Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deep phosphoproteomic analaysis of the response to EGF in HEK293 cells

ABSTRACT: In this study, we adopt the perspective of a naive researcher with the goal of learning a new signaling pathway, starting from differential phosphoproteomic data and a kinase-substrate network. Focusing on the well-characterized epidermal growth factor (EGF) response, we perform a meta-analysis of recent studies and complement those with three deep and time-resolved phosphoproteomic experiments. We also combine multiple kinase-substrate networks using protein language models and data from peptide-array screenings, generating a state-of-the-art resource. We use these datasets and networks to generate context-specific signaling subnetworks through various computational approaches, and compare the results to different sets of ground truth interactions.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: Martin Garrido-Rodriguez

LAB HEAD: Mikhail Savitski

PROVIDER: PXD056666 | Pride | 2026-02-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Eve_230607_S3603_CP_EGF_timecourse_phospho_F1.raw	Raw
	Eve_230607_S3603_CP_EGF_timecourse_phospho_F10.raw	Raw
	Eve_230607_S3603_CP_EGF_timecourse_phospho_F11.raw	Raw
	Eve_230607_S3603_CP_EGF_timecourse_phospho_F12.raw	Raw
	Eve_230607_S3603_CP_EGF_timecourse_phospho_F13.raw	Raw

Items per page:

1 - 5 of 99

Similar Datasets

Hdac6 regulates Tip60-p400 function in stem cells (sequencing)

Project description:The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. In contrast to differentiated cells, where Hdac6 is mainly cytoplasmic and does not interact with Tip60, Hdac6 is largely nuclear in ESCs and neural stem cells (NSCs) and interacts with Tip60-p400 in both cell types. Hdac6 is enriched at promoters bound by Tip60-p400 in ESCs, but while Tip60 binds on both sides of transcription start sites (TSSs), Hdac6 binding overlaps with only the downstream Tip60 peak. Surprisingly, Hdac6 does not deacetylate histones at these sites, but rather is required for Tip60 binding. These data suggest that nuclear exclusion of Hdac6 during differentiation plays a major role in modulation of Tip60-p400 function. We determined the genome-wide localization of Tip60 and Hdac6 in mouse ES cells, and examined genomic binding profiles of Tip60 and Hdac6 upon indicated knockdown by ChIP-seq. We examined genomic binding profiles of p400 upon indicated knockdown by ChIP-seq.

2013-11-20 | E-GEOD-42209 | biostudies-arrayexpress

Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome

Project description:Protein glycosylation is a highly diverse post-translational modification, modulating key cellular processes such as cell signaling, adhesion and cell-cell interactions. Its deregulation has been associated with various pathologies, including cancer and neurological diseases. Methods capable of quantifying glycosylation dynamics are essential to start unraveling the biological functions of protein glycosylation. Here we present Deep Quantitative Glycoprofiling (DQGlyco), a method that combines high-throughput sample preparation, high-sensitivity detection, and precise multiplexed quantification of protein glycosylation. We used DQGlyco to profile the mouse brain glycoproteome, in which we identify more than 200,000 unique N-glycopeptides - this amounts to 25-fold more glycopeptides identified compared to previous studies. We observed extensive heterogeneity of glycoforms and determined their functional and structural preferences. We used our quantitative approach to map surface-exposed glycoforms as well as to characterize glycosites tissue-specificity. The presence of a defined gut microbiota resulted in extensive remodeling of the brain glycoproteome when compared to that of germ-free animals, exemplifying how the gut microbiome may affect brain protein functions.

2025-02-07 | PXD052447 | Pride

In-depth phosphoproteomic profiling of the insulin signaling response in heart tissue and cardiomyocytes unveils canonical and spezialized regulation

Project description:Insulin signaling regulates cardiac substrate utilization and is implicated in physiological adapations of the heart. While extensively investigated in several metabolic organs using phosphoproteomic strategies, the signaling response elicited in cardiac tissue in general, and specifically in the spezialized cardiomyocyte cells, has not yet been investigated to the same extend.

2024-08-10 | PXD050545 | Pride

Quantitative Phosphoproteomics of whole-body sponge collapse

Project description:Sponges (Porifera) are early-branching Metazoa who do not possess muscles or neurons, however are able to undergo a whole-body movement that involves the closure of their canal system and collapse of an epithelial tent. In this study we profile the proteomic responses of the freshwater sponge Spongilla lacustris during nitric oxide (NO) and agitation induced movements to elucidate the early evolution of coordination in animals. Specifically, we used tandem mass tag (TMT) labeling-based quantification of enriched phosphopeptides to systematically measure quantitative differences in protein phosphorylation. We identified and quantified 12165 unique phosphopeptides in the sponge. NO treatment resulted in quantitative changes of phosphorylation levels on 390 unique phosphopeptides mapping to 270 unique proteins. In turn, agitation led to quantitative changes of phosphorylation levels on 303 unique phosphopeptides (229 proteins).

