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Protocols

PaxDb specifications

Information


Unique identifier OMICS_03912
Name PaxDb
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline C. von Mering

Publication for PaxDb

PaxDb citations

 (14)
library_books

Expitope 2.0: a tool to assess immunotherapeutic antigens for their potential cross reactivity against naturally expressed proteins in human tissues

2017
BMC Cancer
PMCID: 5745885
PMID: 29282079
DOI: 10.1186/s12885-017-3854-8

[…] brain expression data from Wang et al. []. The new version 2.0 of Expitope incorporates three gene expression and four protein abundance datasets (Table ). It should be noted that in contrast to the PaxDB and Human Proteome Map datasets, which contain ppm values, the Human Protein Atlas data has been generated by immunohistochemistry, which makes the accuracy of the data dependent on the specific […]

library_books

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples

2017
Plant J
PMCID: 5863471
PMID: 29024340
DOI: 10.1111/tpj.13743

[…] obtaining comparative protein abundance data can be bypassed by referring to standard abundance values derived from publicly available mass spectrometry data, such as has been done for Arabidopsis at paxdb.org (Wang et al., ). However, in silico values cannot describe changes in protein or organelle abundance in response to external factors. Furthermore, low‐abundance proteins that are poorly repr […]

call_split

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

2017
Sci Rep
PMCID: 5622118
PMID: 28963504
DOI: 10.1038/s41598-017-12619-6
call_split See protocol

[…] Integrated protein abundance levels for E. coli K12 MG1655 were downloaded from PaxDb. Each protein id was mapped to its RefSeq geneID, for which the start codon was extracted from the whole genome sequence NC_000913.3. Taking into account only genes with protein abundance above […]

call_split

Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein–Protein Interaction Network

2017
Genome Biol Evol
PMCID: 5570066
PMID: 28854629
DOI: 10.1093/gbe/evx117
call_split See protocol

[…] ng information from different sources: Protein abundance: For each human, fly, worm and yeast gene, an estimate of the total abundance of the encoded proteins in the entire body was obtained from the PaxDb database, version 3 (). These estimates were obtained by combining multiple protein abundance data sets.Protein expression breadth: For each human gene, protein expression data across six differ […]

library_books

Intrinsic protein disorder reduces small scale gene duplicability

2017
PMCID: 5737077
PMID: 28430886
DOI: 10.1093/dnares/dsx015

[…] e was considered to be expressed at a certain tissue if it was annotated as ‘present’ in at least two of the three biological replicates.For all species, protein abundance data were obtained from the PaxDb database, version 4.0. We used the whole-organism integrated datasets, which is the result of a weighted combination of the results of numerous proteomics studies. […]

library_books

How Changes in Anti SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis

2017
PMCID: 5427494
PMID: 28364038
DOI: 10.1534/g3.117.039305

[…] 80 sequences annotated as pseudogenes in the E. coli genome from the analysis resulted in a final total of 4139 genes from E. coli and 4175 from B. subtilis.Protein abundance data were retrieved from PaxDB () at www.pax-db.org. The integrated data sets were downloaded for both B. subtilis and E. coli in order to maximize coverage and consistency scores. We downloaded the paxdb-uniprot-links file r […]


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