BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Bai, Jinwen; Bandla, Chakradhar; Guo, Jiaxin; Alvarez, Roberto Vera; Bai, Mingze; Vizcaíno, Juan Antonio; Moreno, Pablo; Grüning, Björn; Sallou, Olivier; Perez‐Riverol, Yasset

doi:10.1021/acs.jproteome.0c00904

Cited by 22 publications

(16 citation statements)

References 18 publications

(58 reference statements)

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“…As shown above, we are already working on developing open and reproducible data analysis pipelines for different flavours of proteomics workflows (e.g., DDA, DIA, proteogenomics) ( 49 , 53 , 57 ). The main rationale is to make possible the use of that software in cloud infrastructures so that in the future the pipelines can be used by the community in the cloud using software container technologies ( 58 ).…”

Section: Discussion and Future Plansmentioning

confidence: 99%

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

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4,383

2,678

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The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.

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Section: Discussion and Future Plansmentioning

confidence: 99%

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol

Bai

Bandla

et al. 2021

Nucleic Acids Research

Self Cite

4,383

2,678

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“…Phospholipids include platelet-activating factor (PAF), phosphatidylcholine, and lysophosphatidic acid (LPA). Previous studies (31,32) have shown that PAF induces rat fibroblasts to secrete type I and IV collagen and fibronectin tubular cells, leading to renal fibrosis. Furthermore, LPA exerts therapeutic effects on myoblasts and induces significant expression of connective tissue growth factor.…”

Section: Discussionmentioning

confidence: 95%

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

Wang¹,

Wu²,

Li³

et al. 2022

Transl Androl Urol

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Background: This paper aimed to identify the key genes and potential mechanisms of renal fibrosis, and provide methods of evaluation and new ideas for the early diagnosis and treatment of renal fibrosis. Methods:The GSE102515 dataset was searched from the Gene Expression Omnibus (GEO) database was searched, the differential genes were screened out, and the down-regulated and up-regulated genes were identified. Enrichment analysis of differential genes in the development of renal fibrosis was carried out using the DAVID database, differential genes were analyzed using the STRING database, and Cytoscape software was used for visual processing.Results: Eighteen up-regulated genes and ten down-regulated genes were screened. Differential genes are mainly involved in the integrin-mediated signaling pathway and mitotic sister chromatid binding, etc. We found that the molecular functions (MFs) of the differential genes are phospholipid binding and regulatory region DNA binding, etc. Moreover, the cellular components (CCs) of the differential genes are mainly related to low-density lipoprotein (LDL) particles and nuclei. Screening revealed that ADM, ARRB1, AVPR2, CCR1, MTNR1A, PTH, and S1PR2 were core genes in the interaction network of renal fibrosis riskrelated proteins.Conclusions: In this study, the differential genes in the occurrence of renal fibrosis were screened out via dataset analysis. It was found that ADM, ARRB1, AVPR2, CCR1, MTNR1A, PTH, and S1PR2 may be important participants in the development of renal fibrosis, which provides analytical support for the identification of valuable markers of renal fibrosis.

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“…Docker (https://www.docker.com/) was used to run the bioinformatics software. Docker containers of software were obtained from the BioContainers Registry (Bai et al, 2021).…”

Section: Microscopymentioning

confidence: 99%

Phage Genes Induce Quorum Sensing Signal Release through Membrane Vesicle Formation

et al. 2022

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Membrane vesicles (MVs) released from the bacterium Paracoccus denitrificans Pd1222 are enriched with the quorum sensing (QS) signaling molecule N-hexadecanoyl-l-homoserine lactone (C16-HSL). However, the biogenesis of MVs in Pd1222 remains unclear. Investigations on MV formation are crucial for obtaining a more detailed understanding of the dynamics of MV-assisted signaling. In the present study, live-cell imaging showed that P. denitrificans Pd1222 produced MVs through cell lysis under DNA-damaging conditions. DNA sequencing of MVs and a transcriptome analysis of cells indicated that the expression of a prophage region was up-regulated at the onset of MV formation under DNA-damaging conditions. A further sequence analysis identified a putative endolysin (Pden_0381) and holin (Pden_0382) in the prophage region. The expression of these genes was regulated by RecA. Using gene knockout mutants, we showed that prophageencoded endolysin was critical for MV formation by P. denitrificans Pd1222 under DNA-damaging conditions. MV triggering by endolysin was dependent on the putative holin, which presumably transported endolysin to the periplasmic space. C16-HSL quantification revealed that more signals were released into the milieu as a consequence of the effects of endolysin. Using a QS reporter strain, we found that the QS response in P. denitrificans was stimulated by inducing the expression of endolysin. Collectively, these results provide novel insights into the mechanisms by which a bacterial cell-to-cell communication system is manipulated by phage genes.

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BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Cited by 22 publications

References 18 publications

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

Phage Genes Induce Quorum Sensing Signal Release through Membrane Vesicle Formation

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