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rna seq expression data  (Human Protein Atlas)

 
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    Human Protein Atlas rna seq expression data
    a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), <t>while</t> <t>RNA-seq</t> data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).
    Rna Seq Expression Data, supplied by Human Protein Atlas, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Autoantibody repertoire analysis in paraneoplastic pemphigus reveals novel targets linked to mucocutaneous blistering and bronchiolitis obliterans"

    Article Title: Autoantibody repertoire analysis in paraneoplastic pemphigus reveals novel targets linked to mucocutaneous blistering and bronchiolitis obliterans

    Journal: Communications Medicine

    doi: 10.1038/s43856-025-01335-2

    a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), while RNA-seq data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).
    Figure Legend Snippet: a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), while RNA-seq data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).

    Techniques Used: Expressing, Immunopeptidomics, Comparison, RNA Sequencing, Transformation Assay, Protein Array, Fluorescence

    Related Articles

    Clinical Proteomics:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Identification of cell type-enriched plasma proteins The Human Protein Atlas single-cell RNA-seq database (Human Protein Atlas version 24.1 www.proteinatlas.org/humanproteome) was used to map the putative cell type-specific plasma proteome. ..

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 1 | Identification of cell type-specific plasma proteins. (a) Z-scored gene expression of cell type-enriched plasma protein encoding genes in the Human Protein Atlas (HPA, version 24.1) single-cell transcriptomics dataset, labeled by cell type and grouped according to HPA cell type family categorizations. (b) Coverage of cell type-specific proteins across the 7,289 proteins measured by the 7k SomaScan platform. (c) Coverage of cell typespecific proteins across the 2,923 proteins measured by the 3k Olink platform. ..

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Leveraging single-cell transcriptomic data in the Human Protein Atlas (Methods and Extended Data Fig. 1), we linked 60 cell types to their corresponding plasma proteins. ..

    Single Cell:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Identification of cell type-enriched plasma proteins The Human Protein Atlas single-cell RNA-seq database (Human Protein Atlas version 24.1 www.proteinatlas.org/humanproteome) was used to map the putative cell type-specific plasma proteome. ..

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 2 | Enrichment profile examples of cell type-specific proteins. (a) Fold change of enriched proteins for pancreatic endocrine cells based on the Human Protein Atlas single-cell transcriptomic dataset (version 24.1): blue bars represent fold change compared to average expression across all other cell types; red bars show fold change relative to the second-highest expressing cell type. ..

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 1 | Identification of cell type-specific plasma proteins. (a) Z-scored gene expression of cell type-enriched plasma protein encoding genes in the Human Protein Atlas (HPA, version 24.1) single-cell transcriptomics dataset, labeled by cell type and grouped according to HPA cell type family categorizations. (b) Coverage of cell type-specific proteins across the 7,289 proteins measured by the 7k SomaScan platform. (c) Coverage of cell typespecific proteins across the 2,923 proteins measured by the 3k Olink platform. ..

    Article Title: Neuroprotective effects of Chaihu-Longgu-Muli Decoction in an insomnia-depression comorbidity model via Galectin-3-dependent JAK2/STAT3 inhibition.
    Article Snippet: 21 Ethnopharmacological relevance: Chaihu-Longgu-Muli Decoction (CLMD) is a classical 22 Traditional Chinese Medicine (TCM) formula from the Shanghan Lun comprising Bupleureum 23 chinense DC., Os Draconis, Concha Ostreae, and the other herbs.. Traditionally used to 24 harmonize Shaoyang, calm Shen (spirit), and treat emotional disturbances and insomnia related 25 to liver qi stagnation.. 26 Aim of the study: To evaluate CLMD’s therapeutic efficacy in insomnia-depression 27 comorbidity and elucidate molecular mechanisms through bioinformatics and experimental 28 validation.

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Leveraging single-cell transcriptomic data in the Human Protein Atlas (Methods and Extended Data Fig. 1), we linked 60 cell types to their corresponding plasma proteins. ..

    Article Title:
    Article Snippet: .. To test this hypothesis, we calculated median expression levels of genes up- or down-regulated by HSAN and/or 1-deoxysphingosines in different cell types of the human heart using single cell data from the Human Protein Atlas Project ( Uhlen et al., 2015 ). ..

    RNA Sequencing:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Identification of cell type-enriched plasma proteins The Human Protein Atlas single-cell RNA-seq database (Human Protein Atlas version 24.1 www.proteinatlas.org/humanproteome) was used to map the putative cell type-specific plasma proteome. ..

    Article Title: ALDH3A2-mediated fatty acid synthesis induces ferroptosis and AML drug resistance
    Article Snippet: .. Analysis of RNA sequencing (RNA-seq) results for 88 leukemia cell lines in the Human Protein Atlas website (HPA) database showed that the top 25% of cell lines with the highest ALDH3A2 expression included fifteen AML cell lines, 4 chronic myeloid leukemia (CML) cell lines, 2 pediatric acute B-lymphoblastic leukemia cell lines, and one T-lymphoblastic leukemia cell line. ..

