tissue specific gene expression data  (Human Protein Atlas)

Journal: PLOS One

Article Title: Comparative genomics of human brain and immune gene preservation across species

doi: 10.1371/journal.pone.0348713

Figure Lengend Snippet: (A) Cohen’s h values for pairwise comparisons between 𝒞 and the other two groups: ℬ and ℐ . Primate Specific Ratios are calculated as in . A higher absolute Cohen’s h indicates a greater difference in ratios between the two compared groups. Green bar represents ℬ , orange bar represents ℐ , and blue bars represent 𝒞 . (B) Results of Fisher’s exact tests for pairwise comparisons between each of ℬ , ℐ , and 𝒞 and each control group ( ℱ and ℛ ), together with the comparison between ℱ and ℛ . Primate Specific Ratios are calculated as in . Statistical significance is denoted by asterisks. Results with p-values less than 0.01 are indicated by two asterisks (**), results with p-values less than 0.05 are indicated by one asterisk (*), and all other results are marked as ns . Green bar represents ℬ , orange bar represents ℐ , blue bar represents 𝒞 , gray bars represent ℛ , and purple bars represent ℱ . (C) The number of tissues corresponding to each quantile for the brain genes and immune-related genes. Green bars represent ℬ , orange bars represent ℐ , and gray bars represent all genes that have at least one highly expressed tissue in Human Protein Atlas [ , ]. (D) The number and ratio of genes highly expressed specifically in brain tissues or immune-related tissues, out of 1019 brain genes and 586 immune-related genes, respectively.

Article Snippet: There are six types of data used in this work: (1) CDS (coding sequence) data of 32 primate species and 4 non-primate species [ , ]; (2) tissue specific gene expression data obtained from the Human Protein Atlas 23.0 [ , ]; (3) 1360 human genes highly expressed in the brain or the immune system [ , ]; (4) 295 random human genes selected using the random.sample() function in Python 3.10.8; (5) 369 human genes each from a distinct HGNC [ ] gene family group; and (6) protein sequences of the genes obtained from UniProt [ ].

Techniques: Control, Comparison

Journal: Cell Metabolism

Article Title: Integrative systems analysis identifies genetic and dietary modulators of bile acid homeostasis

doi: 10.1016/j.cmet.2022.08.015

Figure Lengend Snippet: Genetic mapping of BA modulators and the identification of Ces1c as a potential regulator of plasma TUDCA levels (A) The genetic effects of the TUDCA QTL on chromosome 8 on plasma TUDCA levels of the BXD animals at 30 min after a test meal. Plasma TUDCA concentrations (log 2 transformed data) were compared between strains inheriting the genetic allele from the reference C57BL/6J strain at the QTL (indicated as B/B) and those inheriting from the DBA/2J strain (indicated as D/D). ∗∗∗ p < 0.001 by two-tailed Student’s t test. (B) Heatmap presenting the correlations between the TUDCA levels across different biological compartments and phenotypic traits. ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001, for Pearson correlation coefficient. (C) Systems genetics pipeline applied to filter for genes responsible for the plasma TUDCA QTL at T30 by integrating 3 major criteria, that is, (1) whether genes have high-impact genetic variants or cis -eQTLs in the liver, (2) whether their liver expression level correlates with plasma TUDCA levels at T30, and (3) whether they associate with the primary BA biosynthesis (KEGG 0120) pathway in GMAD ( Li et al., 2019 ). The numbers of genes that fulfill each or several of these criteria are listed in the Venn diagram. (D) Heatmap listing the genes under the plasma TUDCA QTL at T30 on chromosome 8 reveals the potential modulators of TUDCA. Only genes fulfilling at least 2 criteria were included in the heatmap. The first block of the heatmap represents whether the genes have high-impact variants or cis -eQTLs in liver transcriptome datasets of the BXDs. The second block (Corr) indicates the correlations between the liver expression of these genes and plasma TUDCA levels at T30 in CD or HFD. The third block shows the association between these genes and the primary BA biosynthesis pathway predicted by GMAD ( Li et al., 2019 ) in human, mouse, and rat. The last block shows the enrichment of the expression of these genes in the liver, retrieved from the Human Protein Atlas ( https://www.proteinatlas.org/ ) ( Uhlén et al., 2015 ). r , Pearson correlation coefficient. GMAS, gene-module association score. Asterisk ( ∗ p < 0.05) and hash (#) indicate statistical significance in correlation and GMAD, respectively. The 3 selected candidates are in bold and underlined. Full list of the 191 genes under the TUDCA QTL on chromosome 8 is in Table S7 . (E) Zonation protein (left) or mRNA (right) profiles of key BA synthesis and transport genes, as well as candidate TUDCA modulators in the mouse liver. Protein or mRNA expression of each gene was scaled to 0–1. See also Figure S6 and Tables S1 , , and .

Article Snippet: The tissue specificity gene expression data was downloaded from the Human Protein Atlas ( https://proteinatlas.org/humanproteome/tissue/liver ) ( ) on 2019.12.18.

Techniques: Clinical Proteomics, Transformation Assay, Two Tailed Test, Expressing, Blocking Assay