GSGP

Welcome to the Gene Somatic Genome Pattern (GSGP)

Assessing contributions of genes to the COSMIC SBS signatures

Introduction

GSGP is an algorithm for evaluating the contributions of genes to the Catalogue Of Somatic Mutations In Cancer (COSMIC) Single Base Substitution (SBS) signatures. It provides a new dimension for somatic signature analysis. In addition to exploring the cancer aetiology at the sample level, the GSGP can be used for digging deeper to explore which and how much the aetiologies affect the gene of interest (or which and how much the genes are affected by the aetiology of interest), offering a new perspective on the interactions between environment and cancer genome.

Please cite

Ji X, Wang E, Cui Q. Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Brief Bioinform. 2023;bbad017. PMID: 36682004

Quick Start

1. Analysis a Variant Calling Format (VCF) file (multi-sample VCF is also supported) in one of a human genome (GRCh37/GRCh38). A Task ID will be given after submitting.
2. Search the Task ID in Result page. Select the sample(s), gene(s), and signature(s) of interest and click refresh.
3. If needed, download the heatmap in SVG format and the GSGP in CSV format.
4. For more detailed tutorial, please click Help.

Contact us

Dr. Qinghua Cui, 38 Xueyuan Rd, Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China
Email: cuiqinghua@hsc.pku.edu.cn
Homepage: http://www.cuilab.cn/

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