Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of INDEL variants in apoptosis: the relevance to gastric cancer

ABSTRACT: Variants of INDEL in gastric cancer

PROVIDER: PRJEB40351 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Investigation of INDEL variants in apoptosis: the relevance to gastric cancer.

Project description: Not available

| S-EPMC7574166 | biostudies-literature

Blocking protein quality degradation leads to structural stabilization of DHFR indel variants

Project description:Gene variants leading to insertions or deletions of amino acid residues (indels) often have detrimental consequences for the folding of the encoded protein. Yet at some positions indels are tolerated or only result in partial unfolding. Typically unfolded proteins are targeted for protein quality control (PQC) degradation via ubiquitin-proteasome system, which in yeast is mediated by specific E3 ubiquitin-protein ligases, including Ubr1 and San1. Here we systematically probed the folding of a library of indel variants in the DHFR protein using sensitive yeast-based protein folding reporter. We show that deletion of Ubr1 and San1 leads to a greater fraction of folded DHFR indel variants, primarily positioned towards the N- and C-termini regions in DHFR. Intriguingly, most of the DHFR indels that are structurally stabilized in the E3 knockout strains, are also stabilized at lowered temperatures and upon binding the DHFR inhibitor methotrexate. This suggests that blocking PQC degradation can restore function to partially unfolded hypomorph variants, thus providing a potential therapeutic avenue for protein misfolding diseases.

2025-12-22 | GSE302176 | GEO

Systematic characterization of indel variants using a yeast-based protein folding sensor

Project description:Gene variants resulting in insertions or deletions of amino acid residues (indels) have important consequences for evolution and are often linked to disease, yet compared to missense variants the effects of indels are poorly understood and ineptly predicted. To approach this issue, we developed a sensitive protein folding sensor based on complementation of uracil auxotrophy in yeast by circular permutated orotate phosphoribosyltransferase (CPOP). The sensor accurately reports on the folding of disease-linked missense variants and artificially designed proteins. Applying the folding sensor to a saturated library of single amino acid indel variants in human DHFR revealed that most regions which tolerate indels are confined to internal loops and the N- and C-termini. Surprisingly, indels are also allowed at a central α-helix. Several indels are temperature-sensitive and the folding of most indels is rescued upon binding to the competitive DHFR inhibitor methotrexate. Predictions using Rosetta and AlphaFold2 correlate with the observed effects, suggesting that most indels operate by destabilizing the native fold and that these computational tools may be useful for classification of indels observed in population sequencing.

2024-07-25 | GSE270811 | GEO

Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Project description:Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.

2023-09-28 | GSE244096 | GEO

Blocking protein quality degradation leads to structural stabilization of DHFR indel variants

Project description:Blocking protein quality degradation leads to structural stabilization of DHFR indel variants

| PRJNA1289146 | ENA

Systematic characterization of indel variants using a yeast-based protein folding sensor

Project description:Systematic characterization of indel variants using a yeast-based protein folding sensor

| PRJNA1128549 | ENA

Effect of indel in promoter of CDC20 on gene expression in A375 human melanoma cell line.

Project description:CDC20 promoter variants are present in ~26% of cutaneous melanomas. We generated an indel in the promoter of CDC20 and performed RNA-sequencing to determine the effect on CDC20 expression and other secondary transcriptional changes.

2023-11-01 | GSE206639 | GEO

Familial clustering of gastric cancer

Project description:Discovering Rare Variants in Gastric Cancer Susceptibility in Gastric Cancer Family

| PRJEB29071 | ENA

AxiomM-BM-. Exome 319 Array data to identify susceptible genetic variations of gastric cancer

Project description:To efficiently identify genetic susceptibility variants for gastric cancer, including rare coding variants, we performed an exome chip-based array study. We found that a linkage disequilibrium (LD) block containing 2 significant variants in PSCA gene increased the risk and two blocks that included 15 suggested variants including TRIM31, TRIM 40, TRIM 10, and TRIM26 regions, and included one suggested variant and OR2H2 gene showed protective associations with gastric cancer susceptibility. In addition, the PLEC region (rs200893203), FBLN2 region (rs201192415), and EPHA2 region (rs3754334) were associated with increased susceptibility We performed an exome chip-based array study in 329 gastric cancer cases and 683 controls.

2014-06-11 | E-GEOD-58356 | biostudies-arrayexpress

HITI and INDEL analysis by next-generation sequencing

Project description:SpCas9 INDEL frequency and HITI was evaluated at the on-target site of guide RNA targeting either the mouse or pig rhodopsin by next-generation sequencing.

2021-11-11 | GSE180875 | 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