Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.

Software Proteins Data Mining

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
01 08 2023
Historique:
received: 17 02 2023
revised: 31 05 2023
accepted: 03 08 2023
medline: 14 8 2023
pubmed: 4 8 2023
entrez: 4 8 2023
Statut: ppublish

Résumé

Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts, and scatter plots. Users can also: (i) handle multiple protein/gene lists and analyse union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes, or (iv) analyse multiple lists of differentially expressed proteins/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14 436 organisms. Web Application: http://flame.pavlopouloslab.info. Code: https://github.com/PavlopoulosLab/Flame. Docker: https://hub.docker.com/r/pavlopouloslab/flame.

Identifiants

DOI: 10.1093/bioinformatics/btad490 PMID: 37540207 PMC: PMC10423032
pubmed: 37540207
pii: 7237254
doi: 10.1093/bioinformatics/btad490
pmc: PMC10423032
pii:
doi:

Substances chimiques

Proteins 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© The Author(s) 2023. Published by Oxford University Press.

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Auteurs

Evangelos Karatzas (E)

Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari (Athens), 16672, Greece.
ORCID: 0000-0001-9132-8981

Fotis A Baltoumas (FA)

Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari (Athens), 16672, Greece.
ORCID: 0000-0002-2870-2931

Eleni Aplakidou (E)

Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari (Athens), 16672, Greece.

Panagiota I Kontou (PI)

Department of Mathematics, University of Thessaly, Lamia, 35100, Greece.
Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece.

Panos Stathopoulos (P)

1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece.
School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece.

Leonidas Stefanis (L)

1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece.

Pantelis G Bagos (PG)

Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece.
ORCID: 0000-0003-4935-2325

Georgios A Pavlopoulos (GA)

Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari (Athens), 16672, Greece.
Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece.
Hellenic Army Academy, Vari, 16673, Greece.
ORCID: 0000-0002-4577-8276

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Flame (v2.0): advanced integration and...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Flame (v2.0): advanced integration and...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Fouille de données › Flame (v2.0): advanced integration and...