2024-01-04 | PXD044171 | Pride

Endogenous, tissue-specific short-interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats

Project description:We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype. In order to compare the population of chalcone synthase related small RNAs, we sequenced 3 to 6 million small RNAs using the Illumina Genome Analyzer from the following four soybean cultivars and tissues with specific genotypes at the I locus: Richland immature seed coats (homozygous for the dominant I allele that specifies yellow seed coat); Williams immature seed coats (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum) Williams (i-i/i-i yellow) immature cotyledons (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum); Williams 55 immature seed coats (a Williams isogenic line homozygous for the recessive i allele that specifics pigmented seed coats. All seed coats and cotyledons were dissected from green stage immature seeds within the fresh weight range of 50-75 mg.

2010-05-13 | E-GEOD-21825 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Arabidopsis thaliana Phosphoproteomic

| PRJNA946358 | ENA

NHS esters are non-innocent protein acylating reagents

Project description:N-Hydroxysuccinimide (NHS)-ester derivatives represent one of the most widely used reagents in biological chemistry and chemical biology. Their perceived utility as acylating agents –intermediates that are sufficiently stable to be isolated (even in commercial form) yet active enough to allow direct and acylation simply upon addition – has seen their widespread application. Their efficacy relies critically on the exclusive chemoselectivity of activated acyl over that of the imidic acyl moieties in the succinimide, such that NHS acts simply as an innocent nucleofuge ‘leaving group’. Here, through systematic structural variation that modulates acyl reactivity, coupled with a statistically controlled ultra-rapid screen for unknown modifications in tandem mass spectra and lysine profiling within the native E. coli proteome, which presents complex lysine environments, we reveal that ring-opening reaction of the succinimide to afford several N-succinamide derivatives is a present, sometimes dominant, side-reaction of certain NHS esters. Moreover, the extent of side-reaction is shown to be lysine nucleophile and therefore site-dependent, with both side-reaction and desired reaction occurring within the same protein substrate. The resulting formation of bioconjugates with unintended, unstable linkages and modifications – that may have previously gone undetected – not only suggests re-evaluation of i) use of potentially several hundred of the many-thousand, known commercial reagents; and ii) the functional conclusions previously drawn using NHS esters where these hinge crucially on the precise identity of conjugates in areas as diverse as antibody-drug biotherapy, vaccination to cross-link-enabled structural analyses.

2025-04-27 | PXD056949 | Pride

CRISPR Display: A modular method for locus-specific targeting of long noncoding RNAs and synthetic RNA devices in vivo [RIP-Seq]

Project description:Noncoding RNAs (ncRNAs) comprise an important class of natural regulators that mediate a vast array of biological processes, including the modulation of chromatin architecture. Moreover, artificial ncRNAs have revealed that the functional capabilities of RNA are extremely broad. To further investigate and harness these capabilities, we developed CRISPR-Display ("CRISP-Disp"), a targeted localization strategy that uses Cas9 to deploy large RNA cargos to specific DNA loci. We demonstrate that exogenous RNA domains can be functionally appended onto the CRISPR scaffold at multiple insertion points, allowing the construction of Cas9 complexes with RNAs nearing one kilobase in length, with structured RNAs, protein-binding cassettes, artificial aptamers and pools of random sequences. CRISP-Disp also allows the simultaneous multiplexing of disparate functions at multiple targets. We anticipate that this technology will provide a powerful method with which to ectopically localize functional RNAs and ribonuceloprotein complexes at specified genomic loci. RNA Immunoprecipitation (RIP) against FLAG-tagged Cas9 protein, coexpressed with a large pool of CRISPR RNAs bearing random internal insertions

2015-05-11 | E-GEOD-62305 | biostudies-arrayexpress

Integrated Systems Biology Analysis of KSHV Latent Infection Reveals Viral Induction and Reliance on Peroxisome Mediated Lipid Metabolism

Project description:Kaposi’s Sarcoma herpesvirus (KSHV), an oncogenic virus, modulates host cell signaling and metabolism to maintain latent infection. To unravel the underlying cellular mechanisms modulated by KSHV, we identified changes in the host proteome, phosphoproteome and transcriptome landscape upon KSHV infection of endothelial cells. A Steiner Forest algorithm was used to integrate proteomic, phosphoproteomic and transcriptomic data with transcriptome based predicted transcription factor activity to identify cellular networks altered by latent KSHV.

2017-02-08 | GSE84237 | GEO

Linking oncogenic signaling to transcriptional changes by epigenomic data in a cell line model of human glioblastoma

Project description:We present a computational method for building a regulatory network from global phosphoproteomic and transcription profiling data. To recover the critical missing links between signaling events and transcriptional responses, we relate changes in chromatin accessibility to changes in expression and then uses these links to connect proteomic and transcriptome data. We applied our approach to integrate epigenomic, phosphoproteomic and transcriptome changes induced by the variant III mutation of the epidermal growth factor receptor (EGFRvIII) in a cell line model of glioblastoma multiforme (GBM). Genome-wide DNase I hypersensitivity followed by sequencing (DNase-Seq) to measure chromatin accessibility in a cell line derived from the U87MG glioblastoma cell line to express high level of EGFRvIII (U87H; 2 million copies of EGFRvIII per cell) and a control cell line expressing kinase dead EGFRvIII (U87DK; 2 million kinase dead EGFRvIII per cell). A prediction from the computational method, the transcriptional co-regulator p300, was experimentally validated by chromatin immunoprecipitation followed by sequencing (ChIP-Seq).

2013-01-01 | E-GEOD-36900 | biostudies-arrayexpress

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