Am J Cancer Res 2011;1(1):85-97
Original Article
Expression profiling and pathway analysis of Krüppel-Like Factor 4 in mouse
embryonic fibroblasts
Engda G. Hagos, Amr M. Ghaleb, Amrita Kumar, Andrew S. Neish, Vincent W. Yang
Division of Digestive Diseases, Department of Medicine, Department of Pathology, and Department of Hematology and
Oncology, Emory University School of Medicine, Atlanta, Georgia
Received October 12, 2010; accepted October 19, 2010; Epub October 21, 2010; Published January 1, 2011
Abstract: Background: Krüppel-like factor 4 (KLF4) is a zinc-finger transcription factor with diverse regulatory functions in
proliferation, differentiation, and development. KLF4 also plays a role in inflammation, tumorigenesis, and reprogramming of
somatic cells to induced pluripotent stem (iPS) cells. To gain insight into the mechanisms by which KLF4 regulates these
processes, we conducted DNA microarray analyses to identify differentially expressed genes in mouse embryonic fibroblasts
(MEFs) wild type and null for Klf4. Methods: Expression profiles of fibroblasts isolated from mouse embryos wild type or null for
the Klf4 alleles were examined by DNA microarrays. Differentially expressed genes were subjected to the Database for
Annotation, Visualization and Integrated Discovery (DAVID). The microarray data were also interrogated with the Ingenuity
Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) for pathway identification. Results obtained from the
microarray analysis were confirmed by Western blotting for select genes with biological relevance to determine the correlation
between mRNA and protein levels. Results: One hundred and sixty three up-regulated and 88 down-regulated genes were
identified that demonstrated a fold-change of at least 1.5 and a P-value < 0.05 in Klf4-null MEFs compared to wild type MEFs.
Many of the up-regulated genes in Klf4-null MEFs encode proto-oncogenes, growth factors, extracellular matrix, and cell cycle
activators. In contrast, genes encoding tumor suppressors and those involved in JAK-STAT signaling pathways are down-
regulated in Klf4-null MEFs. IPA and GSEA also identified various pathways that are regulated by KLF4. Lastly, Western blotting of
select target genes confirmed the changes revealed by microarray data. Conclusions: These data are not only consistent with
previous functional studies of KLF4’s role in tumor suppression and somatic cell reprogramming, but also revealed novel target
genes that mediate KLF4’s functions (AJCR0000006).
Keywords: KLF4; Microarray; MEF; DAVID; GSEA; IPA; SAM; FDR
Full Text PDF
Address all correspondence to:
Vincent W. Yang, MD, PhD
Division of Digestive Diseases
Department of Medicine, Emory University
201 Whitehead Research Building
615 Michael Street
Atlanta, GA 30322, USA.
Tel: (404) 727-5638; FAX: (404) 727-5767
E-mail: vyang@emory.edu
Original Article
Expression profiling and pathway analysis of Krüppel-Like Factor 4 in mouse
embryonic fibroblasts
Engda G. Hagos, Amr M. Ghaleb, Amrita Kumar, Andrew S. Neish, Vincent W. Yang
Division of Digestive Diseases, Department of Medicine, Department of Pathology, and Department of Hematology and
Oncology, Emory University School of Medicine, Atlanta, Georgia
Received October 12, 2010; accepted October 19, 2010; Epub October 21, 2010; Published January 1, 2011
Abstract: Background: Krüppel-like factor 4 (KLF4) is a zinc-finger transcription factor with diverse regulatory functions in
proliferation, differentiation, and development. KLF4 also plays a role in inflammation, tumorigenesis, and reprogramming of
somatic cells to induced pluripotent stem (iPS) cells. To gain insight into the mechanisms by which KLF4 regulates these
processes, we conducted DNA microarray analyses to identify differentially expressed genes in mouse embryonic fibroblasts
(MEFs) wild type and null for Klf4. Methods: Expression profiles of fibroblasts isolated from mouse embryos wild type or null for
the Klf4 alleles were examined by DNA microarrays. Differentially expressed genes were subjected to the Database for
Annotation, Visualization and Integrated Discovery (DAVID). The microarray data were also interrogated with the Ingenuity
Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) for pathway identification. Results obtained from the
microarray analysis were confirmed by Western blotting for select genes with biological relevance to determine the correlation
between mRNA and protein levels. Results: One hundred and sixty three up-regulated and 88 down-regulated genes were
identified that demonstrated a fold-change of at least 1.5 and a P-value < 0.05 in Klf4-null MEFs compared to wild type MEFs.
Many of the up-regulated genes in Klf4-null MEFs encode proto-oncogenes, growth factors, extracellular matrix, and cell cycle
activators. In contrast, genes encoding tumor suppressors and those involved in JAK-STAT signaling pathways are down-
regulated in Klf4-null MEFs. IPA and GSEA also identified various pathways that are regulated by KLF4. Lastly, Western blotting of
select target genes confirmed the changes revealed by microarray data. Conclusions: These data are not only consistent with
previous functional studies of KLF4’s role in tumor suppression and somatic cell reprogramming, but also revealed novel target
genes that mediate KLF4’s functions (AJCR0000006).
Keywords: KLF4; Microarray; MEF; DAVID; GSEA; IPA; SAM; FDR
Full Text PDF
Address all correspondence to:
Vincent W. Yang, MD, PhD
Division of Digestive Diseases
Department of Medicine, Emory University
201 Whitehead Research Building
615 Michael Street
Atlanta, GA 30322, USA.
Tel: (404) 727-5638; FAX: (404) 727-5767
E-mail: vyang@emory.edu
| AJCR Copyright © 2010-present, All rights reserved. Published by e-Century Publishing Corporation, Madison, WI 53711, USA |
 | |  | |  | |  | |  | |  | |  | |  |
American Journal of Cancer Research
| ISSN: 2156-6976 |