Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis
Q1
- Autores:
-
Otálora-Otálora, Beatriz Andrea
Osuna-Garzón, Daniel Alejandro
Carvajal-Parra, Michael Steven
Canas, Alejandra
Montecino, Martín
López-Kleine, Liliana
Rojas, Adriana
- Tipo de recurso:
- Article of journal
- Fecha de publicación:
- 2022
- Institución:
- Pontificia Universidad Javeriana
- Repositorio:
- Repositorio Universidad Javeriana
- Idioma:
- eng
- OAI Identifier:
- oai:repository.javeriana.edu.co:10554/61981
- Acceso en línea:
- https://www.mdpi.com/2079-7737/11/7/1082/htm
http://hdl.handle.net/10554/61981
https://doi.org/10.3390/biology11071082
- Palabra clave:
- Lung cancer (LC)
Breast cancer (BC)
Leukemia (LK)
Differentially expressed genes (DEGs)
Coexpression networks
Early detection and prognosis biomarkers
- Rights
- License
- Atribución-NoComercial 4.0 Internacional
| id |
JAVERIANA2_ab58a95ef3223f84f982e0c12ab4e97f |
|---|---|
| oai_identifier_str |
oai:repository.javeriana.edu.co:10554/61981 |
| network_acronym_str |
JAVERIANA2 |
| network_name_str |
Repositorio Universidad Javeriana |
| repository_id_str |
|
| dc.title.spa.fl_str_mv |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| title |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| spellingShingle |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis Lung cancer (LC) Breast cancer (BC) Leukemia (LK) Differentially expressed genes (DEGs) Coexpression networks Early detection and prognosis biomarkers |
| title_short |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| title_full |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| title_fullStr |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| title_full_unstemmed |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| title_sort |
Identifying general tumoral and specific lung cancer biomarkers by transcriptomic analysis |
| dc.creator.fl_str_mv |
Otálora-Otálora, Beatriz Andrea Osuna-Garzón, Daniel Alejandro Carvajal-Parra, Michael Steven Canas, Alejandra Montecino, Martín López-Kleine, Liliana Rojas, Adriana |
| dc.contributor.author.none.fl_str_mv |
Otálora-Otálora, Beatriz Andrea Osuna-Garzón, Daniel Alejandro Carvajal-Parra, Michael Steven Canas, Alejandra Montecino, Martín López-Kleine, Liliana Rojas, Adriana |
| dc.contributor.corporatename.spa.fl_str_mv |
Pontificia Universidad Javeriana. Facultad de Medicina. Departamento de Medicina Interna. Neumología |
| dc.contributor.corporatename.none.fl_str_mv |
Pontificia Universidad Javeriana. Facultad de Medicina. Instituto de Genética Humana. Grupo de investigación Instituto de Genética Humana |
| dc.contributor.javerianateacher.none.fl_str_mv |
Canas, Alejandra Rojas, Adriana |
| dc.subject.keyword.spa.fl_str_mv |
Lung cancer (LC) Breast cancer (BC) Leukemia (LK) Differentially expressed genes (DEGs) Coexpression networks Early detection and prognosis biomarkers |
