Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

OTHER RELATED OMICS DATASETS IN: MSV000079669

PROVIDER: PRJNA340076 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR4063770_1.fastq.gz	Fastqsanger.gz
	SRR4063770_2.fastq.gz	Fastqsanger.gz
	SRR4063780_1.fastq.gz	Fastqsanger.gz
	SRR4063780_2.fastq.gz	Fastqsanger.gz
	SRR4063790_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 56

Similar Datasets

SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

Project description:RNA metabolism is controlled by an expanding yet incomplete catalog of RNA binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull-down of twelve nuclear and cytoplasmic RBPs followed by quantitative mass-spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1923 human, 489 fly and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.

2016-10-06 | GSE86035 | GEO

Large-scale tethering of RNA binding proteins discovers alternative splicing regulators

Project description:Large-scale tethering of RNA binding proteins discovers alternative splicing regulators

| PRJNA392334 | ENA

Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [microarray]

Project description:Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [microarray]

| PRJNA392278 | ENA

Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [RIP-Seq]

Project description:Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [RIP-Seq]

| PRJNA392336 | ENA

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Project description:Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

| PRJNA962448 | ENA

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Project description:TRIM25 E3 ubiquitin ligase is a new RNA-binding protein. We present the first high-throughput analysis of the molecular interactomes of TRIM25. We show that TRIM25 is a bona fide RNA-binding protein that interacts with numerous coding and non-coding transcripts. This suggests that TRIM25 could play a role in the regulation of RNA metabolism.

2018-07-27 | GSE104949 | GEO

Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response (PIP-Seq)

Project description:Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.

2022-06-15 | GSE148423 | GEO

Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response (mRNA)

2022-06-15 | GSE148422 | GEO

A compendium of RNA-binding motifs for analysis of gene regulation

Project description:RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized. Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukaryotes. The sequence specificities of RBPs display deep evolutionary conservation, such that the recognition preferences for a large fraction of metazoan RNA binding proteins can be inferred from the sequences of their binding domains. The motifs we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA binding proteins in both normal physiology and in human disease. These data provide an unprecedented global view of RBPs and their targets and constitute an invaluable resource for defining post-transcriptional regulatory mechanisms in eukaryotes.

2013-05-10 | GSE41235 | GEO

Cisplatin, Carboplatin, and Oxaliplatin Interactions With Plasma Proteins

Project description:Cisplatin is a widely used anti-tumor agent for the treatment of testicular and ovarian cancers. Carboplatin is used extensively for small cell, non small cell lung cancer and ovarian cancer. Oxaliplatin has recently been approved in the United States (US) for treatment of colorectal cancer. A large portion (in the range of 65% to 98%) of cisplatin in the blood plasma was bound to protein within a day after intravenous administration. The binding of cisplatin and other analogues to proteins and enzymes is generally believed to be the cause of several severe side effects such as ototoxicity and nephrotoxicity. The interactions between platinum based chemotherapy drugs and proteins is proposed to play important roles in both drug activity and toxicity. Therefore, a better understanding of the molecular mechanism of platinum-protein interactions may have an impact on optimization of strategies for treatment. The objective is to develop novel approaches and techniques to provide detailed mechanistic, kinetic and high-resolution structural information on the binding of platinum analogues to blood proteins, and to improve treatment efficacy and reduce side effects.

| 2014357 | ecrin-mdr-crc

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