Browse
Submit Data
Databases
API
Help

Dataset Information

336 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 provided DB analysis

ABSTRACT: This dataset is no actual new study but the results of the benchmark of the iPRG2008 benchmark dataset used in the manuscript "In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics".

INSTRUMENT(S): Q TRAP

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Julian Uszkoreit

LAB HEAD: Katrin Marcus

PROVIDER: PXD003956 | Pride | 2016-08-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MGI_UniProtMouse_20071203_iPRG2008_fixed__tdr.fasta	Fasta
	PT_model.txt	Txt
	iPRG2008_combined_faked_rt.mgf	Mgf
	mascot-iPRG2008_combined_faked_rt.idXML	Other
	merge1-mascot-fdr_filtered-iPRG2008_combined_faked_rt.idXML	Other

Items per page:

1 - 5 of 31

Publications

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain Enrique E Uszkoreit Julian J Sachsenberg Timo T Pfeuffer Julianus J Liang Xiao X Hermjakob Henning H Sanchez Aniel A Eisenacher Martin M Reinert Knut K Tabb David L DL Kohlbacher Oliver O Perez-Riverol Yasset Y

Journal of proteomics 20160804

In mass spectrometry-based shotgun proteomics, protein identifications are usually the desired result. However, most of the analytical methods are based on the identification of reliable peptides and not the direct identification of intact proteins. Thus, assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Currently, different protein inference algorithms and tools are available for the prot ...[more]

PMID: 27498275

Similar Datasets

In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 UniProt proteome analysis

Project description:This dataset is no actual new study but the results of the benchmark of the iPRG2008 benchmark dataset used in the manuscript "In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics".

2016-08-10 | PXD003954 | Pride

In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 Swiss-Prot analysis

2016-08-10 | PXD003953 | Pride

In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 UniProt proteome with isoforms analysis

2016-08-10 | PXD003955 | Pride

PIA - iPRG2008 Benchmark Dataset

Project description:This dataset is no actual new study but the iPRG2008 benchmark dataset used in the PIA manuscript.

2015-05-08 | PXD000793 | Pride

The Rice Annotation Project Database (RAP-DB): 2008 update.

Project description:The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

| S-EPMC2238920 | biostudies-literature

Integrative analysis of histone ChIP-seq and gene expression microarray data using Bayesian mixture models

Project description:Histone modifications are a key epigenetic mechanism to activate or repress the expression of genes. Data sets of matched microarray expression data and histone modification data measured by ChIP-seq exist, but methods for integrative analysis of both data types are still rare. Here, we present a novel bioinformatic approach to detect genes that are differentially expressed between two conditions putatively caused by alterations in histone modification. We introduce a correlation measure for integrative analysis of ChIP-seq and gene expression data and demonstrate that a proper normalization of the ChIP-seq data is crucial. We suggest applying Bayesian mixture models of different distributions to further study the distribution of the correlation measure. The implicit classification of the mixture models is used to detect genes with differences between two conditions in both gene expression and histone modification. The method is applied to different data sets and its superiority to a naive separate analysis of both data types is demonstrated. This GEO series contains the expression data of the Cebpa example data set. This data set was derived from sorted Cebpafl/fl and Cebpafl/fl;Mx1Cre murine hematopoietic LSKCD150- 18 post pIpC injections (conditional deletion of Cebpa). The specimens from three Cebpafl/fl and three Cebpafl/fl;Mx1Cre mice were hybridized separately on six Affymetrix Mouse Gene 1.0 ST arrays. Associated histone modification ChIP-seq data is provided by series GSE43007.

2014-02-05 | E-GEOD-49975 | biostudies-arrayexpress

Pre-leukemic Cebpa mutant myeloid progenitors

Project description:In this study, we use pre-malignant cells from different Cebpa mutant acute myeloid leukemia (AML) models. We have used conditional KO models (CreLoxP) and isolated hematopoietic cells shortly after induction of recombination, in order to look at pre-leukemic cells, which have acquired the first hit, but not yet undergone full malignant transformation. We have sorted granulocyte-macrophage progenitors (GMPs) and the more immature population pre-granulocyte-macrophages (preGMs) from pre-leukemic mice. We analyzed gene-expression profiles in order to find deregulated genes, which make the cells more prone to undergo transformation.

2013-07-08 | E-GEOD-47813 | biostudies-arrayexpress

Development of MLL-rearranged leukemia is dependent on a transcriptional program orchestradt by C/EBPα

Project description:Translocations involving the MLL genes are frequently found in Acute Myeloid Leukemia (AML) and are associated with poor prognosis. The MLL fusion proteins act as aberrant transcription factor activating a transcriptional program that transforms the cells, potentially through collaboration with other transcription factors. To investigate this we searched gene expression profiles from patients with MLL-rearranged AML compared with normal hematopoietic progenitor cells for transcriptional regulators and found targets of C/EBPα to be up-regulated in the AML samples, suggesting that C/EBPα might collaborate with MLL fusion proteins in the initial transformation process. We could show that transformation by MLL fusion proteins is dependent on C/EBPα activity both in early progenitors as well as in GMPs. In contrast, C/EBPα was found to be indispensable in an already established leukemia. These results suggest that C/EBPα play an important role in the early transforming event of leukemogenesis. We used microarray to study the early transcriptional changes induced by MLL-ENL expression and we identified a combined C/EBPα / MLL-ENL transcriptional signature. 3 Cebpaflox/flox;Mx1Cre and 3 Cebpaflox/flox;Mx1Cre- mice were sacrificed 14 days after pIpC injection and bone marrow cells were harvested, enriched for cKit-expression and transduced with a pMIG retroviral vector expressing the MLL-ENL fusion protein and GFP. 72 h post first transduction, GFP-positive or negative PreGM cells were sorted.

2013-12-10 | E-GEOD-46534 | biostudies-arrayexpress

CD-1mice: db/db vs db/+

2015-09-01 | GSE70527 | GEO

CD-1mice: db/db vs db/+

Project description:Transcriptional profiling of mouse white adipose tissues. The objective of this study is to explore gene expression profiles of obese adipose tissue by DNA microarray data analysis. Male db/db (BKS.Cg-m+/+ Lepr db/J, 6 weeks old) and db/+ (BKS.Cg-Dock7m +/+ Lepr db/J, 6 weeks old) mice were used in this experiment.

2015-09-01 | E-GEOD-70527 | 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