| topic |
Lung cancer (LC) Breast cancer (BC) Leukemia (LK) Differentially expressed genes (DEGs) Coexpression networks Early detection and prognosis biomarkers |
| description |
Q1 |
| publishDate |
2022 |
| dc.date.accessioned.none.fl_str_mv |
2022-10-03T13:27:59Z |
| dc.date.available.none.fl_str_mv |
2022-10-03T13:27:59Z |
| dc.date.created.none.fl_str_mv |
2022-07-20 |
| dc.type.local.spa.fl_str_mv |
Artículo de revista |
| dc.type.coar.spa.fl_str_mv |
http://purl.org/coar/resource_type/c_6501 |
| format |
http://purl.org/coar/resource_type/c_6501 |
| dc.identifier.spa.fl_str_mv |
https://www.mdpi.com/2079-7737/11/7/1082/htm |
| dc.identifier.issn.spa.fl_str_mv |
2079-7737 |
| dc.identifier.uri.none.fl_str_mv |
http://hdl.handle.net/10554/61981 |
| dc.identifier.doi.spa.fl_str_mv |
https://doi.org/10.3390/biology11071082 |
| dc.identifier.instname.spa.fl_str_mv |
instname:Pontificia Universidad Javeriana |
| dc.identifier.reponame.spa.fl_str_mv |
reponame:Repositorio Institucional - Pontificia Universidad Javeriana |
| dc.identifier.repourl.spa.fl_str_mv |
repourl:https://repository.javeriana.edu.co |
| url |
https://www.mdpi.com/2079-7737/11/7/1082/htm http://hdl.handle.net/10554/61981 https://doi.org/10.3390/biology11071082 |
| identifier_str_mv |
2079-7737 instname:Pontificia Universidad Javeriana reponame:Repositorio Institucional - Pontificia Universidad Javeriana repourl:https://repository.javeriana.edu.co |
| dc.language.iso.spa.fl_str_mv |
eng |
| language |
eng |
| dc.relation.citationstartpage.spa.fl_str_mv |
1 |
| dc.relation.citationendpage.spa.fl_str_mv |
37 |
| dc.relation.ispartofjournal.spa.fl_str_mv |
Biology |
| dc.relation.citationvolume.spa.fl_str_mv |
11 |
| dc.relation.citationissue.spa.fl_str_mv |
7 |
| dc.rights.licence.*.fl_str_mv |
Atribución-NoComercial 4.0 Internacional |
| dc.rights.uri.*.fl_str_mv |
http://creativecommons.org/licenses/by-nc/4.0/ |
| dc.rights.coar.spa.fl_str_mv |
http://purl.org/coar/access_right/c_abf2 |
| rights_invalid_str_mv |
Atribución-NoComercial 4.0 Internacional http://creativecommons.org/licenses/by-nc/4.0/ http://purl.org/coar/access_right/c_abf2 |
| dc.format.spa.fl_str_mv |
PDF |
| dc.format.mimetype.spa.fl_str_mv |
application/pdf |
| institution |
Pontificia Universidad Javeriana |
| bitstream.url.fl_str_mv |
http://repository.javeriana.edu.co/bitstream/10554/61981/1/biology-11-01082.pdf http://repository.javeriana.edu.co/bitstream/10554/61981/2/license.txt http://repository.javeriana.edu.co/bitstream/10554/61981/4/biology-11-01082.pdf.jpg |
| bitstream.checksum.fl_str_mv |
da8c2424b866e12046f503ee90f338ef 2070d280cc89439d983d9eee1b17df53 2c0f40d67bcf32716b9545966b970d53 |
| bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 |
