Browse
Submit Data
Databases
API
Help

Dataset Information

492 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Re-analysis of: ‘CSF proteome mapping: Human cerebrospinal fluid LC-MS/MS, Part 2’ (PXD000652) to demonstrate the ProteoAnnotator software for mapping identifications to Ensembl genomes

ABSTRACT: We have performed a re-analysis of PXD000652 - a human proteome CSF fluid sample, originally queried versus UniProt. We have used our ProteoAnnotator package to re-search the data against Ensembl Human build 76 to demonstrate the capability of the pipeline to perform genome mapping on a large scale.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Fawaz Ghali

LAB HEAD: Andy Jones

PROVIDER: PXD001390 | Pride | 2014-10-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HV_map_B1.mgf	Mgf
	HV_map_B1.pride.mgf.gz	Mgf
	HV_map_B1.raw	Raw
	HV_map_B10.mgf	Mgf
	HV_map_B10.pride.mgf.gz	Mgf

Items per page:

1 - 5 of 145

Publications

ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

Ghali Fawaz F Krishna Ritesh R Perkins Simon S Collins Andrew A Xia Dong D Wastling Jonathan J Jones Andrew R AR

Proteomics 20141119 23-24

The recent massive increase in capability for sequencing genomes is producing enormous advances in our understanding of biological systems. However, there is a bottleneck in genome annotation--determining the structure of all transcribed genes. Experimental data from MS studies can play a major role in confirming and correcting gene structure--proteogenomics. However, there are some technical and practical challenges to overcome, since proteogenomics requires pipelines comprising a complex set o ...[more]

PMID: 25297486

Similar Datasets

Re-analysis of: ‘CSF proteome mapping: Human cerebrospinal fluid LC-MS/MS, Part 2’ (PXD000652) to demonstrate the ProteoAnnotator software for mapping identifications to Ensembl genomes

Project description:We have performed a re-analysis of PXD000652 - a human proteome CSF fluid sample, originally queried versus UniProt. We have used our ProteoAnnotator package to re-search the data against Ensembl Human build 76 to demonstrate the capability of the pipeline to perform genome mapping on a large scale.

| MSV000080193 | MassIVE

Proteogenomic analysis of Toxoplasma gondii (comparing genome releases 6 and 10) to demonstrate the performance of the ProteoAnnotator software

Project description:Testing the performance of the ProteoAnnotator software via comparing analysis of annotating the Toxoplasma gondii gene models 6 and 10

2014-10-20 | PXD001042 | Pride

Host imprinting on bacterial genomes-rapid, divergent evolution in individual hosts

Project description:Transcriptional profiling of Asymptomatic Bacteriuria (ABU) Escherichia coli strain 83972 comparing the progenitor wild type strain ABU83972 with its re-isolates from human bladder colonization (PI-2, PII-4, PIII-4) and in vitro cultivation experiment (4.9). Wild type vs. re-isolate cells. Biological replicates: 3 wild type, 3 re-isolates, independently grown and harvested. One replicate per array.

2011-01-15 | E-GEOD-19917 | biostudies-arrayexpress

Proteomic and phosphoproteomic profilings in fibroblasts of 11 common mammalian species

Project description:A central goal of modern biology is to understand the molecular basis of phenotype evolution between species. Previously, the evolutionary profiling at the molecular level has been largely limited to the nucleotide level. Nevertheless, the genotype is translated to proteotype through comprehensive and gene-specific post-transcriptional regulations. Harnessing recently emerged consistent proteomic quantification methods, we here investigate the co-evolution processes across the transcriptomic, proteomic, and phosphoproteomic layers in skin fibroblasts from 11 common mammalian species. Altogether, we have generated a multi-species, multi-omics resource, the analysis of which significantly facilitates the understanding of gene expression, proteotype co-evolution, and biodiversity in mammals.

2022-09-22 | PXD028979 | Pride

Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset

Project description:A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generati on by the algorithm DecoyPyrat.

