OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data

Candace C Liu; Yongjian Guo; Kiera L Vrindten; William W Lau; Rachel Sparks; John S Tsang

doi:10.1016/j.xpro.2022.101474

OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data

STAR Protoc. 2022 Jul 20;3(3):101474. doi: 10.1016/j.xpro.2022.101474. eCollection 2022 Sep 16.

Authors

Candace C Liu¹, Yongjian Guo², Kiera L Vrindten², William W Lau², Rachel Sparks², John S Tsang³

Affiliations

¹ Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: cliu72@stanford.edu.
² Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
³ Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIH Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: john.tsang@nih.gov.

Abstract

OMiCC (OMics Compendia Commons) is a biologist-friendly web platform that facilitates data reuse and integration. Users can search over 40,000 publicly available gene expression studies, annotate and curate samples, and perform meta-analysis. Since the initial publication, we have incorporated RNA-seq datasets, compendia sharing, RESTful API support, and an additional meta-analysis method based on random effects. Here, we provide a step-by-step guide for using OMiCC. For complete details on the use and execution of this protocol, please refer to Shah et al. (2016).

Keywords: Bioinformatics; Gene Expression; Genomics; RNAseq.

Publication types

Research Support, N.I.H., Intramural

MeSH terms

Gene Expression* / genetics