Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of PBX3-binding sites and Quantitative Analysis of PBX3-Regulated Transcriptomes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE71262 | GEO | 2015/09/24

SECONDARY ACCESSION(S): PRJNA290719

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide maps of PBX3-binding site

Project description:We report the high-throughput profiling of PBX3-binding sites under liver cancer stem cell reprogramming driven by PBX3 overexpression. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide PBX3-binding maps of SMMC-7721 cells. This study provides a prediction of regulated genes by the PBX3.

2015-09-24 | GSE71260 | GEO

Genome-wide maps of XBP1 binding sites in different breast cancer cell lines

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

| S-ECPF-GEOD-49955 | biostudies-other

Next Generation Sequencing Facilitates Quantitative Analysis of PBX3 Regulated Transcriptomes

Project description:The goals of this study are to analyze the transcriptome profiling (RNA-seq) after PBX3 overexpression in SMMC-7721 cells.

2015-09-24 | GSE71261 | GEO

Genome-wide maps of PRDM16 binding sites and histone modifications

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-21 | GSE111661 | GEO

Genome-wide maps of XBP1 binding sites in different breast cancer cell lines.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-26 | E-GEOD-49955 | biostudies-arrayexpress

Genome-wide maps of RAP1 binding sites.

Project description:By performing chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq), we find that RAP1 binds to telomeres as well as to extra-telomeric sites through the (TTAGGG)2 consensus motif. Extra-telomeric RAP1 binding sites are particularly abundant at subtelomeric regions, and this is in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. Significantly, more than 70% of extratelomeric RAP1 binding sites are located in the vicinity of known genes and about 40% of the genes deregulated in Rap1-null cells contain binding sites for RAP1, suggesting a role of RAP1 in transcriptional control.

2010-07-10 | GSE20867 | GEO

Genome-wide maps of RAP1 binding sites.

2010-07-10 | E-GEOD-20867 | biostudies-arrayexpress

Genome-wide maps of XBP1 binding sites in different breast cancer cell lines.

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-09-26 | GSE49955 | GEO

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells.

Project description:Aberrant expression of HOXC6 and HOXC4 is commonly detected in prostate cancer. The high expression of these transcription factors is associated with aggressive prostate cancer and can predict cancer recurrence after treatment. Thus, HOXC4 and HOXC6 are clinically relevant biomarkers of aggressive prostate cancer. However, the molecular mechanisms by which these HOXC genes contribute to prostate cancer is not yet understood. To begin to address the role of HOXC4 and HOXC6 in prostate cancer, we performed RNA-seq analyses before and after siRNA-mediated knockdown of HOXC4 and/or HOXC6 and also performed ChIP-seq to identify genomic binding sites for both of these transcription factors. Our studies demonstrate that HOXC4 and HOXC6 co-localize with HOXB13, FOXA1 and AR, three transcription factors previously shown to contribute to the development of prostate cancer. We suggest that the aberrantly upregulated HOXC4 and HOXC6 proteins may compete with HOXB13 for binding sites, thus altering the prostate transcriptome. This competition model may be applicable to many different human cancers that display increased expression of a HOX transcription factor.

| S-EPMC6996832 | biostudies-literature

MotifMap: integrative genome-wide maps of regulatory motif sites for model species.

Project description:BACKGROUND:A central challenge of biology is to map and understand gene regulation on a genome-wide scale. For any given genome, only a small fraction of the regulatory elements embedded in the DNA sequence have been characterized, and there is great interest in developing computational methods to systematically map all these elements and understand their relationships. Such computational efforts, however, are significantly hindered by the overwhelming size of non-coding regions and the statistical variability and complex spatial organizations of regulatory elements and interactions. Genome-wide catalogs of regulatory elements for all model species simply do not yet exist. RESULTS:The MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate regulatory elements encoded in the genomes of model species. The system is used to derive new genome-wide maps for yeast, fly, worm, mouse, and human. The human map contains 519,108 sites for 570 matrices with a False Discovery Rate of 0.1 or less. The new maps are assessed in several ways, for instance using high-throughput experimental ChIP-seq data and AUC statistics, providing strong evidence for their accuracy and coverage. The maps can be usefully integrated with many other kinds of omic data and are available at http://motifmap.igb.uci.edu/. CONCLUSIONS:MotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses. The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathways as examples.

| S-EPMC3293935 | 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