tissue 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: bioRxiv

Article Title: Inhibition of the gut ceramidase Asah2 decelerates the vertebrate ageing rate

doi: 10.64898/2026.04.30.721799

Figure Lengend Snippet: a , Schematic representation of ceramide hydrolysis by membrane-tethered Asah2. Cer, ceramide; Sph, sphingosine. Image was created with BioRender.com. b , Loss of Asah2 activity is associated with a longer lifespan. Protein domain architectures of Asah2 are shown. Blue box, catalytic domain; orange box, immunoglobulin (Ig)-like domain; white box, other regions; grey box, N. furzeri MZM-specific region; red vertical lines in human ASAH2, essential amino acid residues required for enzymatic activity. c, e , asah2 is specifically expressed in the intestine and increases with age. Expression levels of asah2 mRNA in various tissues ( c ) and in the intestine ( e ) of 2- and 4-month-old wild-type (WT) and asah2 knockout (KO) N. furzeri are shown. In c and e , mRNA levels were analysed by reverse transcription quantitative PCR (RT–qPCR) and RNA sequencing (RNA-seq), respectively. CPM, counts per million; FDR, false discovery rate. FDR values were derived from quasi-likelihood methods in edgeR. d , Asah2 protein localises to the apical /luminal side of intestinal epithelium in short-lived GRZ fish but is absent in long-lived MZM fish and asah2 KO fish. Representative images of intestinal sections immunostained with anti-Asah2 antibody (green) and 4′,6-diamidino-2-phenylindole (DAPI; blue) are shown. Scale bar, 200 μm. f , Pooled censoring-aware parental survival analysis showing that higher participant plasma ASAH2 z-score was associated with higher pooled parental hazard, consistent with lower parental longevity. The displayed p-value tests the overall ASAH2-parental hazard association in the stratified cubic B-spline Cox model. Primary statistical inference was based on the cluster-robust linear Cox model. g , CRISPR/Cas9-mediated asah2 knockout. Top, schematic representation of the asah2 locus (black boxes, exons; ATG, start codon) and two sgRNA target sites (orange boxes). Bottom left, DNA sequences of WT and asah2 KO. The red horizontal line denotes the 4 bp deletion. Bottom right, the mutation was predicted to result in loss of the C-terminal domain of the Asah2 protein. Blue, catalytic domain; orange, Ig-like domain; white, other regions; grey, asah2 KO N. furzeri- specific region. h , Expression of Asah2 in the intestine of short-lived N. furzeri analysed by Western blotting. i, j , asah2 KO extends lifespan ( i ) and improves locomotor activity ( j ). In i , survival curves of male WT (blue) and asah2 KO (orange) fish are shown on the left; the corresponding statistical results, mean lifespan and maximum lifespan are shown on the right. Black dots indicate censored individuals. Graphs in j show exploratory behaviour in male WT (blue) and asah2 KO (orange) fish. The y-axis indicates the average velocity. The log-rank test, fixed-time survival test, and unpaired two-tailed t -test were used for i , and a Brown–Forsythe and Welch ANOVA followed by Dunnett’s T3 multiple-comparisons test were used for j . Bars and error bars represent the mean ± SD.

Article Snippet: Human tissue expression data were obtained from the Human Protein Atlas , .

Techniques: Membrane, Activity Assay, Expressing, Knock-Out, Reverse Transcription, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, RNA Sequencing, Derivative Assay, Clinical Proteomics, CRISPR, Mutagenesis, Western Blot, Two Tailed Test

Journal: bioRxiv

Article Title: Inhibition of the gut ceramidase Asah2 decelerates the vertebrate ageing rate

doi: 10.64898/2026.04.30.721799

Figure Lengend Snippet: a , Asah2 expression increases with age in the human terminal ileum of the small intestine. Data were obtained from voyAGEr . CPM, counts per million. b , Sex-stratified pooled censoring-aware parental survival analysis of participant plasma ASAH2 z-score and pooled parental hazard in male and female participants. Displayed p-values denote the overall ASAH2-parental hazard association from stratified cubic B-spline Cox models. c, d , asah2 KO does not affect body size or body mass index ( c ) or reproductive capacity ( d ). Graphs in c show body weight, body length, and body mass index in WT (blue) and asah2 KO (orange) male fish. Animals measured at each time point were different individuals. In d , the graph shows the number of fertilized eggs in WT (blue) and asah2 KO (orange) fish. Bars and error bars ( c, d ) represent the mean ± SD. An unpaired two-tailed t -test was used in c , and a Brown–Forsythe and Welch ANOVA followed by Dunnett’s T3 multiple-comparisons test were used in d .

Article Snippet: Human tissue expression data were obtained from the Human Protein Atlas , .

Techniques: Expressing, Clinical Proteomics, Two Tailed Test

Journal: Nature Communications

Article Title: Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development

doi: 10.1038/s41467-026-68675-y

Figure Lengend Snippet: a Reaggregation of iPSc-derived TEPs with primary human ETPs to form hTOs (human Thymic Organoids) cultured in a 3D fibrin hydrogel at an air-liquid interface in medium supplemented with RANKL, IL7, SCF, and FLT3L (Created in BioRender. Guillonneau, C. (2025) https://BioRender.com/apk8n61 ). b Bright-field images of hTOs (human Thymic Organoids) at 24 h and D4 showing a compact spheroid core with a peripheral cellular crown (identical magnification) ( n = 12 from independent differentiations and ETP donors). c scRNA-seq of EPCAM + CD45 − cells from D7 organoids with UMAP embedding and cell-cycle scoring (10x Genomics; Seurat workflow). d Module score for a TEP gene set: PDPN , PAX9 , IL7 , EBF1 , FN1 . e Integration of the EPCAM + CD45 − scRNA-seq dataset (Clusters 1, 2, and 3) with the Bautista human TEC atlas; with reference cells in gray. f Cell type deconvolution of TEPs and CD205 + TEPs against the EPCAM + CD45 − scRNA-seq dataset. g Distribution of the Tau tissue-specific variability index within clusters 3 and 1. Tau was computed from GTEx tissue expression data; TRA enrichment was assessed on the top-200 cluster-specific genes. Source data are provided as a file. h Assessment of the TRA repertoire in Cluster 3, showing enrichment for brain antigens. Source data are provided as a file.

Article Snippet: The Tau was calculated for a list of genes using the gene tissue expression data (GTEx) from the Human Protein Atlas database ( https://www.proteinatlas.org/about/download ).

Techniques: Derivative Assay, Cell Culture, Expressing