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UniPathway specifications

Information


Unique identifier OMICS_21397
Name UniPathway
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Maintainer


  • person_outline Anne Morgat

Publication for UniPathway

UniPathway citations

 (7)
library_books

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

2018
Nat Commun
PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] the dataset after host subtraction and quality filtering (Average reads per sample = 27 million; range = 12–40 million). HUMAnN2 v0.5.0 (http://huttenhower.sph.harvard.edu/humann2) was used with the UniPathway database for functional metagenomic profiling of filtered, host-subtracted metagenomic reads. Gene families were normalized to counts per million (cpm) prior to superpathway- and pathway-le […]

library_books

Metagenomic characterization of ambulances across the USA

2017
Microbiome
PMCID: 5610413
PMID: 28938903
DOI: 10.1186/s40168-017-0339-6

[…] Functional genomic profiles of the dataset were generated using HUMAnN2 version 0.5.0. HUMAnN2 utilizes the MetaCyc, UniPathway, and KEGG databases as well as the UniRef gene family catalog to characterize the microbial pathways present in samples. HUMAnN2 was run under default parameters (see Additional file for c […]

library_books

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

2016
mSystems
PMCID: 5069760
PMID: 27822528
DOI: 10.1128/mSystems.00018-16

[…] l genomic profiles were generated with HUMAnN2 version 0.3.0 () (http://huttenhower.sph.harvard.edu/humann2), which leverages the UniRef () orthologous gene family catalog, along with the MetaCyc (), UniPathway (), and KEGG () databases. HUMAnN2 gives three outputs: the (i) UniRef proteins and their abundances in reads per kilobase (RPK); (ii) the MetaCyc pathways and their abundances in RPK; and […]

library_books

De novo assembly and sex specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

2015
BMC Genomics
PMCID: 4619268
PMID: 26493315
DOI: 10.1186/s12864-015-2088-x

[…] yme hit in the ENZYME database (http://enzyme.expasy.org/); (iii) 10,790 (36.8 %) had at least one domain annotation in PFAM database (http://pfam.sanger.ac.uk/); (iv) 763 (2.6 %) were assigned to an UniPathway metabolic pathway (www.grenoble.prabi.fr/obiwarehouse/unipathway) (Additional file : Figure S2). Similarly to other recently released transcriptomes of dipteran insects [, , ], among the 81 […]

library_books

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

2015
PLoS One
PMCID: 4569324
PMID: 26366735
DOI: 10.1371/journal.pone.0137908

[…] sisting of InterPro entries that are connected to the InterPro database []. Additionally, using InterProScan, we inferred potential Gene Ontology (GO) terms [], EC-numbers [], KEGG [], MetaCyc [] and UniPathway [] pathway identifiers, which we used for further biological interpretation of gene function. InterProScan analysis of the 121 Streptococci strains was carried out using multi-threading com […]

library_books

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.)

2015
PLoS One
PMCID: 4521873
PMID: 26230730
DOI: 10.1371/journal.pone.0133696

[…] ome Annotation [] website. Circos diagrams [] were also used to analysis the differences at various growth stages. Proteins that were differentially expressed in the booting stage were analyzed using UniPathway [] to identify molecular pathways that may be different in this growth stage compared with the other two stages. […]

Citations

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UniPathway institution(s)
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Equipe BAMBOO, INRIA Grenoble Rhone-Alpes, Montbonnot Saint-Martin, France; Laboratoire d’Ecologie Alpine, UMR UJF-CNRS 5553, Universite Joseph Fourier, Grenoble, France; CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
UniPathway funding source(s)
Supported by Swiss Federal Government through the Federal Office of Education and Science, European Union (SLING: Serving Life-science Information for the Next Generation: 226073, Microme: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics: 222886-2 and ERC Advanced Grant SISYPHE), French government through ANR MIRI BLAN08-1335497 and MetaNetX project of the Swiss SystemsX.ch initiative.

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