In silico analysis of gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity.

y otros autores.

doi:10.1186/1476-4598-7-22

In silico analysis of gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity.

Título traducido de la contribución: Análisis in silico del carcinoma gástrico El análisis seriado de bibliotecas de expresión genética revela diferentes perfiles asociados con la etnicidad.

y otros autores.

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22 Citas (Scopus)

Resumen

El carcinoma gástrico a nivel mundial presenta marcadas variaciones geográficas y peores resultados en pacientes de Occidente en comparación con Oriente. Aunque estas diferencias se han explicado por mejores criterios diagnósticos, métodos de estadificación mejorados y cirugía más radical, la evidencia emergente apoya el concepto de que las diferencias en la expresión génica asociadas a la etnicidad podrían contribuir a este resultado dispar. Aquí, recopilamos conjuntos de datos de 4 bibliotecas de análisis de expresión génica seriada (SAGE) de carcinoma gástrico normal y 11 de dos etnias diferentes. Todas las bibliotecas de SAGE normales, así como 7 bibliotecas de tumores, eran de Occidente y 4 bibliotecas de tumores eran de Oriente. Comparamos estos conjuntos de datos mediante análisis de correspondencia y análisis de árbol de soporte, y las diferencias específicas en la expresión de etiquetas se identificaron mediante análisis de significancia para microarray. Las asignaciones de etiquetas a genes se realizaron mediante CGAP-SAGE Genie o TAGmapper. El análisis del transcriptoma global muestra una clara separación entre las bibliotecas normales y tumorales con 90 etiquetas expresadas de forma diferencial. También se encontró una clara separación entre las bibliotecas de tumores de Occidente y Oriente con 54 etiquetas expresadas de forma diferencial. Las etiquetas para la asignación de genes identificaron 15 genes, 5 de ellos con una expresión significativamente mayor en las bibliotecas occidentales que en las orientales. La qRT-PCR en líneas celulares de origen occidental y oriental confirmó estas diferencias. Curiosamente, dos de estos genes se han asociado con la agresividad (COL1A1 y KLK10). En conclusión, encontramos que el análisis in silico de bibliotecas SAGE de dos etnias diferentes revela diferencias en el perfil de expresión génica. Estas diferencias de expresión podrían explicar los resultados dispares entre Occidente y Oriente.

Título traducido de la contribución	Análisis in silico del carcinoma gástrico El análisis seriado de bibliotecas de expresión genética revela diferentes perfiles asociados con la etnicidad.
Idioma original	Inglés
Número de artículo	22
Publicación	Molecular Cancer
Volumen	7
N.º	22
DOI	https://doi.org/10.1186/1476-4598-7-22
Estado	Publicada - 27 feb. 2008
Publicado de forma externa	Sí

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title = "In silico analysis of gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity.",

abstract = "Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East.",

author = "Ossandon, \{Francisco J.\} and Francisco Aguayo and Corval{\'a}n, \{Alejandro H.\} and \{and other authors.\}",

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AU - Ossandon, Francisco J.

AU - Aguayo, Francisco

AU - Corvalán, Alejandro H.

AU - and other authors.

PY - 2008/2/27

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N2 - Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East.

AB - Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East.

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In silico analysis of gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity.

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