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Fig. 4 | BMC Molecular and Cell Biology

Fig. 4

From: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

Fig. 4

Data visualization The figure shows the output displayed when a user clicks on the “View link” for the GM12878 dataset. The red highlighted section shows the information about the Resolution(s) available for the Hi-C data. The blue highlighted section displays the structure available for the Hi-C data. The green highlighted section shows the evaluation result available for the Hi-C data. It displays the Spearman Correlation between the output structure and the input Hi-C data, and other evaluation result obtained. To evaluate each 3D structure, we compute the distance Spearman’s correlation coefficient (dSCC) between reconstructed distances and distances obtained from the Hi-C datasets. The value of dSCC is in the range of − 1 to + 1, where a higher value is better. For distance-based methods, we report the conversion factor (α) used for the IF to distance conversion. For LorDG and 3DMax, which use gradient ascent optimization algorithm, we report the learning rate used for the optimization process. The parameters used by each method to generate 3D structures are available on GSDB GitHub page

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