Cell annotation using scRNA-seq data: A protein-protein interaction network approach
- Autores
- Senra, Daniela; Guisoni, Nara Cristina; Diambra, Luis Anibal
- Año de publicación
- 2023
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Pathway analysis is an important step in the interpretation of single cell transcriptomic data, as it provides powerful information to detect which cellular processes are active in each individual cell. We have recently developed a protein-protein interaction network-based framework to quantify pluripotency associated pathways from scRNA-seq data. On this occasion, we extend this approach to quantify the activity of a pathway associated with any biological process, or even any list of genes. A systems-level characterization of pathway activities across multiple cell types provides a broadly applicable tool for the analysis of pathways in both healthy and disease conditions. Dysregulated cellular functions are a hallmark of a wide spectrum of human disorders, including cancer and autoimmune diseases. Here, we illustrate our method by analyzing various biological processes in healthy and cancer breast samples. Using this approach we found that tumor breast cells, even when they form a single group in the UMAP space, keep diverse biological programs active in a differentiated manner within the cluster. • We implement a protein-protein interaction network-based approach to quantify the activity of different biological processes. • The methodology can be used for cell annotation in scRNA-seq studies and is freely available as R package.
Fil: Senra, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Guisoni, Nara Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina - Materia
-
BIOLOGICAL PROCESSES
BREAST CANCER
CELL ANNOTATION
PROTEIN-PROTEIN INTERACTION NETWORKS
SCRNA-SEQ - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/221884
Ver los metadatos del registro completo
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Cell annotation using scRNA-seq data: A protein-protein interaction network approachSenra, DanielaGuisoni, Nara CristinaDiambra, Luis AnibalBIOLOGICAL PROCESSESBREAST CANCERCELL ANNOTATIONPROTEIN-PROTEIN INTERACTION NETWORKSSCRNA-SEQhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Pathway analysis is an important step in the interpretation of single cell transcriptomic data, as it provides powerful information to detect which cellular processes are active in each individual cell. We have recently developed a protein-protein interaction network-based framework to quantify pluripotency associated pathways from scRNA-seq data. On this occasion, we extend this approach to quantify the activity of a pathway associated with any biological process, or even any list of genes. A systems-level characterization of pathway activities across multiple cell types provides a broadly applicable tool for the analysis of pathways in both healthy and disease conditions. Dysregulated cellular functions are a hallmark of a wide spectrum of human disorders, including cancer and autoimmune diseases. Here, we illustrate our method by analyzing various biological processes in healthy and cancer breast samples. Using this approach we found that tumor breast cells, even when they form a single group in the UMAP space, keep diverse biological programs active in a differentiated manner within the cluster. • We implement a protein-protein interaction network-based approach to quantify the activity of different biological processes. • The methodology can be used for cell annotation in scRNA-seq studies and is freely available as R package.Fil: Senra, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Guisoni, Nara Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaElsevier2023-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/221884Senra, Daniela; Guisoni, Nara Cristina; Diambra, Luis Anibal; Cell annotation using scRNA-seq data: A protein-protein interaction network approach; Elsevier; MethodsX; 10; 102179; 4-2023; 1-82215-0161CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S2215016123001796info:eu-repo/semantics/altIdentifier/doi/10.1016/j.mex.2023.102179info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:37:46Zoai:ri.conicet.gov.ar:11336/221884instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:37:47.067CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
title |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
spellingShingle |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach Senra, Daniela BIOLOGICAL PROCESSES BREAST CANCER CELL ANNOTATION PROTEIN-PROTEIN INTERACTION NETWORKS SCRNA-SEQ |
title_short |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
title_full |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
title_fullStr |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
title_full_unstemmed |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
title_sort |
Cell annotation using scRNA-seq data: A protein-protein interaction network approach |
dc.creator.none.fl_str_mv |
Senra, Daniela Guisoni, Nara Cristina Diambra, Luis Anibal |
author |
Senra, Daniela |
author_facet |
Senra, Daniela Guisoni, Nara Cristina Diambra, Luis Anibal |
author_role |
author |
author2 |
Guisoni, Nara Cristina Diambra, Luis Anibal |
author2_role |
author author |
dc.subject.none.fl_str_mv |
BIOLOGICAL PROCESSES BREAST CANCER CELL ANNOTATION PROTEIN-PROTEIN INTERACTION NETWORKS SCRNA-SEQ |
topic |
BIOLOGICAL PROCESSES BREAST CANCER CELL ANNOTATION PROTEIN-PROTEIN INTERACTION NETWORKS SCRNA-SEQ |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Pathway analysis is an important step in the interpretation of single cell transcriptomic data, as it provides powerful information to detect which cellular processes are active in each individual cell. We have recently developed a protein-protein interaction network-based framework to quantify pluripotency associated pathways from scRNA-seq data. On this occasion, we extend this approach to quantify the activity of a pathway associated with any biological process, or even any list of genes. A systems-level characterization of pathway activities across multiple cell types provides a broadly applicable tool for the analysis of pathways in both healthy and disease conditions. Dysregulated cellular functions are a hallmark of a wide spectrum of human disorders, including cancer and autoimmune diseases. Here, we illustrate our method by analyzing various biological processes in healthy and cancer breast samples. Using this approach we found that tumor breast cells, even when they form a single group in the UMAP space, keep diverse biological programs active in a differentiated manner within the cluster. • We implement a protein-protein interaction network-based approach to quantify the activity of different biological processes. • The methodology can be used for cell annotation in scRNA-seq studies and is freely available as R package. Fil: Senra, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina Fil: Guisoni, Nara Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina |
description |
Pathway analysis is an important step in the interpretation of single cell transcriptomic data, as it provides powerful information to detect which cellular processes are active in each individual cell. We have recently developed a protein-protein interaction network-based framework to quantify pluripotency associated pathways from scRNA-seq data. On this occasion, we extend this approach to quantify the activity of a pathway associated with any biological process, or even any list of genes. A systems-level characterization of pathway activities across multiple cell types provides a broadly applicable tool for the analysis of pathways in both healthy and disease conditions. Dysregulated cellular functions are a hallmark of a wide spectrum of human disorders, including cancer and autoimmune diseases. Here, we illustrate our method by analyzing various biological processes in healthy and cancer breast samples. Using this approach we found that tumor breast cells, even when they form a single group in the UMAP space, keep diverse biological programs active in a differentiated manner within the cluster. • We implement a protein-protein interaction network-based approach to quantify the activity of different biological processes. • The methodology can be used for cell annotation in scRNA-seq studies and is freely available as R package. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-04 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/221884 Senra, Daniela; Guisoni, Nara Cristina; Diambra, Luis Anibal; Cell annotation using scRNA-seq data: A protein-protein interaction network approach; Elsevier; MethodsX; 10; 102179; 4-2023; 1-8 2215-0161 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/221884 |
identifier_str_mv |
Senra, Daniela; Guisoni, Nara Cristina; Diambra, Luis Anibal; Cell annotation using scRNA-seq data: A protein-protein interaction network approach; Elsevier; MethodsX; 10; 102179; 4-2023; 1-8 2215-0161 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S2215016123001796 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.mex.2023.102179 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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13.070432 |