Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Population-associated molecular variation in histologically normal breast tissue is context-dependent and associated with distinct transcriptional states

ABSTRACT: Population-associated molecular variation in breast tissue may contribute to differences in tissue biology and disease susceptibility, yet the extent to which such variation is shaped by underlying tissue states remains unclear. We performed integrated transcriptomic and lipidomic profiling of histologically normal breast tissue samples from African American and Caucasian White individuals. Unsupervised transcriptomic analysis revealed two baseline transcriptional states, G1 and G2, that defined the primary axis of molecular variation and corresponded to epithelial-enriched and vascular-enriched tissue contexts. Global comparisons between African American and Caucasian White samples showed limited transcriptomic differences. However, when samples were stratified by baseline transcriptional state, 191 genes were differentially expressed within G1, with coordinated upregulation of extracellular matrix organization and proliferative/cytoskeletal programs in African American samples. No comparable population-associated differences were observed within G2. Lipidomic analyses showed partial but non-significant trends consistent with transcriptomic structure. These findings suggest that population-associated molecular differences in normal breast tissue are context-dependent and emerge within specific baseline transcriptional states.

ORGANISM(S): Homo sapiens

PROVIDER: GSE333857 | GEO | 2026/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA methylation contributes to natural human variation

2013-07-22 | GSE36369 | GEO

Differences in Timely Cancer Diagnosis in African American and Caucasian Patients With Newly Diagnosed Colorectal Cancer

Project description:RATIONALE: Gathering information about timely diagnosis in African American and Caucasian patients with newly diagnosed colorectal cancer may help doctors learn more about factors that influence a diagnosis and plan the best treatment. PURPOSE: This phase I trial is studying differences in timely cancer diagnosis in African American patients and in Caucasian patients with newly diagnosed colorectal cancer.

| 2068885 | ecrin-mdr-crc

Transcription profiling of human optic nerve head astrocytes in Caucasian and African americans with or without glaucoma

Project description:To determine whether optic nerve head astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary culture of astrocytes from African American donors with or without glaucoma, compared to astrocytes from Caucasian American donors with or without glaucoma. Experiment Overall Design: We divided samples into four group: Caucasian American normal, Caucasian American with glaucoma, African American normal and African American with glaucoma. We analyzed data from Affymetrix Human Genome U133A 2.0 and U95 chips.

2008-04-07 | E-GEOD-9944 | biostudies-arrayexpress

Circulating miRNAs as biomarkers and potential functional mediators of early stage breast cancer

Project description:Analysis of the levels of circulating miRNAs from women with early stage breast cancer and matched healthy controls. miRNAs in plasma samples from 20 women with early stage breast cancer (10 Caucasian American and 10 African American) compared with 20 matched healthy controls (10 Caucasian American and 10 African American).

2011-01-16 | E-GEOD-22981 | biostudies-arrayexpress

Differential Expression of miRNAs: Implication in Colon Cancer Racial Health Disparity

Project description:We have demonstrated that the miR-182 level, in addition to being significantly increased in colon cancer compared to adjacent normal colon tissue, is also significantly increased in African American(AA) compared to Caucasian American (CA) colon cancer. Since miR-182 has been previously associated with decreased survival in colon cancer patients and with increased liver metastases, this observation supports the concept that biological differences between AA and CA colon cancers may contribute to AA disparities in colon cancer survival.

2015-06-25 | GSE48267 | GEO

Transcription profiling of human optic nerve head astrocytes in normal Caucasian and African americans

Project description:To determine whether optic nerve head astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary culture of astrocytes from normal African American donors, compared to astrocytes from normal Caucasian American donors. All donors have no histories of eye disease, diabetes, or chronic CNS disease. Experiment Overall Design: We divided samples into two groups: normal Caucasian American and normal African American. We analyzed data from Affymetrix Human Genome Human Genome U133A and U133A 2.0 chips.

2008-06-17 | E-GEOD-9939 | biostudies-arrayexpress

Human T cells isolated from healthy European and African American blood donors: Control vs. Interferon alpha 2b-treated

Project description:Transcriptional profiling of human T cells analyzing the impact of race on the responsiveness to IFNa in healthy blood donors. Control and IFNa-treated samples derived from healthy Caucasian American vs. African American blood donors are compared.

2010-01-27 | GSE17952 | GEO

DNA methylation contributes to natural human variation

Project description:DNA methylation analysis using the Infinium HumanMethylation450 BeadChip platform (Illumina) of 96 Caucasian American, 96 Han Chinese American and 96 African American LCL samples determined differences in terms of differentially methylated sites. Importantly, the observed differences were confirmed in primary blood samples of 10 healthy Caucasian, 10 African American (GSE36064) and 10 Asian individuals. Genes associated to differentially methylated site suggest an influence of DNA methylation on phenotype differences. Interestingly, methylation differences could be partially traced back to genetic polymorphisms. DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

2013-07-22 | E-GEOD-36369 | biostudies-arrayexpress

Gene expression data on human optic nerve head astrocytes in Caucasian and African americans with or without glaucoma

2008-01-31 | GSE9944 | GEO

Tumor Immunobiological Differences in Prostate Cancer between African-American and European-American Men

Project description:The incidence and mortality rates of prostate cancer are significantly higher in African-American men when compared to European-American men. We tested the hypothesis that differences in tumor biology contribute to this survival health disparity. Using microarray technology, we obtained gene expression profiles of primary prostate tumors resected from 33 African-American and 36 European-American patients. These tumors were matched on clinical parameters. We also evaluated 18 non-tumor prostate tissues from 7 African-American and 11 European-American patients. The resulting datasets were analyzed for expression differences on the gene and pathway level comparing African-American with European-American patients. Our analysis revealed a significant number of genes, e.g., 162 transcripts at a false-discovery rate less than 5%, to be differently expressed between African-American and European-American patients. Using a disease association analysis, we identified a common relationship of these transcripts with autoimmunity and inflammation. These findings were corroborated on the pathway level with numerous differently expressed genes clustering in immune response, stress response, cytokine signaling, and chemotaxis pathways. Furthermore, a two-gene tumor signature was identified that accurately differentiated between African-American and European-American patients. This finding was confirmed in a blinded analysis of a second sample set. In conclusion, the gene expression profiles of prostate tumors indicate prominent differences in tumor immunobiology between African-American and European-American men. The profiles portray the existence of a distinct tumor microenvironment in these two patient groups. Keywords: Microdissected tissue analysis

2008-01-01 | GSE6956 | GEO

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