| repository.name.fl_str_mv |
Repositorio Institucional - Pontificia Universidad Javeriana |
| repository.mail.fl_str_mv |
repositorio@javeriana.edu.co |
| _version_ |
1811671070528241664 |
| spelling |
Atribución-NoComercial 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc/4.0/http://purl.org/coar/access_right/c_abf2Otálora-Otálora, Beatriz AndreaOsuna-Garzón, Daniel AlejandroCarvajal-Parra, Michael StevenCanas, AlejandraMontecino, MartínLópez-Kleine, LilianaRojas, AdrianaPontificia Universidad Javeriana. Facultad de Medicina. Departamento de Medicina Interna. NeumologíaPontificia Universidad Javeriana. Facultad de Medicina. Instituto de Genética Humana. Grupo de investigación Instituto de Genética HumanaCanas, AlejandraRojas, Adriana2022-10-03T13:27:59Z2022-10-03T13:27:59Z2022-07-20https://www.mdpi.com/2079-7737/11/7/1082/htm2079-7737http://hdl.handle.net/10554/61981https://doi.org/10.3390/biology11071082instname:Pontificia Universidad Javerianareponame:Repositorio Institucional - Pontificia Universidad Javerianarepourl:https://repository.javeriana.edu.coPDFapplication/pdfengIdentifying general tumoral and specific lung cancer biomarkers by transcriptomic analysisArtículo de revistahttp://purl.org/coar/resource_type/c_6501Q1Q1Pacientes con Cáncer de pulmónPacientes con Cáncer de mamaPacientes con LeucemiaThe bioinformatic pipeline previously developed in our research laboratory is used to identify potential general and specific deregulated tumor genes and transcription factors related to the establishment and progression of tumoral diseases, now comparing lung cancer with other two types of cancer. Twenty microarray datasets were selected and analyzed separately to identify hub differentiated expressed genes and compared to identify all the deregulated genes and transcription factors in common between the three types of cancer and those unique to lung cancer. The winning DEGs analysis allowed to identify an important number of TFs deregulated in the majority of microarray datasets, which can become key biomarkers of general tumors and specific to lung cancer. A coexpression network was constructed for every dataset with all deregulated genes associated with lung cancer, according to DAVID’s tool enrichment analysis, and transcription factors capable of regulating them, according to oPOSSUM´s tool. Several genes and transcription factors are coexpressed in the networks, suggesting that they could be related to the establishment or progression of the tumoral pathology in any tissue and specifically in the lung. The comparison of the coexpression networks of lung cancer and other types of cancer allowed the identification of common connectivity patterns with deregulated genes and transcription factors correlated to important tumoral processes