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Naslov:PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases
Avtorji:ID Liu, Tianyuan (Avtor)
ID Salguero, Pedro (Avtor)
ID Petek, Marko (Avtor)
ID Martinez-Mira, Carlos (Avtor)
ID Balzano-Nogueira, Leandro (Avtor)
ID Ramšak, Živa (Avtor)
ID McIntyre, Lauren (Avtor)
ID Gruden, Kristina (Avtor)
ID Tarazona, Sonia (Avtor)
ID Conesa, Ana (Avtor)
Datoteke:URL URL - Izvorni URL, za dostop obiščite https://doi.org/10.1093/nar/gkac352
 
.pdf PDF - Predstavitvena datoteka, prenos (3,53 MB)
MD5: 3B6A31A08FF7A627A2447A7E593E8DE1
 
Jezik:Angleški jezik
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:Logo NIB - Nacionalni inštitut za biologijo
Povzetek:PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology.
Ključne besede:PaintOmics 4, web tools, datasets, analysis methods, molecular biology
Verzija publikacije:Objavljena publikacija
Datum objave:24.05.2022
Leto izida:2022
Št. strani:str. W551-W559
Številčenje:Vol. 50, iss. W1
PID:20.500.12556/DiRROS-19337 Novo okno
UDK:577
ISSN pri članku:0305-1048
DOI:10.1093/nar/gkac352 Novo okno
COBISS.SI-ID:110574851 Novo okno
Opomba:Ostali avtorji: Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa; Članek v PDF formatu obsega 9 str.; First online: 24 May 2022;
Datum objave v DiRROS:17.07.2024
Število ogledov:459
Število prenosov:307
Metapodatki:XML DC-XML DC-RDF
:
LIU, Tianyuan, SALGUERO, Pedro, PETEK, Marko, MARTINEZ-MIRA, Carlos, BALZANO-NOGUEIRA, Leandro, RAMŠAK, Živa, MCINTYRE, Lauren, GRUDEN, Kristina, TARAZONA, Sonia in CONESA, Ana, 2022, PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. Nucleic acids research [na spletu]. 2022. Vol. 50, no. W1, p. w551–w559. [Dostopano 6 april 2025]. DOI 10.1093/nar/gkac352. Pridobljeno s: https://dirros.openscience.si/IzpisGradiva.php?lang=slv&id=19337
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Gradivo je del revije

Naslov:Nucleic acids research
Skrajšan naslov:Nucleic acids res.
Založnik:Oxford University Press
ISSN:0305-1048
COBISS.SI-ID:3269647 Novo okno

Gradivo je financirano iz projekta

Financer:ARIS - Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
Številka projekta:P4-0165-2022
Naslov:Biotehnologija in sistemska biologija rastlin
Financer:Drugi - Drug financer ali več financerjev
Program financ.:Spanish Ministry of Science and Innovation
Številka projekta:BIO2015- 1658-R and PID2020-119537RB-100
Financer:NIH - National Institutes of Health
Številka projekta:R03 CA222444
Financer:EC - European Commission
Številka projekta:GA 2020 862-858
Financer:EC - European Commission
Program financ.:COST Action
Številka projekta:CA15110 STSM
Financer:Drugi - Drug financer ali več financerjev
Program financ.:Generalitat Valenciana
Številka projekta:ACIF2019/081

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

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