Saman Khakmardan1, Mohsen Rezvani2, Ali Akbar Pouyan1, Mansoor Fateh1, Hamid Alinejad-Rokny3,4. 1. Faculty of Computer Engineering, Shahrood University of Technology, Shahrood, Iran. 2. Faculty of Computer Engineering, Shahrood University of Technology, Shahrood, Iran. mrezvani@shahroodut.ac.ir. 3. Systems Biology and Health Data Analytics Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, 2052, Australia. h.alinejad@ieee.org. 4. School of Computer Science and Engineering, The University of New South Wales (UNSW Sydney), Sydney, 2052, Australia. h.alinejad@ieee.org.
Abstract
BACKGROUND: Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and identify significant interactions. Each method receives its own Hi-C data structure and only work on specific operating systems. RESULTS: We introduce MHiC (Multi-function Hi-C data analysis tool), a tool to identify and visualize statistically signifiant interactions from Hi-C data. The MHiC tool (i) works on different operating systems, (ii) accepts various Hi-C data structures from different Hi-C analysis tools such as HiCUP or HiC-Pro, (iii) identify significant Hi-C interactions with GOTHiC, HiCNorm and Fit-Hi-C methods and (iv) visualizes interactions in Arc or Heatmap diagram. MHiC is an open-source tool which is freely available for download on https://github.com/MHi-C. CONCLUSIONS: MHiC is an integrated tool for the analysis of high-throughput chromosome conformation capture (Hi-C) data.
BACKGROUND:Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and identify significant interactions. Each method receives its own Hi-C data structure and only work on specific operating systems. RESULTS: We introduce MHiC (Multi-function Hi-C data analysis tool), a tool to identify and visualize statistically signifiant interactions from Hi-C data. The MHiC tool (i) works on different operating systems, (ii) accepts various Hi-C data structures from different Hi-C analysis tools such as HiCUP or HiC-Pro, (iii) identify significant Hi-C interactions with GOTHiC, HiCNorm and Fit-Hi-C methods and (iv) visualizes interactions in Arc or Heatmap diagram. MHiC is an open-source tool which is freely available for download on https://github.com/MHi-C. CONCLUSIONS: MHiC is an integrated tool for the analysis of high-throughput chromosome conformation capture (Hi-C) data.
Authors: Shahab S Band; Sina Ardabili; Atefeh Yarahmadi; Bahareh Pahlevanzadeh; Adiqa Kausar Kiani; Amin Beheshti; Hamid Alinejad-Rokny; Iman Dehzangi; Arthur Chang; Amir Mosavi; Massoud Moslehpour Journal: Front Public Health Date: 2022-06-23