Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic Atlas of Embryonic Human Heart Development

ABSTRACT: Human heart tissue transcriptome was analyzed over a developmental period of 4-8 weeks post-conception. The analysis identifies several modules of co-expressed genes. These modules were tested for significance and disease relevance using other publically available data. This gene expression data was also integrated with the epigenetic data generated in this study to elucidate complex regulatory networks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138799 | GEO | 2020/07/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Epigenomic Atlas of Embryonic Human Heart Development

Project description:Chromatin State Profilining using multiple histone modifications in human embryonic heart tissue spanning 4 post conception weeks (pcw) to 8 pcw

2020-07-29 | GSE137731 | GEO

Transcriptomic Atlas of Embryonic Human Craniofacial Development

Project description:A majority of craniofacial development occurs early in pregnancy and to fully understand how craniofacial defects arise, it is essential to observe gene expression during this critical time period. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from embryonic development -4 to 8 weeks post conception. To observe how genes are organized in this system, we have constructed co-expression networks from the bulk RNA-seq. Strong disease candidates are likely genes that are co-expressed with many other genes, serving as regulatory hubs within these networks. We have identified 29 modules of co-expressed genes and ~1800 hub genes and found enrichment of craniofacial relevant biology suggesting that these networks could reveal new disease genes and potential targets of previously identified disease genes. We leveraged large functional genomics databases including GTEx and GnomAD to reveal genes that are specifically expressed in craniofacial tissue. We integrate these data with our co-expression networks in order to prioritize the genes in this study. Our analysis revealed 268 novel or underappreciated disease candidate genes.

2023-06-26 | GSE197513 | GEO

An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks

Project description:The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets (745 samples, from over 100 separate studies) derived from human primary cells and analysed on the Affymetrix U133plus2.0 array. Using the network analysis tool BioLayout Express3D we have constructed and clustered large correlation graphs of these data in order to identify robust co-associations of genes expressed in a wide variety of cell lineages. We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control. We consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system. Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (www.biogps.org) and on macrophages.com (www.macrophages.com). Meta-analysis of publically available human primary cell data run on the Affymetrix U133plus2.0 array.

2013-08-16 | E-GEOD-49910 | biostudies-arrayexpress

Genomic atlas of human adrenal and gonad development

Project description:Microarray analysis of human adrenal and gonad (testis and ovary) samples between six and ten weeks post-conception. This dataset consists of 17 adrenal glands, 20 testes and 10 ovaries, as well as 6 control samples from spine, brain, muscle, heart, kidney and liver.

2017-03-27 | E-MTAB-5525 | biostudies-arrayexpress

Epigenomic Atlas of Early Human Craniofacial Development

Project description:Chromatin State Profilining using multiple histone modifications in human craniofacial tissue spanning 4.5 post conception weeks to 10 pcw The raw FASTQ sequence files are being deposited in dbGAP

2017-05-04 | GSE97752 | GEO

An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks

2013-08-16 | GSE49910 | GEO

SECRETORY PROTEOMIC RESPONSES OF ENDOMETRIAL EPITHELIAL CELLS TO TROPHOBLAST DERIVED EXTRACELLULAR VESICLES

Project description:Synchronized cross talk between embryo and endometrium during pre-implantation period is critical for establishment of pregnancy. Extracellular vesicels(EVs) of both embryo and endometrial origin are known to be integral in regulating embryo maternal communication during this time. However, exact molecular signalling pathways or factors that regulate the embryo endometrial communication during pre-conception period remains elusive. Here in this study extracellular vesicles from trophoblast cells were shown to modulate endometrial epithelial cell secretome in favour of embryo implantation and embryo development.

2023-10-24 | PXD040311 | Pride

Gene expression atlas of a developing tissue by single cell expression correlation analysis

Project description:The Drosophila wing disc has been a fundamental model system for the discovery of key signaling pathways and for our understanding of developmental processes. However, a complete map of gene expression in this tissue is lacking. To obtain a complete gene expression atlas in the wing disc, we employed single-cell sequencing (scRNA-seq) and developed a new method for analyzing scRNA-seq data based on gene expression correlations rather than cell mappings. This enables us to discover 824 genes with spatially restricted expression patterns, and to compute expression maps for all genes in the wing disc. This approach identifies both known and new clusters of genes with similar expression patterns and functional relevance. As proof of concept, we characterize the previously unstudied gene CG5151 and show it regulates Wnt signaling. This novel method will enable the leveraging of scRNA-seq data for generating expression atlases of undifferentiated tissues during development.

2019-06-01 | GSE127832 | GEO

Molecular Atlas of Postnatal Mouse Heart Development.

Project description: Not available

| S-EPMC6474944 | biostudies-literature

Two microRNA Signatures for Malignancy and Immune Infiltration Predict Overall Survival in Advanced Epithelial Ovarian Cancer

Project description:MicroRNAs have been established as key regulators of tumor gene expression and as prime biomarker candidates for clinical phenotypes in epithelial ovarian cancer (EOC). We analyzed the coexpression and regulatory structure of microRNAs and their colocalized gene targets in primary tumor tissue of 20 advanced epithelial ovarian cancer patients in order to construct a regulatory signature for clinical prognosis. We performed an integrative analysis to identify two prognostic microRNA/mRNA coexpression modules, each enriched for consistent biological functions. One module, enriched for malignancy related functions, was found to be upregulated in malignant versus benign samples. The second module, enriched for immune related functions, was strongly correlated with intratumoral immune infiltrates of T cells, NK cells, Cytotoxic Lymphocytes, and Macrophages. We validated the prognostic relevance of the immunological module microRNAs in the publically available TCGA dataset. These findings provide novel functional roles for microRNAs in the progression of advanced EOC and possible prognostic signatures for survival.

2017-04-01 | GSE81873 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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