Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Improved functional annotation of posttranslationally modified proteins

ABSTRACT: Identification of posttranslational modifications (PTMs) by mass spectrometry is biased towards abundant proteins, skewing our understanding of PTMs towards readily detected proteins. To uncover specifically enriched Gene Ontology (GO) terms associated with PTMs, we developed a method to account for protein abundance bias when performing GO term enrichment analyses on PTM datasets. GO term enrichment analysis is frequently used to examine “-omics” datasets for overrepresented functional terms within a subset of the dataset, such as regulated genes or modified proteins. However, the identification of PTMs is biased to abundant proteins that are more readily detected in the mass spectrometer. Therefore, GO enrichment analyses comparing posttranslationally modified proteins (referred to here as modified proteins) to unmodified proteins are likely to reveal overrepresented GO terms associated with abundant proteins, rather than modified proteins specifically. The method we developed here provides more accurate GO term enrichment analysis of PTMs and identifies terms whose enrichment results from the bias to identify PTMs on abundant proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Brian Weinert

LAB HEAD: Brian Tate Weinert

PROVIDER: PXD002800 | Pride | 2020-07-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of differentiated NSC after lnc-OPC knockdown)

Project description:To quantitative analysis of transcriptome changes caused by lnc-OPC knockdown during OPC differentiation from NSC, lentivirus-based short hairpin RNAs were used to knockdown the lnc-OPC expression in a neural stem cell culture . Subsequently, puromycin-selected NSCs were differentiated to OPC in culture for three days.RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. DEseq was used for differential gene expression analysis caused by lnc-OPC knockdown. GO functional term enrichment analysis of differential gene expression caused by lnc-OPC knockdown, revealed significant enrichment of âoligodendrocyte developmentâ, âoligodendrocyte differentiationâ, âglia cell developmentâ, and âaxon ensheathmentâ terms that are associated with oligodendrogenesis. mRNA profiles of differentiiated NSC samples after lnc-OPC knockdown by RNA-sequencing.

2015-11-04 | E-GEOD-74647 | biostudies-arrayexpress

Large-Scale Analysis of Protein Crotonylation Reveals Its Diverse Functions in Pinellia ternate

Project description:We generated a global crotonylome analysis of the leaves in Pinellia ternata. We found 4509 crotonylated sites on 1757 proteins totally, and three specific amino acids surrounding crotonylation sites were identified in Pinellia ternata: KcrF, K***Y**Kcr and Kcr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participate in the carbohydrate metabolism pathway, were modified also by lysine crotonylation.

2022-04-13 | PXD033154 | Pride

Large-Scale Analysis of Protein Crotonylation Reveals Its Diverse Functions in Pinellia ternate

2022-07-31 | PXD033142 | Pride

Human and murine serum reactivity to specific histone posttranslational modifications in neutrophil extracellular traps

Project description:Introduction: Autoreactivity to histones is a pervasive feature of several human autoimmune disorders including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutrophil extracellular traps (NETs) may potentially drive the process by which tolerance to these chromatin-associated proteins is broken. We hypothesized that NETs and their unique histone PTMs might be capable of inducing autoantibodies that target histones. Methods: We developed a novel and efficient method for the in vitro production, visualization, and broad profiling of histone-PTMs of human and murine NETs. We also immunized Balb/c mice with murine NETs and profiled their sera on autoantigen and histone peptide microarrays for evidence of autoantibody production to their immunogen. Results: We confirmed specificity toward acetyl-modified histone H2B as well as to other histone PTMs in sera from patients with SLE known to have autoreactivity against histones. We observed enrichment for distinctive histone marks of transcriptionally silent DNA during NETosis triggered by diverse stimuli. However, NETs derived from human and murine sources did not harbor many of the PTMs toward which autoreactivity was observed in patients with SLE or in MRL/lpr mice. Further, while murine NETs were weak autoantigens in vivo, there was only partial overlap in the IgG and IgM autoantibody profiles induced by vaccination of mice with NETs and those seen in patients with SLE. Conclusions: Isolated in vivo exposure to NETs is insufficient to break tolerance and may involve additional factors that have yet to be identified.

2012-01-26 | GSE32543 | GEO

Murine serum reactivity to common autoantigens in response to immunization with neutrophil extracellular traps

2012-01-26 | GSE32542 | GEO

Transforming chemical proteomics into high-throughput method using SP2E workflow.