    Expressing:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 2 | Enrichment profile examples of cell type-specific proteins. (a) Fold change of enriched proteins for pancreatic endocrine cells based on the Human Protein Atlas single-cell transcriptomic dataset (version 24.1): blue bars represent fold change compared to average expression across all other cell types; red bars show fold change relative to the second-highest expressing cell type. ..

    Article Title: ALDH3A2-mediated fatty acid synthesis induces ferroptosis and AML drug resistance
    Article Snippet: .. Analysis of RNA sequencing (RNA-seq) results for 88 leukemia cell lines in the Human Protein Atlas website (HPA) database showed that the top 25% of cell lines with the highest ALDH3A2 expression included fifteen AML cell lines, 4 chronic myeloid leukemia (CML) cell lines, 2 pediatric acute B-lymphoblastic leukemia cell lines, and one T-lymphoblastic leukemia cell line. ..

    Article Title: Neuroprotective effects of Chaihu-Longgu-Muli Decoction in an insomnia-depression comorbidity model via Galectin-3-dependent JAK2/STAT3 inhibition.
    Article Snippet: 21 Ethnopharmacological relevance: Chaihu-Longgu-Muli Decoction (CLMD) is a classical 22 Traditional Chinese Medicine (TCM) formula from the Shanghan Lun comprising Bupleureum 23 chinense DC., Os Draconis, Concha Ostreae, and the other herbs.. Traditionally used to 24 harmonize Shaoyang, calm Shen (spirit), and treat emotional disturbances and insomnia related 25 to liver qi stagnation.. 26 Aim of the study: To evaluate CLMD’s therapeutic efficacy in insomnia-depression 27 comorbidity and elucidate molecular mechanisms through bioinformatics and experimental 28 validation.

    Article Title:
    Article Snippet: .. To test this hypothesis, we calculated median expression levels of genes up- or down-regulated by HSAN and/or 1-deoxysphingosines in different cell types of the human heart using single cell data from the Human Protein Atlas Project ( Uhlen et al., 2015 ). ..

    Gene Expression:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 1 | Identification of cell type-specific plasma proteins. (a) Z-scored gene expression of cell type-enriched plasma protein encoding genes in the Human Protein Atlas (HPA, version 24.1) single-cell transcriptomics dataset, labeled by cell type and grouped according to HPA cell type family categorizations. (b) Coverage of cell type-specific proteins across the 7,289 proteins measured by the 7k SomaScan platform. (c) Coverage of cell typespecific proteins across the 2,923 proteins measured by the 3k Olink platform. ..

    Transcriptomics:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 1 | Identification of cell type-specific plasma proteins. (a) Z-scored gene expression of cell type-enriched plasma protein encoding genes in the Human Protein Atlas (HPA, version 24.1) single-cell transcriptomics dataset, labeled by cell type and grouped according to HPA cell type family categorizations. (b) Coverage of cell type-specific proteins across the 7,289 proteins measured by the 7k SomaScan platform. (c) Coverage of cell typespecific proteins across the 2,923 proteins measured by the 3k Olink platform. ..

    Labeling:

    Article Title: Plasma proteomic signatures of cellular aging predict human disease.
    Article Snippet: .. Nature Medicine Article https://doi.org/10.1038/s41591-026-04446-y Extended Data Fig. 1 | Identification of cell type-specific plasma proteins. (a) Z-scored gene expression of cell type-enriched plasma protein encoding genes in the Human Protein Atlas (HPA, version 24.1) single-cell transcriptomics dataset, labeled by cell type and grouped according to HPA cell type family categorizations. (b) Coverage of cell type-specific proteins across the 7,289 proteins measured by the 7k SomaScan platform. (c) Coverage of cell typespecific proteins across the 2,923 proteins measured by the 3k Olink platform. ..



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    a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), <t>while</t> <t>RNA-seq</t> data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).
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    Image Search Results


    a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), while RNA-seq data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).

    Journal: Communications Medicine

    Article Title: Autoantibody repertoire analysis in paraneoplastic pemphigus reveals novel targets linked to mucocutaneous blistering and bronchiolitis obliterans

