» Articles » PMID: 36494766

Robust and Rigorous Identification of Tissue-specific Genes by Statistically Extending Tau Score

Overview
Journal BioData Min
Publisher Biomed Central
Specialty Biology
Date 2022 Dec 10
PMID 36494766
Authors
Affiliations
Soon will be listed here.
Abstract

Objectives: In this study, we aimed to identify tissue-specific genes for various human tissues/organs more robustly and rigorously by extending the tau score algorithm.

Introduction: Tissue-specific genes are a class of genes whose functions and expressions are preferred in one or several tissues restrictedly. Identification of tissue-specific genes is essential for discovering multi-cellular biological processes such as tissue-specific molecular regulations, tissue development, physiology, and the pathogenesis of tissue-associated diseases.

Materials And Methods: Gene expression data derived from five large RNA sequencing (RNA-seq) projects, spanning 96 different human tissues, were retrieved from ArrayExpress and ExpressionAtlas. The first step is categorizing genes using significant filters and tau score as a specificity index. After calculating tau for each gene in all datasets separately, statistical distance from the maximum expression level was estimated using a new meaningful procedure. Specific expression of a gene in one or several tissues was calculated after the integration of tau and statistical distance estimation, which is called as extended tau approach. Obtained tissue-specific genes for 96 different human tissues were functionally annotated, and some comparisons were carried out to show the effectiveness of the extended tau method.

Results And Discussion: Categorization of genes based on expression level and identification of tissue-specific genes for a large number of tissues/organs were executed. Genes were successfully assigned to multiple tissues by generating the extended tau approach as opposed to the original tau score, which can assign tissue specificity to single tissue only.

Citing Articles

Mining of Root-Specific Expression Genes and Their Core Cis-Regulatory Elements in Plants.

Gao S, Chai Y, Zhou X, Chen S Int J Mol Sci. 2025; 26(4).

PMID: 40004183 PMC: 11855845. DOI: 10.3390/ijms26041720.


Gene expression atlas of the Colorado potato beetle (Leptinotarsa decemlineata).

Wilhelm L, Wang Y, Xu S Sci Data. 2025; 12(1):299.

PMID: 39971983 PMC: 11840028. DOI: 10.1038/s41597-025-04607-7.


Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet.

Luo W, Sun M, Zhang A, Lin C, Jin Y, Wang X BMC Genomics. 2024; 25(1):1199.

PMID: 39695372 PMC: 11653590. DOI: 10.1186/s12864-024-11114-3.


Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery.

Li G, Schnell D, Bhattacharjee A, Yarmarkovich M, Salomonis N Cell Rep Methods. 2024; 4(11):100900.

PMID: 39515334 PMC: 11705768. DOI: 10.1016/j.crmeth.2024.100900.


FEAtl: a comprehensive web-based expression atlas for functional genomics in tropical and subtropical fruit crops.

Roy A, Chaurasia H, Kumar B, Kumari N, Jaiswal S, Srivastava M BMC Plant Biol. 2024; 24(1):890.

PMID: 39343895 PMC: 11440752. DOI: 10.1186/s12870-024-05595-3.


References
1.
Fonseca N, Marioni J, Brazma A . RNA-Seq gene profiling--a systematic empirical comparison. PLoS One. 2014; 9(9):e107026. PMC: 4182317. DOI: 10.1371/journal.pone.0107026. View

2.
Schuster E, Blanc E, Partridge L, Thornton J . Correcting for sequence biases in present/absent calls. Genome Biol. 2007; 8(6):R125. PMC: 2394774. DOI: 10.1186/gb-2007-8-6-r125. View

3.
Schug J, Schuller W, Kappen C, Salbaum J, Bucan M, Stoeckert Jr C . Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol. 2005; 6(4):R33. PMC: 1088961. DOI: 10.1186/gb-2005-6-4-r33. View

4.
Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Schutz F . Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 2012; 10(5):e1001328. PMC: 3352821. DOI: 10.1371/journal.pbio.1001328. View

5.
Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A . Evolutionary analysis of the female-specific avian W chromosome. Nat Commun. 2015; 6:7330. PMC: 4468903. DOI: 10.1038/ncomms8330. View