Project description:Protein post-translational modifications (PTMs) play a critical role in regulation of protein catalytic activity, localization and protein-protein interactions. An attachment of PTMs onto proteins significantly diversify their structure and function resulting in so called proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease specific, is still a highly challenging task. Sub-stoichiometric amounts and modification of low abundant proteins necessitate purification or enrichment of the modified proteins. Introduction of the mass spectrometry-based chemical proteomic strategy has enabled to screen protein PTMs with increased throughput, but the sample preparation has remained highly time consuming and tedious. Here, we report an optimized workflow for enrichment of PTM proteins in 96-well plate format which could be extended to robotic automation. This platform allows to significantly lower the input of total protein, which opens up the possibility to screen specialized and difficult to culture cell lines in high-throughput manner. The presented SP2E protocol is robust, time- and cost-effective as well as suitable for large-scale screening of proteoforms. Application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration and cancer. This may contribute to an overall acceleration of the recently launched Human Proteoform Project.

2022-07-04 | PXD033644 | Pride

Gene expression analysis of intestinal stem cells (ISCs) from polyI:C treated WT mice or Ifnar1-/- mice.

Project description:To explore the influence of IFNR-mediated singnaling in ISCs, we performed microarray analysis of the ISCs from control Lgr5ki mice versus Ifnar1-/-Lgr5ki mice after treating for 1 weeks with low doses of poly(I:C), which potentially induce type I and -III IFNs. The Gene Ontology (GO) analysis indicated that the GO terms overrepresented among the genes upregulated in ISCs from poly(I:C)-treated WT mice compared with those from poly(I:C)-treated Ifnar1−/− mice included “defense response to virus”, “immune system process”, “response to virus”, and “innate immune response”, all from the GOTERM_Biological Processes (BP) category. We compared these results against the Interferome database, which contains genes regulated by type I, II, or III IFN, compiled by analyzing the expression data of IFN-treated cells (http://www.interferome.org), and found that most of the genes found for the GO term “defense response to virus” were IFN-inducible genes, indicating that IFNs act directly on ISCs. The GO analysis also showed an enrichment of defense response to bacteria. In the GOTERM_Cellular Component (CC) category, “extracellular space” and “extracellular region” ranked at the top, indicating a dramatic change in the expression pattern of secretory molecules. Notably, these GO terms included genes encoding antibacterial proteins and endocrine hormones such as angiogenin, defensin, lysozyme, chromogranin, and glucagon, all of which are produced by secretory IECs. Thus, we hypothesized that excess IFN signals force ISCs to lose stemness and differentiate into secretory progenitors.

2020-07-21 | GSE137189 | GEO

Whole transcriptome analysis of leaves and petioles in Chinese cabbage [miRNA]

Project description:We use Chinese cabbage PHL as the material and sample during maturing repeating three times. 44796 differentially expressed mRNAs were identified by complete transcriptome sequencing of leaf and petiole, of which 10646 were significant differentially expressed. There were 10422 significant differentially expressed mRNAs annotated into molecular function, biological process and cell components. There were 723 GO terms, and the most enriched GO term was membrane component (GO: 0016021) . KEGG analysis showed that there were 31 significant pathways. Among them, the plant hormone signal transduction pathway (Ko04075) is the pathway with the most differentially enriched genes.A total of 2553 differentially expressed lncRNAs were obtained, of which 303 were significant differentially expressed lncRNAs. Target genes of significantly differentially expressed lncRNAs were predicted, and the predicted target genes were analyzed by GO and KEGG. There were 2425 GO terms and 127 pathways. The most enriched GO term was nucleus (GO: 0005634) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 1070 differentially expressed miRNAs were obtained, of which 195 were significant differentially expressed. Go and KEGG analyses of the predicted target genes were performed. There were 551 GO terms and 24 pathways. The most abundant GO terms were membrane components (GO: 0016021) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 886 differentially expressed circRNAs were obtained, including 7 significant differentially expressed circRNAs, which have 3 up-regulated circRNAs and 4 down-regulated circRNAs.

2022-08-26 | GSE182326 | GEO

Whole transcriptome analysis of leaves and petioles in Chinese cabbage [circRNA]

2022-08-26 | GSE182325 | GEO

High fat diet enriched in eicosapentaenoic and docosahexaenoic acids delays the development of fatty liver in mice.

Project description:To investigate the effects of quality of fat in a high fat diet (HFD) over time on hepatic lipid storage and transcriptome in mice. In this dataset, we include the expression data obtained from dissected mouse liver after being fed with Control, HFD-EPA/DHA and HFD-corn oil diet for 8 and 12 weeks. In total, 24 samples were analyzed. Based on hierarchical clustering and scatter plots, one microarray from the HFD-corn oil group at 8 weeks was removed from subsequent analyses. The Piano package was used for Gene Set Enrichment Analysis (GSEA) to identify the total number of genes regulated and the direction of regulation. Gene Ontology (GO) terms were annotated to each probe-set after performing GSEA. The reporter algorithm was used to analyse the functional enrichment level of individual GO term. Heatmaps were generated using the log10p-values to visualize enriched GO biological processes (BPs) terms.

2015-06-30 | E-GEOD-65370 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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