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1.
Figure 6

Figure 6. Classification of genes by specific molecular and biological function.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

(A) Biological processes up-regulated in ESCs, IPSCs, and ECCs compared to PGCs. (B) Biological processes up-regulated in EGCs compared to PGCs. The allocation of specific biological functions in pluripotent stem cells and EGCs are represented by percentages in the table legend.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
2.
Figure 1

Figure 1. Phase contrast images representing different stem cells studied in gene expression analyses.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

(A) primordial germ cells (PGCs), (B) embryonic germ cells (EGCs), (C) induced pluripotent stem cells (IPSCs), (D) embryonic stem cells (ESCs), and (E) embryonal carcinoma cells (ECCs).

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
3.
Figure 7

Figure 7. Graphical representation of biological relationships in genes responsible for human embryonic stem cell pluripotency detected by IPA analysis.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

Green color represents genes of the pathway that are up-regulated in the pluripotent stem cells compared to PGCs and gray color represents genes that are expressed at similar levels between both groups. White signifies genes whose expression was not detected in the cell lines.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
4.
Figure 5

Figure 5. Hierarchical clustering of potential signature genes.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

Gene expression levels of (A) PGC signature, (B) EGC and common PGC/EGC signature and (C) ESC, IPSC and ECC group genes are represented in a heat map. Lists of genes corresponding to each group are on the right hand side of the cluster tree. Order of the genes in the tables corresponds to their order in the heat map (high expression in red, log10 = >1.00; low expression in green; log10 = <–1.00).

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
5.
Figure 4

Figure 4. Identification of potential signature genes of PGCs, ECCs, EGCs, IPSCs, and ESCs.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

The vertical axis of each graph shows the log ratio of the expression data relative to the population mean. (A) Genes that are up-regulated in PGCs include (A) SPO11, DMRT1, TEX13, and HBA1. (B) Genes up-regulated in ECCs include SALL4, GDF3, MYCN, and PIWIL2. (C) Genes up-regulated in EGCs include FN1, FKBP6, AXL, and SOX9. (D) Genes up-regulated in IPSCs include MAD2L1, PIK3R3, BAX and APC. (E) Genes up-regulated in ESCs include DAZL, CCNG1, JARID2, and ZSCAN1.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
6.
Figure 2

Figure 2. Real-time qRT-PCR analysis of several key pluripotent and germ cell associated genes in primordial germ cells and pluripotent stem cells.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

OCT4, SOX2, NANOG, and DNMT3B were normalized to the beta-actin gene using the comparative CT method, and plotted relative to the human foreskin fibroblast line, HFF1 (0 baseline) (N  = 3 biological samples with technical triplicates for each cell type, P<0.05). Asterisks denote statistical significant differences in cell lines compared to PGCs.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
7.
Figure 8

Figure 8. Graphical representation of biological relationships in known or suspected genes associated with controlling cell cycle, replication, DNA repair, recombination, and cell death.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

This network is specifically showing genes that are up-regulated in pluripotent stem cells compared to PGCs. Green color represents genes in this network that are highly up-regulated in the ESC, IPSC, and ECC group and gray color represents genes that are expressed in similar levels across all cell types. White signifies that the gene was not detected in the cell lines. Solid and dotted arrows represent direct and indirect interactions, respectively. Elevated levels of KRAS and HSPD1 were also detected in EGCs.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.
8.
Figure 3

Figure 3. Principal component analysis (PCA) of the expression profiles of primordial germ cells and pluripotent stem cells.. From: Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.

(A) Two-dimensional PCA map of cell types, comparing PC1 and PC3. (B) Three-dimensional map comparing all cell types. (C) A loading scatter plot for the identification of signature genes. Red dots represent the top 1000 differentially genes expressed across the mean of all lines with FDR adjusted P<0.0001. “PGC signature” genes include HBA1, TEX13, and SPO11 located on the lower left half of the scatter plot. In contrast, XIST was upregulated in PGCs compared to other pluripotent stem cell lines as expected given their differentiated state. “PGC/EGC common” genes include H19, BGN, ITGA8, IGFB5, MOV10L1, and TGF-B1. “EGC signature” genes include SOX9, KLF4, FN1, AXL, and FKBP6. “ECC, ESC, and IPSC” signature genes include DPPA4, NANOG, SOX2, PIWIL2, MYCN, GDF3, and OCT4.

Nikta Pashai, et al. PLoS One. 2012;7(6):e39088.

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