Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.

ABSTRACT: Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68 cancer types, and 64 other diseases. This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available from the GeneSapiens website.

SUBMITTER: Kilpinen S

PROVIDER: S-EPMC2592717 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.

Kilpinen Sami S Autio Reija R Ojala Kalle K Iljin Kristiina K Bucher Elmar E Sara Henri H Pisto Tommi T Saarela Matti M Skotheim Rolf I RI Björkman Mari M Mpindi John-Patrick JP Haapa-Paananen Saija S Vainio Paula P Edgren Henrik H Wolf Maija M Astola Jaakko J Nees Matthias M Hautaniemi Sampsa S Kallioniemi Olli O

Genome biology 20080919 9

Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68 cancer types, and 64 other diseases. This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available fr ...[more]

PMID: 18803840

Similar Datasets

The Beta3 Adrenergic Receptor in Healthy and Pathological Cardiovascular Tissues.

Project description:The third isotype of beta-adrenoreceptors (?3-AR) has recently come (back) into focus after the observation of its expression in white and beige human adipocytes and its implication in metabolic regulation. This coincides with the recent development and marketing of agonists at the human receptor with superior specificity. Twenty years ago, however, we and others described the expression of ?3-AR in human myocardium and its regulation of contractility and cardiac remodeling. Subsequent work from many laboratories has since expanded the characterization of ?3-AR involvement in many aspects of cardiovascular physio(patho)logy, justifying the present effort to update current paradigms under the light of the most recent evidence.

| S-EPMC7761574 | biostudies-literature

Frequency and Types of Pathological Upper Gastrointestinal Endoscopy Findings in Clinically Healthy Individuals.

Project description:Background and objectiveBeyond its application for diagnostics in patients, esophagogastroduodenoscopy (EGD) is used to assess gastrointestinal drug effects in clinical trials, where the interpretation of any pathological findings depends on the respective background variability. The objective of this analysis was to characterize the occurrence of pathological findings in the upper gastrointestinal tract in symptom-free healthy individuals.MethodsA baseline EGD was performed in clinically healthy individuals in three clinical trials aimed to assess gastrointestinal tolerability of drugs. Pathological findings were described by type (redness, erosion, ulcer or other), number, size and location, and by clinical relevance as assessed by the endoscopist. Characteristics of volunteers were tested as potential covariates.ResultsA total of 294 EGDs were assessed. Characteristics of individuals were as follows: 257 (87.4%) males, age (mean ± SD) 32.0 ± 8.1 years, body weight 76.0 ± 10.6 kg, body mass index (BMI) 24.0 ± 2.5 kg/m2, 200 consumed alcohol, 250 (of 290 where this information was available) consumed caffeine and 39 (of 152) were smokers, 30 (of 151) tested positive for H. pylori. Any pathological finding was present in 79.6%. Clinically relevant findings occurred in 44.2%, mainly erosions (39.1%). Nine stomach ulcers were observed. Only age and BMI had a statistically significant relationship to overall pathological findings [age 3.4 years higher (p = 0.027), and BMI 1.6 kg/m2 higher (p < 0.001); for clinically relevant vs no findings].ConclusionUpper gastrointestinal tract mucosal lesions, including those assessed as clinically relevant, are frequent in clinically healthy individuals, impeding the assessment of causality for both disease and drug effects on gastrointestinal health.

| S-EPMC7221033 | biostudies-literature

Erastin‑induced ferroptosis causes physiological and pathological changes in healthy tissues of mice.

