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Murtaza et al. |

GrapHiC

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Omics
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Step 1: Upload your data

Upload HiC Dataset

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    • Dataset file should be provided in .tar.gz format. In tar.gz file, there must be one folder that contains .hic files. An indexed binary format called .hic was created to provide quick random access to contact matrix heatmaps.
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Upload Epigenetic Dataset

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  • Your file can be in the following formats:tar.gz
    • Dataset file should be provided in .tar.gz format. In tar.gz file, there must be one folder that contains .bigwig files. File names in folder must contain same name in epigenetic feautures. File names cannot be random names. For example, you have epigenetic factor in your dataset and .bigWig file name should be the same (e.g. H3K4ME1.bigwig, DNASE-Seq.bigwig). Genome-wide signal data are stored in BigWig files, a compressed, indexed, binary format used for calculations (like GC percent) or studies (like ChIP-seq/RNA-seq read depth).
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Step 2: Set Parameters
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The three-dimensional (3D) architecture of the genome at various structural scales can be comprehended and investigated by scientists using Hi-C, a high-throughput chromosomal conformation capture technique. Generally, Hi-C experiment data is stored in a contact map of size N × N. Each row and column correspond to fixed-width N windows (“bins”) in the range of 1 kbps to 1 mbps. The examination of these contact maps revealed significant structural features such as topologically associated domains (TADs).

Building high-resolution Hi-C contact maps often necessitate billions of reads, which is often impossible. GrapHiC imputes Hi-C contact maps by reformulating the Hi-C data as a position-aware graph, using less expensive ChIP-seq signals, and proposing a generative graph-autoencoder that first encodes the input graph into a latent representation.

Example use case: Imputation of Hi-C data

Technology: Graph Auto-Encoder (GAE)

Limitation:
- Some of the parameters were left as default. Please check this page for more information.

Metrics: Detailed metrics of the study can be found in the supplementary file.

Epigenetic Features:

All: ['RAD-21', 'RNA-Pol2','CTCF', 'DNASE-Seq', 'H3K27ME3', 'H3K27AC', 'H3K36ME3', 'H3K4ME1', 'H3K4ME2', 'H3K4ME3', 'H3K79ME2', 'H3K9AC', 'H4K20ME1', 'H3K9ME3']
DNA-Acessibility: ['RAD-21', 'RNA-Pol2','CTCF', 'DNASE-Seq']
Repression-Marker: ['H3K27ME3', 'H3K4ME2', 'H4K20ME1']
Activating-Marker: ['H3K4ME3', 'H3K9AC', 'H3K9ME3']
Enchancer-Interaction-Marker: ['H3K36ME3', 'H3K79ME2']
Gene-Related: ['H3K36ME3', 'H3K79ME2']
HiC-Reg-Reduced: ['CTCF', 'DNASE-Seq', 'H4K20ME1', 'H3K27ME3', 'H3K9ME3', 'H3K9AC', 'H3K4ME1', 'H3K27AC']

Citation:
GrapHiC: An integrative graph based approach for imputing missing Hi-C reads Ghulam Murtaza, Justin Wagner, Justin M. Zook, Ritambhara Singh bioRxiv 2022.10.19.512942; doi: https://doi.org/10.1101/2022.10.19.512942
Released:
Dec-01-2022
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