Dataset Information

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

ABSTRACT:

Summary

Ordino is a web-based analysis tool for cancer genomics that allows users to flexibly rank, filter and explore genes, cell lines and tissue samples based on pre-loaded data, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia and manually uploaded information. Interactive tabular data visualization that facilitates the user-driven prioritization process forms a core component of Ordino. Detail views of selected items complement the exploration. Findings can be stored, shared and reproduced via the integrated session management.

Availability and implementation

Ordino is publicly available at https://ordino.caleydoapp.org. The source code is released at https://github.com/Caleydo/ordino under the Mozilla Public License 2.0.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Streit M

PROVIDER: S-EPMC6736116 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Publications

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

Streit Marc M Gratzl Samuel S Stitz Holger H Wernitznig Andreas A Zichner Thomas T Haslinger Christian C

Bioinformatics (Oxford, England) 20190901 17

<h4>Summary</h4>Ordino is a web-based analysis tool for cancer genomics that allows users to flexibly rank, filter and explore genes, cell lines and tissue samples based on pre-loaded data, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia and manually uploaded information. Interactive tabular data visualization that facilitates the user-driven prioritization process forms a core component of Ordino. Detail views of selected items complement the exploration. Findings can be st ...[more]

PMID: 30657871

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Project description:MotivationThe recent advance in high-throughput sequencing technologies is generating a huge amount of data that are becoming an important resource for deciphering the genotype underlying a given phenotype. Genome sequencing has been extensively applied to the study of the cancer genomes. Although a few methods have been already proposed for the detection of cancer-related genes, their automatic identification is still a challenging task. Using the genomic data made available by The Cancer Genome Atlas Consortium (TCGA), we propose a new prioritization approach based on the analysis of the distribution of putative deleterious variants in a large cohort of cancer samples.ResultsIn this paper, we present ContastRank, a new method for the prioritization of putative impaired genes in cancer. The method is based on the comparison of the putative defective rate of each gene in tumor versus normal and 1000 genome samples. We show that the method is able to provide a ranked list of putative impaired genes for colon, lung and prostate adenocarcinomas. The list significantly overlaps with the list of known cancer driver genes previously published. More importantly, by using our scoring approach, we can successfully discriminate between TCGA normal and tumor samples. A binary classifier based on ContrastRank score reaches an overall accuracy >90% and the area under the curve (AUC) of receiver operating characteristics (ROC) >0.95 for all the three types of adenocarcinoma analyzed in this paper. In addition, using ContrastRank score, we are able to discriminate the three tumor types with a minimum overall accuracy of 77% and AUC of 0.83.ConclusionsWe describe ContrastRank, a method for prioritizing putative impaired genes in cancer. The method is based on the comparison of exome sequencing data from different cohorts and can detect putative cancer driver genes. ContrastRank can also be used to estimate a global score for an individual genome about the risk of adenocarcinoma based on the genetic variants information from a whole-exome VCF (Variant Calling Format) file. We believe that the application of ContrastRank can be an important step in genomic medicine to enable genome-based diagnosis.Availability and implementationThe lists of ContrastRank scores of all genes in each tumor type are available as supplementary materials. A webserver for evaluating the risk of the three studied adenocarcinomas starting from whole-exome VCF file is under development.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

Summary

Availability and implementation

Supplementary information

Publications

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

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