Project description:Ferroptosis is a non‑apoptotic form of cell death that relies on iron and lipid peroxidation, which is associated with multiple pathological processes in several diseases. Erastin is a small molecule capable of initiating ferroptotic cell death in cancer cells, which has shown great potential for cancer therapy. However, the physiological and pathological role of erastin‑induced ferroptosis on healthy tissues has not been well characterized. The present study intraperitoneally injected erastin into healthy mice to detect the metabolic changes of several tissues of mice. Erastin injection induced typical characteristics of ferroptosis with higher level of serum iron and malondialdehyde and lower level of glutathione and glutathione peroxidase 4 protein. Erastin injection enhanced iron deposition in the brain, duodenum, kidney and spleen of mice. Erastin‑induced ferroptosis altered the blood index values, causing mild cerebral infarction of brain and enlarged glomerular volume of kidney. It also promoted the growth of duodenal epithelium with thicker, longer and denser villi in erastin‑treated mice. The findings provided evidence that erastin induced ferroptosis and caused pathological changes in healthy tissues of mice. This suggested that the anti‑tumor drug erastin was somewhat toxic to healthy tissues.

| S-EPMC8383038 | biostudies-literature

Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues.

Project description:BACKGROUND: Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST) data. METHODS: Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. RESULTS: Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. CONCLUSION: Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer.

| S-EPMC1459866 | biostudies-other

Identification of genes associated with laryngeal squamous cell carcinoma samples based on bioinformatic analysis.

Project description:The present study aimed to investigate the differentially expressed genes (DEGs) between laryngeal squamous cell carcinoma (LSCC) samples and non‑neoplastic laryngeal squamous cell samples, and the underlying biological mechanism. Gene expression profile data of GSE51985 and GSE10288 were obtained from the Gene Expression Omnibus database. The DEGs between the LSCC and normal samples were identified using the rowtest function in the genefilter package. Hierarchical clustering for DEGs was performed to confirm the distinction between the identified DEGs, and Gene Ontology term and pathway enrichment analyses were performed to determine the underlying function of the DEGs. In addition, protein‑protein interaction networks were established to investigate the interactive mechanism of the DEGs. A total of 1,288 upregulated genes and 317 downregulated genes were identified between the LSCC samples and non‑neoplastic LSC samples in the GSE51985 dataset, and five upregulated and 26 downregulated genes were identified in the samples from the GSE10288 dataset. The DEGs were clearly distinguished between the LSCC sample and the non‑neoplastic LSCC sample by hierarchical clustering. The upregulated genes were predominantly involved in the cell cycle, cell division or focal adhesion, and the 295 upregulated genes formed 374 protein interaction pairs in interaction network analysis. The results revealed that the genes involved in the cell cycle, in cell division or in focal adhesion were associated with the development and progression of LSCC.

| S-EPMC4526082 | biostudies-literature

Complete genome sequences of three novel human papillomavirus types, 175, 178, and 180.

Project description:We report the characterization of three novel human papillomavirus (HPV) types of the genus Gammapapillomavirus. HPV175 and HPV180 were isolated from a condyloma. HPV178 was isolated from healthy skin adjacent to an actinic keratosis.

| S-EPMC4031336 | biostudies-literature

A Systematic Characterization of Aquaporin-9 Expression in Human Normal and Pathological Tissues.

Project description:AQP9 is known to facilitate hepatocyte glycerol uptake. Murine AQP9 protein expression has been verified in liver, skin, epididymis, epidermis and neuronal cells using knockout mice. Further expression sites have been reported in humans. We aimed to verify AQP9 expression in a large set of human normal organs, different cancer types, rheumatoid arthritis synovial biopsies as well as in cell lines and primary cells. Combining standardized immunohistochemistry with high-throughput mRNA sequencing, we found that AQP9 expression in normal tissues was limited, with high membranous expression only in hepatocytes. In cancer tissues, AQP9 expression was mainly found in hepatocellular carcinomas, suggesting no general contribution of AQP9 to carcinogenesis. AQP9 expression in a subset of rheumatoid arthritis synovial tissue samples was affected by Humira, thereby supporting a suggested role of TNFα in AQP9 regulation in this disease. Among cell lines and primary cells, LP-1 myeloma cells expressed high levels of AQP9, whereas low expression was observed in a few other lymphoid cell lines. AQP9 mRNA and protein expression was absent in HepG2 hepatocellular carcinoma cells. Overall, AQP9 expression in human tissues appears to be more selective than in mice.

| S-EPMC4851273 | biostudies-literature

Characterization of three novel human papillomavirus types isolated from oral rinse samples of healthy individuals.