and signaling pathways that have not been studied yet to experimentally validate their role in lung cancer. The Kaplan–Meier estimator determined the association of thirteen deregulated top winning transcription factors with the survival of lung cancer patients. The coregulatory analysis identified two top winning transcription factors networks related to the regulatory control of gene expression in lung and breast cancer. Our transcriptomic analysis suggests that cancer has an important coregulatory network of transcription factors related to the acquisition of the hallmarks of cancer. Moreover, lung cancer has a group of genes and transcription factors unique to pulmonary tissue that are coexpressed during tumorigenesis and must be studied experimentally to fully understand their role in the pathogenesis within its very complex transcriptomic scenario. Therefore, the downstream bioinformatic analysis developed was able to identify a coregulatory metafirm of cancer in general and specific to lung cancer taking into account the great heterogeneity of the tumoral process at cellular and population levels.https://orcid.org/0000-0003-3975-2835https://orcid.org/0000-0001-8528-4433Revista Internacional - IndexadaA1NoLung cancer (LC)Breast cancer (BC)Leukemia (LK)Differentially expressed genes (DEGs)Coexpression networksEarly detection and prognosis biomarkers137Biology117ORIGINALbiology-11-01082.pdfbiology-11-01082.pdfArtículoapplication/pdf4977488http://repository.javeriana.edu.co/bitstream/10554/61981/1/biology-11-01082.pdfda8c2424b866e12046f503ee90f338efMD51open accessLICENSElicense.txtlicense.txttext/plain; charset=utf-82603http://repository.javeriana.edu.co/bitstream/10554/61981/2/license.txt2070d280cc89439d983d9eee1b17df53MD52open accessTHUMBNAILbiology-11-01082.pdf.jpgbiology-11-01082.pdf.jpgIM Thumbnailimage/jpeg12976http://repository.javeriana.edu.co/bitstream/10554/61981/4/biology-11-01082.pdf.jpg2c0f40d67bcf32716b9545966b970d53MD54open access10554/61981oai:repository.javeriana.edu.co:10554/619812023-05-18 12:39:36.177Repositorio Institucional - Pontificia Universidad Javerianarepositorio@javeriana.edu.coTElDRU5DSUEgWSBBVVRPUklaQUNJw5NOIERFIExPUyBBVVRPUkVTIFBBUkEgUFVCTElDQVIgWSBQRVJNSVRJUiBMQSBDT05TVUxUQSBZIFVTTy4KClBhcnRlIDEuIFTDqXJtaW5vcyBkZSBsYSBsaWNlbmNpYSBnZW5lcmFsIHBhcmEgcHVibGljYWNpw7NuIGRlIG9icmFzIGVuIGVsIHJlcG9zaXRvcmlvIGluc3RpdHVjaW9uYWwKQ29tbyB0aXR1bGFyIChlcykgZGVsIGRlcmVjaG8gZGUgYXV0b3IsIGNvbmZpZXJvIChlcmltb3MpIGEgbGEgUG9udGlmaWNpYSBVbml2ZXJzaWRhZCBKYXZlcmlhbmEgdW5hIGxpY2VuY2lhIG5vIGV4Y2x1c2l2YSwgbGltaXRhZGEgeSBncmF0dWl0YSBzb2JyZSBsYSBvYnJhIHF1ZSBzZSBpbnRlZ3JhcsOhIGVuIGVsIFJlcG9zaXRvcmlvIEluc3RpdHVjaW9uYWwsIHF1ZSBzZSBhanVzdGEgYSBsYXMgc2lndWllbnRlcyBjYXJhY3RlcsOtc3RpY2FzOgphKSAgICAgIEVzdGFyw6EgdmlnZW50ZSBhIHBhcnRpciBkZSBsYSBmZWNoYSBkZSBpbmNsdXNpw7NuIGVuIGVsIHJlcG9zaXRvcmlvLCBwb3IgdW4gcGxhem8gZGUgNSBhw7FvcywgcXVlIHNlcsOhbiBwcm9ycm9nYWJsZXMgaW5kZWZpbmlkYW1lbnRlIHBvciBlbCB0aWVtcG8gcXVlIGR1cmUgZWwgZGVyZWNobyBwYXRyaW1vbmlhbCBkZWwgYXV0b3IuIEVsIGF1dG9yIHBvZHLDoSBkYXIgcG9yIHRlcm1pbmFkYSBsYSBsaWNlbmNpYSBzb2xpY2l0w6FuZG9sbyBhIGxhIFVuaXZlcnNpZGFkIHBvciBlc2NyaXRvLgpiKSAgICAgIEF1dG9yaXphIGEgbGEgUG9udGlmaWNpYSBVbml2ZXJzaWRhZCBKYXZlcmlhbmEgYSBwdWJsaWNhciBsYSBvYnJhIGVuIGRpZ2l0YWwsIGNvbm9jaWVuZG8gcXVlLCBkYWRvIHF1ZSBzZSBwdWJsaWNhIGVuIEludGVybmV0LCBwb3IgZXN0ZSBoZWNobyBjaXJjdWxhIGNvbiB1biBhbGNhbmNlIG11bmRpYWwuCmMpICAgICAgTG9zIGF1dG9yZXMgYWNlcHRhbiBxdWUgbGEgYXV0b3JpemFjacOzbiBzZSBoYWNlIGEgdMOtdHVsbyBncmF0dWl0bywgcG9yIGxvIHRhbnRvIHJlbnVuY2lhbiBhIHJlY2liaXIgYmVuZWZpY2lvIGFsZ3VubyBwb3IgbGEgcHVibGljYWNpw7NuLCBkaXN0cmlidWNpw7NuLCBjb211bmljYWNpw7NuIHDDumJsaWNhIHkgY3VhbHF1aWVyIG90cm8gdXNvIHF1ZSBzZSBoYWdhIGVuIGxvcyB0w6lybWlub3MgZGUgbGEgcHJlc2VudGUgbGljZW5jaWEgeSBkZSBsYSBsaWNlbmNpYSBkZSB1c28gY29uIHF1ZSBzZSBwdWJsaWNhLgpkKSAgICAgIExvcyBhdXRvcmVzIG1hbmlmaWVzdGFuIHF1ZSBzZSB0cmF0YSBkZSB1bmEgb2JyYSBvcmlnaW5hbCBzb2JyZSBsYSBxdWUgdGllbmVuIGxvcyBkZXJlY2hvcyBxdWUgYXV0b3JpemFuIHkgcXVlIHNvbiBlbGxvcyBxdWllbmVzIGFzdW1lbiB0b3RhbCByZXNwb25zYWJpbGlkYWQgcG9yIGVsIGNvbnRlbmlkbyBkZSBzdSBvYnJhIGFudGUgbGEgUG9udGlmaWNpYSBVbml2ZXJzaWRhZCBKYXZlcmlhbmEgeSBhbnRlIHRlcmNlcm9zLiBFbiB0b2RvIGNhc28gbGEgUG9udGlmaWNpYSBVbml2ZXJzaWRhZCBKYXZlcmlhbmEgc2UgY29tcHJvbWV0ZSBhIGluZGljYXIgc2llbXByZSBsYSBhdXRvcsOtYSBpbmNsdXllbmRvIGVsIG5vbWJyZSBkZWwgYXV0b3IgeSBsYSBmZWNoYSBkZSBwdWJsaWNhY2nDs24uCmUpICAgICAgQXV0b3Jpem8gKGFtb3MpIGEgbGEgVW5pdmVyc2lkYWQgcGFyYSBpbmNsdWlyIGxhIG9icmEgZW4gbG9zIMOtbmRpY2VzIHkgYnVzY2Fkb3JlcyBxdWUgZXN0aW1lbiBuZWNlc2FyaW9zIHBhcmEgcHJvbW92ZXIgc3UgZGlmdXNpw7NuLgpmKSAgICAgIEFjZXB0byAoYW1vcykgcXVlIGxhIFBvbnRpZmljaWEgVW5pdmVyc2lkYWQgSmF2ZXJpYW5hIHB1ZWRhIGNvbnZlcnRpciBlbCBkb2N1bWVudG8gYSBjdWFscXVpZXIgbWVkaW8gbyBmb3JtYXRvIHBhcmEgcHJvcMOzc2l0b3MgZGUgcHJlc2VydmFjacOzbiBkaWdpdGFsLgpnKSAgICAgIEF1dG9yaXpvIChhbW9zKSBxdWUgbGEgb2JyYSBzZWEgcHVlc3RhIGEgZGlzcG9zaWNpw7NuIGRlbCBww7pibGljbyBlbiBsb3MgdMOpcm1pbm9zIGF1dG9yaXphZG9zIGVuIGxvcyBsaXRlcmFsZXMgYW50ZXJpb3JlcyBiYWpvIGxvcyBsw61taXRlcyBkZWZpbmlkb3MgcG9yIGxhIHVuaXZlcnNpZGFkIGVuIGxhcyDigJxDb25kaWNpb25lcyBkZSB1c28gZGUgZXN0cmljdG8gY3VtcGxpbWllbnRv4oCdIGRlIGxvcyByZWN1cnNvcyBwdWJsaWNhZG9zIGVuIFJlcG9zaXRvcmlvIEluc3RpdHVjaW9uYWwgUFVKICwgY3V5byB0ZXh0byBjb21wbGV0byBzZSBwdWVkZSBjb25zdWx0YXIgZW4gaHR0cDovL3JlcG9zaXRvcnkuamF2ZXJpYW5hLmVkdS5jby8KClNJIEVMIERPQ1VNRU5UTyBTRSBCQVNBIEVOIFVOIFRSQUJBSk8gUVVFIEhBIFNJRE8gUEFUUk9DSU5BRE8gTyBBUE9ZQURPIFBPUiBVTkEgQUdFTkNJQSBPIFVOQSBPUkdBTklaQUNJw5NOLCBDT04gRVhDRVBDScOTTiBERSBMQSBQT05USUZJQ0lBIFVOSVZFUlNJREFEIEpBVkVSSUFOQSwgRUwgKExPUykgQVVUT1IoRVMpIEdBUkFOVElaQShNT1MpIFFVRSBTRSBIQSBDVU1QTElETyBDT04gTE9TIERFUkVDSE9TIFkgT0JMSUdBQ0lPTkVTIFJFUVVFUklET1MgUE9SIEVMIFJFU1BFQ1RJVk8gQ09OVFJBVE8gTyBBQ1VFUkRPLgo= |