Results: 5

1.
Figure 5

Figure 5. From: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X.

System Analysis using Ingenuity. Ingenuity analysis shows that while known players of stemness (Nanog and Sox-2) are over expressed (red) in nhpESC compared to fibroblast, many other genes are expressed as well indicated by the red tint. Genes denoted by the green tinge are over expressed in fibroblast. For this analysis we compared all genes with a known entrez gene ID.

Ahmi Ben-Yehudah, et al. Stem Cell Res. ;4(1):25.
2.
Figure 3

Figure 3. From: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X.

Chromosome Overabundance of Gene Expression. Genes overexpressed in nhpESC are clustered on rhesus chromosomes 16, 19, 20 and X and under abundant are clustered on rhesus chromosomes 6 and 12. (A) Ratio of overexpressed genes observed divided by the overexpressed genes expected calculated by the ratio of annotations for each gene on the array is shown by the bars. Significance is indicated by the orange graph (-log (p-value)). Only differentially expressed genes with an Entrez gene ID and a chromosome location were analyzed. (B) Ratio of underexpressed calculated as in A.

Ahmi Ben-Yehudah, et al. Stem Cell Res. ;4(1):25.
3.
Figure 2

Figure 2. From: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X.

Differentially Expressed Genes are Detected by Gene Expression Arrays and qPCR. (A) Plotting gene expression levels on the microarray. Black bars denote stem cells, white bars skin fibroblast and gray bars teratoma fibroblast. For each expression level at least 5 samples were used. (B) For verification of array information, we used quantitative-PCR assay. Results denote at least 3 experiments for at least 2 cell lines. Blue- Sox2, Red- Oct4, Yellow- Nanog. Error bars-SD.

Ahmi Ben-Yehudah, et al. Stem Cell Res. ;4(1):25.
4.
Figure 4

Figure 4. From: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X.

Gene Expression Averages of Skin Fibroblast are more closely related to Pluripotent nhpESCs than Genetically Identical Fibroblasts Differentiated within Teratomas. (A) Box plot of average gene expression. Dark solid lines show median expression level off all genes in each group. The interquartile range (IR), or middle 50%, of average gene expression is delimited by a box. Data are expressed on a log base 2 scale. (B) snap shots from a 3-D analysis using BRB ArrayTool shows that nhpESC are different from both types of fibroblast (left), nhpESC are similar to skin fibroblast but different from teratoma fibroblast (middle) and that the 3 groups are slightly different from each other (right). Sex of the cells did not affect results. Red- male nhpESC, green – female nhpESC, pink – male teratoma fibroblast, pink – female teratoma fibroblast, cyan – male skin fibroblast, blue – female skin fibroblast.

Ahmi Ben-Yehudah, et al. Stem Cell Res. ;4(1):25.
5.
Figure 1

Figure 1. From: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X.

Gene Expressed in Pluripotent ESCs Differs Significantly from their Genetically Identical Differentiated Fibroblasts. (A) Experimental design. Gene expression profiles of three different cell types were compared: pluripotent nhpESCs (lines C3106 and C3806), their pedigreed parents and their differentiated progeny in teratomas denoted by the letter T followed by the teratoma number and cell line from which it was derived. Teratoma images are panoramic views at a 4x magnification after H&E staining. (B) Heat map of clustering described in C. 39 samples (6 stem cell samples, 24 teratoma and 9 skin fibroblast) were analyzed for gene expression using Affymetrix Rhesus gene expression chips. We applied agglomerative hierarchical clustering to the gene expression values, using the minimum variance incremental sum of squares method of Ward [80], with dissimilarity measured by one minus the squared Pearson correlation. Yellow = relatively overexpressed, Purple = relatively underexpressed. Color scale is in log ratio to the overall mean of the row. (C) Clustering analysis of 29,000 genes with an Entrez gene ID described in B. The three cell types clustered together with their cellular subtype: pluripotent nhpESCs were significantly different from both types of differentiated fibroblasts. In addition, skin fibroblasts clustered together and separate from the teratoma-derived lines in two distinct nodes.

Ahmi Ben-Yehudah, et al. Stem Cell Res. ;4(1):25.

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk