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Gene transcriptional profiling across tissues

LJ Long Jin
QT Qianzi Tang
SH Silu Hu
ZC Zhongxu Chen
XZ Xuming Zhou
BZ Bo Zeng
YW Yuhao Wang
MH Mengnan He
YL Yan Li
LG Lixuan Gui
LS Linyuan Shen
KL Keren Long
JM Jideng Ma
XW Xun Wang
ZC Zhengli Chen
YJ Yanzhi Jiang
GT Guoqing Tang
LZ Li Zhu
FL Fei Liu
BZ Bo Zhang
ZH Zhiqing Huang
GL Guisen Li
DL Diyan Li
VG Vadim N. Gladyshev
JY Jingdong Yin
YG Yiren Gu
XL Xuewei Li
ML Mingzhou Li
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We calculated the tissue specificity of gene abundance reflected by the tau score (τ)102 (ranging from 0 to 1, with 1 for highly tissue-specific genes and 0 for ubiquitously transcribed genes) for each gene with scaled TPM values. For each tissue, we averaged all replicates and then calculated τ to account for unequal numbers of replicates among tissues. We used τ ≥ 0.75 as the cut-off for tissue-specific genes.

We calculated the abundance distribution (i.e., transcriptome complexity) of distinct transcripts across tissues, reflected as the fraction of total RNAs contributed by the most highly expressed genes.

Differential gene expression analysis was performed using edgeR (version 3.22.5)103, with a false discovery rate (FDR) ≤0.05 and log2(fold change) ≥1 as cut-offs for statistical significance.

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