    doi: 10.1038/s43856-025-01335-2

    Figure Lengend Snippet: a Expression of paraneoplastic pemphigus (PNP) autoantigens in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, Burkitt’s lymphoma, and HIV-positive cervical cancer. The heatmap displays the proportion of samples with expression levels exceeding 10 RPKM. In addition to PNP autoantigens, the heatmap includes reference genes such as GAPDH (housekeeping gene), KRTAP4-7 (skin-specific), CD3 epsilon (T-cell-specific), and CD19 (B-cell-specific) for comparison. Tumor RNA-sequencing summary statistics were obtained from the NIH Center for Cancer Genomics and the Cancer Genome Characterization Initiative (CGCI), while RNA-seq data for normal tissues (ectocervix, endocervix, and EBV-transformed lymphocytes) were retrieved from the GTEx portal (v6p.v1.1.8). b Autoantibody signal intensities in patients with paraneoplastic pemphigus, stratified by the type of neoplasm. Autoantibodies were measured using a bead-based protein array in patients with paraneoplastic pemphigus (PNP, n = 84) and healthy controls (HC, n = 105). c The heatmap displays the proportion of samples with an autoantibody fluorescence signal >1000, categorized by the type of neoplasm group in patients with paraneoplastic pemphigus ( n = 46). Only neoplasms present in two or more patients are included. The color scale is consistent across heatmaps ( a ) and ( c ).

    Article Snippet: RNA-seq expression data for healthy subjects were retrieved from the Human Protein Atlas version 23.0 ( https://www.proteinatlas.org/ ), accessed 2023-12-13 (rna_single_cell_type.tsv, and rna_single_cell_cluster_description.tsv), and the GTEx portal (v6p.v1.1.8), accessed 2022-12-05.

    Techniques: Expressing, Immunopeptidomics, Comparison, RNA Sequencing, Transformation Assay, Protein Array, Fluorescence

    (A) Heatmap of differentially expressed genes from RNA-sequencing analysis of A549 cells with stable RHOV knockdown (sh1, sh2) compared to control. Consistent transcriptional alterations across both shRNAs are observed, with enrichment of MYC-related gene signatures among downregulated transcripts. (B) Gene ontology (GO) of differentially expressed genes shows significant downregulation of pathways associated with RNA biosynthesis, mRNA catabolism, ribosomal assembly, and mitotic cell cycle—all known MYC-driven processes. Upregulated pathways include DNA damage response, chromatin organization, and endocytic trafficking. Enrichment scores are represented along with q-values. (C) Gene Set Enrichment Analysis (GSEA) using Hallmark gene sets confirms strong negative enrichment of hallmark MYC target gene sets (V1 and V2) and oxidative phosphorylation genes in RHOV knockdown cells, indicating suppression of both proliferative and metabolic MYC programs. (D) Expression of MYC was compared between high and Low RHOV expressing patients in four NSCLC patients’ datasets. The expression of MYC was significantly higher in high RHOV patients (Mann-Whitney test). (E, F and G) The patients’ samples with high expression of RHOV (which show poor survival, ) from three cohort, (E) EAC, (F) Microarray and (G) TCGA were divided into two groups based on MYC expression. The analysis shows that RHOV high patients with low MYC expression survive significantly better than the RHOV high patients with high MYC expression. The p-values and Hazard ration are shown.

    Journal: bioRxiv

    Article Title: TGF/J Regulated Small GTPase RHOV interact with PEAK1 and drive MYC Expression to Promote Cellular Proliferation, Migration and Etoposide resistance

    doi: 10.1101/2025.04.18.649622

    Figure Lengend Snippet: (A) Heatmap of differentially expressed genes from RNA-sequencing analysis of A549 cells with stable RHOV knockdown (sh1, sh2) compared to control. Consistent transcriptional alterations across both shRNAs are observed, with enrichment of MYC-related gene signatures among downregulated transcripts. (B) Gene ontology (GO) of differentially expressed genes shows significant downregulation of pathways associated with RNA biosynthesis, mRNA catabolism, ribosomal assembly, and mitotic cell cycle—all known MYC-driven processes. Upregulated pathways include DNA damage response, chromatin organization, and endocytic trafficking. Enrichment scores are represented along with q-values. (C) Gene Set Enrichment Analysis (GSEA) using Hallmark gene sets confirms strong negative enrichment of hallmark MYC target gene sets (V1 and V2) and oxidative phosphorylation genes in RHOV knockdown cells, indicating suppression of both proliferative and metabolic MYC programs. (D) Expression of MYC was compared between high and Low RHOV expressing patients in four NSCLC patients’ datasets. The expression of MYC was significantly higher in high RHOV patients (Mann-Whitney test). (E, F and G) The patients’ samples with high expression of RHOV (which show poor survival, ) from three cohort, (E) EAC, (F) Microarray and (G) TCGA were divided into two groups based on MYC expression. The analysis shows that RHOV high patients with low MYC expression survive significantly better than the RHOV high patients with high MYC expression. The p-values and Hazard ration are shown.

    Article Snippet: RNA-sequencing (RNA-seq) expression data from The Cancer Genome Atlas (TCGA) project were downloaded from the Broad Institute GDAC Firehose platform ( https://gdac.broadinstitute.org ).

    Techniques: RNA Sequencing, Knockdown, Control, Phospho-proteomics, Expressing, MANN-WHITNEY, Microarray