| Accession | GMS-97-1
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| Title | PHi-C2: interpreting Hi-C data as the dynamic 3D genome state |
| Submit date | 2025-05-13 14:43:43 |
| Last update date | 2025-05-13 15:12:15 |
| Contact | Soya SHINKAI soya.shinkai AT riken.jp RIKEN BDR |
| Sharing | |
| Total file size | 2.82 MB |
| Keywords | PHi-C2 Genome DNA Mesoscale Rheology Modeling Viscoelasticity |
| Experiment type | PHi-C2 Rheology analysis |
| Summary | High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into the polymer model’s dynamics, structural conformations and rheological features. The updated optimization algorithm for regenerating a highly similar Hi-C matrix provides a fast and accurate optimal solution compared to the previous version by eliminating the factors underlying the inefficiency of the optimization algorithm in the iterative optimization process. In addition, we have enabled a Google Colab workflow to run the algorithm, wherein users can easily change the parameters and check the results in the notebook. Overall, PHi-C2 represents a valuable tool for mining the dynamic 3D genome state embedded in Hi-C data. |
| Citation(s) | Shinkai, S., Itoga, H., Kyoda, K., Onami, S. (2022) PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. Bioinformatics, 38(21), 4984–4986. https://doi.org/10.1093/bioinformatics/btac613 |
| Organism | Mouse |
| Cell (Tissue) | embryonic stem cell |
| Protocol | |
| Data processing |
| [978] figureS5.pdf
Rheology analysis application/pdf 2.11 MB MD5: 970742562ac1a812ffbb47e3f3234c0e |
| [979] figureS5.png
Rheology analysis image/png 717.12 KB MD5: 16bf47a272a5aa4cce8bfe2b76e98077 |
