|response to organic substances|
|D sim gain||regulation of transcription|
|BCD||A B loss|
|BCD||A vir loss|
|BCD, HKB||C ana gain|
|BCD, MAD||D amel gain|
|DL||B per loss||oxidation reduction|
|DL||C D gain||mitochondrion|
|MAD||B pse gain|
|SLP1||C ana loss||wing disc development|
|leg disc pattern formation|
|TWI||B pse loss|
|TWI||C D loss||gastrulation|
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