Project description:BackgroundDespite the strong evidence of HPV infection as the etiological agent in a subset of oral cancer, oral α-HPV detection is rare in healthy individuals, and little is known of the existing of novel HPV types in oral cavity.ObjectiveWe determined whether novel HPV types can be isolated from oral rinse samples collected from healthy individuals.Study designWe performed rolling circle amplification (RCA) coupled with degenerated PCR assay on 48 oral rinse samples to amplify novel HPV types. Full length HPV DNA was cloned using long range PCR. Quantitative type specific Taqman assays were used to determine the prevalence of novel HPV types in 158 archived oral tissue samples.ResultsWe were able to isolate four novel human papillomavirus types. Full length HPV DNA was cloned for three of the four novel HPV types. All four HPV types belong to the genus Gammapapillomavirus (γ-PV), where HPV 171 is most closely related to HPV 169, showing 88% similarity; HPV 172 is most closely related to HPV 156, showing 70% similarity; HPV 173 is most closely related to HPV 4, showing 73% similarity; oral sample lavage (OSL) 37 is most closely related to HPV 144, showing 69% similarity. Finally, we showed that HPV 173 was rarely present in oral tissues (2/158), HPV 172 was only detected in normal oral tissues (25/76), and HPV 171 was more prevalent in malignant oral tissues (17/82 vs. 10/76, p=0.21).ConclusionsNovel γ-HPV types are present in oral cavity of healthy individuals.

| S-EPMC3898882 | biostudies-literature

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types.

Project description:We introduce an approach to identify disease-relevant tissues and cell types by analyzing gene expression data together with genome-wide association study (GWAS) summary statistics. Our approach uses stratified linkage disequilibrium (LD) score regression to test whether disease heritability is enriched in regions surrounding genes with the highest specific expression in a given tissue. We applied our approach to gene expression data from several sources together with GWAS summary statistics for 48 diseases and traits (average N = 169,331) and found significant tissue-specific enrichments (false discovery rate (FDR) < 5%) for 34 traits. In our analysis of multiple tissues, we detected a broad range of enrichments that recapitulated known biology. In our brain-specific analysis, significant enrichments included an enrichment of inhibitory over excitatory neurons for bipolar disorder, and excitatory over inhibitory neurons for schizophrenia and body mass index. Our results demonstrate that our polygenic approach is a powerful way to leverage gene expression data for interpreting GWAS signals.

| S-EPMC5896795 | biostudies-literature

Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues.

Project description:BACKGROUND: Gene expression microarrays have been intensively applied to screen for genes involved in specific biological processes of interest such as diseases or responses to environmental stimuli. For mammalian species, cataloging of the global gene expression profiles in large tissue collections under normal conditions have been focusing on human and mouse genomes but is lacking for the pig genome. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the results from a large-scale porcine study establishing microarray cDNA expression profiles of approximately 20.000 genes across 23 healthy tissues. As expected, a large portion of the genes show tissue specific expression in agreement with mappings to gene descriptions, Gene Ontology terms and KEGG pathways. Two-way hierarchical clustering identified expected tissue clusters in accordance with tissue type and a number of cDNA clusters having similar gene expression patterns across tissues. For one of these cDNA clusters, we demonstrate that possible tissue associated gene function can be inferred for previously uncharacterized genes based on their shared expression patterns with functionally annotated genes. We show that gene expression in common porcine tissues is similar to the expression in homologous tissues of human. CONCLUSIONS/SIGNIFICANCE: The results from this study constitute a valuable and publicly available resource of basic gene expression profiles in normal porcine tissues and will contribute to the identification and functional annotation of porcine genes.

| S-EPMC2065904 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data