Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of GABP knockdown on the transcriptome of macaque fibroblast cells

ABSTRACT: We identified a total of 2,058 GABP-regulated genes (1,067 up-regulated and 991 down-regulated genes in the GABP knockdown cells) with the threshold of Padj < 0.05 and Fold change > 1.5.

ORGANISM(S): Macaca mulatta

PROVIDER: GSE201987 | GEO | 2025/02/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effects of GABP knockdown on the transcriptome of macaque fibroblast cells

Project description:Effects of GABP knockdown on the transcriptome of macaque fibroblast cells

| PRJNA833936 | ENA

RNA-seq identified GLI1 as the target gene for GABP

Project description:We performed RNA-seq based transcriptomic analysis to evaluate differential protein expression in the kidneys of GABP overexpressing mice in db/m and GABP knockdown mice in db/db. The cluster analysis heat map shows the genetic changes . Compared with db/m mice, 734 differentially expressed genes, 525 upregulated genes and 209 upregulated genes . Compared with db/db mice, 82 genes were up-regulated and 82 genes were down-regulated in the kidneys of mice with GABP knockdown in db/db . Further, the classical pathway map in IPA database found that cell growth, proliferation, organ development and other pathways were activated after GABP overexpression. Cell growth, proliferation, organ development and other pathways were inhibited . It was further confirmed that GABP was associated with proliferation. Among differentially expressed genes, there were 9 differentially expressed genes up-regulated by GABP overexpression and down-regulated by GABP knockdown . Through the analysis of Ingenuity Pathway Analysis database, GABP and GLI1 were most closely related .

2024-10-05 | GSE244715 | GEO

[E-MTAB-115] ChIP-seq for FOXA2 HNF4a and NRF2 / GABP in HepG2

Project description:In each cell type the expression of genes is regulated by the action of a large number of transcription factors, but so far we have only a rudimentary knowledge of the location of the gene regulatory elements where they bind. This can now be addressed with genome-wide ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. HNF4a and FOXA2 binding was found in at least half of the regions previously identified as bound by USF2 but not USF1, showing that they frequently bind the same regulatory elements. GABP peaks were found at transcription start sites whereas 94 % of FOXA2 and 90 % of HNF4a peaks were located at other positions. We developed a method based on the high resolution achieved by ChIP-seq to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An unexpected interaction between HNF4a and GABP was seen at TSS, with as many as 1/3 of the HNF4a positive promoters being bound also by GABP, and co-immunoprecipitations show that these factors are in the same complex in the nucleus. ArrayExpress Release Date: 2009-06-10 Publication Title: Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing Publication Author List: Ola Wallerman, Mehdi Motallebipour, Stefan Enroth, Kalicharan Patra, MadhuSudan Reddy Bysani, Jan Komorowski, Claes Wadelius Person Roles: submitter Person Last Name: Wallerman Person First Name: Ola Person Mid Initials: Person Email: ola.wallerman@genpat.uu.se Person Phone: Person Address: IGP, Rudbecklab Person Affiliation: Uppsala University

2011-02-05 | GSE25694 | GEO

Genome-wide mapping of the transcription factor GABP-alpha binding in human CD34+CD133+ hematopoietic progenitor cells.

Project description:We used ChIP-Seq to map GABP-alpha binding sites in human hematopoietic progenitor cells (HPCs). Coupled with functional assays using GABP-alpha deficient mouse model and bioinformatics analysis, we systematically determined a transcriptional module controlled by GABP in HPCs.

2010-12-10 | GSE24933 | GEO

High throughput sequencing of human HepG2 DNA immunoprecipitated with FOXA2, HNF4a and NRF2/GABP

2009-06-09 | E-MTAB-115 | biostudies-arrayexpress

Genome-wide mapping of the transcription factor GABP-alpha binding in human CD34+CD133+ hematopoietic progenitor cells.

2010-12-10 | E-GEOD-24933 | biostudies-arrayexpress

GABP-dependent gene regulation in T cells

Project description:GABP-dependent gene regulation in T cells

| PRJNA395977 | ENA

RNA-seq identified GLI1 as the target gene for GABP

Project description:RNA-seq identified GLI1 as the target gene for GABP

| PRJNA1024439 | ENA

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

Project description:Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBM), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identify the functional consequence of these mutations in GBM to be recruitment of the multimeric GABP transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native ETS motifs critically cooperate with these mutations to activate TERT, likely by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.

| EGAS00001001242 | EGA

HOTAIRM1 knockdown microarray

Project description:To investigate the target genes of HOTAIRM1 in glioma cells, we conducted a lncRNA + mRNA expression microarray analysis to identify novel HOTAIRM1 regulating genes. Three glioma cell lines U87MG, T98G and A172 stably knockdown HOTAIRM1 were used as the experiments models. We conservatively established a minimum of 2-fold difference between shHOTAIRM1 (knockdown HOTAIRM1) and shNT (control group), and identified 10 up-regulated and 22 down-regulated genes that met the threshold in all cell lines.

2021-12-26 | GSE192627 | 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