2021-10-26 | PXD029362 | Pride

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

Project description:East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations. While TE-derived genetic and epigenetic variability has been associated with phenotypic traits, TE expression and epigenetic silencing remain unexplored in cichlids. Here, we profiled TE expression in African cichlids, and describe dynamic expression patterns during embryogenesis and according to sex. Most TE silencing factors are conserved and expressed in cichlids. We describe an expansion of two truncated Piwil1 genes in Lake Malawi/Nyasa cichlids, encoding a Piwi domain with catalytic potential. To further dissect epigenetic silencing of TEs, we focused on small RNA-driven epigenetic silencing. We detect a small RNA population in gonads consistent with an active Piwi-interacting RNA (piRNA) pathway targeting TEs. We uncover fluid genomic origins of piRNAs in closely related cichlid species. This, along with signatures of positive selection in piRNA pathway factors, points towards fast co-evolution of TEs and the piRNA pathway. Our study is the first step to understand the contribution of ongoing TE-host arms races to the cichlid radiations in Africa.

2024-04-02 | PXD047439 | Pride

Mapping personal functional data to personal genomes.

Project description:The sequencing of personal genomes enabled analysis of variation in transcription factor (TF) binding, chromatin structure and gene expression and indicated how they contribute to phenotypic variation. It is hypothesized that using the reference genome for mapping ChIP-seq or RNA-seq reads may introduce errors, especially at polymorphic genomic regions.We developed a Personal Genome Editor (perEditor) that changes the reference human genome (NCBI36/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure and gene expression.perEditor is available at http://biocomp.bioen.uiuc.edu/perEditor.szhong@illinois.edu.

| S-EPMC3232370 | biostudies-literature

Proteogenomics of Venturia pirina

Project description:This dataset relates to a proteogenomic analysis for Venturia pirina, a fungus that causes scab disease on European pear (Pyrus communis). V. pirina is host specific and infection is thought to be mediated by small, secreted effector proteins. To focus on these effectors we analysed extracts from V. pirina grown in vitro, on cellophane sheets, that mimics the growth habit in infected leaves. LC-MS/MS data was queried against a protein database generated by combining in-silico predicted transcripts with six-frame translations of a whole genome sequence for V. pirina.

2014-07-02 | PXD000710 | Pride

Functional mapping of yeast genomes by saturated transposition.

Project description:Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.

| S-EPMC5466422 | biostudies-literature

Mapping the RNA structural landscape of viral genomes.

Project description:Functional RNA structures are prevalent in viral genomes, and have been shown to play roles in almost every aspect of their biology. However, the majority of viral RNA remains structurally uncharacterized. This is likely to remain true as the cost of sequencing decreases much faster than the cost of structural characterizations. Because of this, there is a need for rapid, inexpensive methods to highlight regions of viral RNA which are ideal candidates for structure-function analyses. The ScanFold method was developed as a single sequence alternative to traditional RNA structural motif discovery pipelines, which rely heavily on well curated sequence alignments to identify conserved RNA structures. ScanFold focuses on identifying (based on their more stable than expected folding energies) the most likely functional structures encoded within a single large RNA sequence, while allowing predicted motifs to be tested for evidence of structural conservation later. Decoupling these processes can be a benefit to researchers studying viruses lacking the ideal phylogenetic depth to yield evidence of structural conservation. Here, we demonstrate how the most significant ScanFold predicted structures correspond to higher base pairing probabilities, SHAPE reactivities, and predict known functional structures within the ZIKV and HIV-1 genomes with accuracy. Best practices and examples are also shown to aid users in utilizing ScanFold for their own systems of interest. ScanFold is available as a Webserver (https://mosslabtools.bb.iastate.edu/scanfold) or can be downloaded (https://github.com/moss-lab/ScanFold) and run locally.

| S-EPMC7205576 | 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