gcrma algorithm using robust multi-array average (rma) with gc-content background correction Search Results


genespring v7 2  (Silicon Genetics Inc)
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Silicon Genetics Inc genespring v7 2
Clustered image maps (heat maps) illustrating all genes (A) and the top thirty genes (B) differentially expressed between prenatal saline- and arsenate-exposed cranial neural crest cells (CNCCs). Each row of the clustered image map represents a gene, and each column represents one array for treatment type examined [saline (S) or arsenate (A)]. The color saturation represents the level of gene expression. The three columns marked ‘S’ represent clusters of genes from the three independent sets of CNCCs prenatally-exposed to saline (control), that exhibit increased (red) and decreased (blue) expression. The three columns marked ‘A’ represent clusters of the same genes from the three independent sets of CNCCs prenatally-exposed to arsenate. Clustered are those genes that were either up regulated (red) or down regulated (blue) in arsenate-exposed CNCCs when compared to their relative expression in saline exposed CNCCs. <t>GeneSpring</t> GX software (v 11.0, Agilent Technologies) was used for hierarchical clustering analysis to create a condition tree representing all of the differentially expressed genes based on their expression profiles. Genes demonstrating a 1.5-fold or greater difference (p <0.05) in expression are included in the map.
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Clustered image maps (heat maps) illustrating all genes (A) and the top thirty genes (B) differentially expressed between prenatal saline- and arsenate-exposed cranial neural crest cells (CNCCs). Each row of the clustered image map represents a gene, and each column represents one array for treatment type examined [saline (S) or arsenate (A)]. The color saturation represents the level of gene expression. The three columns marked ‘S’ represent clusters of genes from the three independent sets of CNCCs prenatally-exposed to saline (control), that exhibit increased (red) and decreased (blue) expression. The three columns marked ‘A’ represent clusters of the same genes from the three independent sets of CNCCs prenatally-exposed to arsenate. Clustered are those genes that were either up regulated (red) or down regulated (blue) in arsenate-exposed CNCCs when compared to their relative expression in saline exposed CNCCs. GeneSpring GX software (v 11.0, Agilent Technologies) was used for hierarchical clustering analysis to create a condition tree representing all of the differentially expressed genes based on their expression profiles. Genes demonstrating a 1.5-fold or greater difference (p <0.05) in expression are included in the map.

Journal: Reproductive toxicology (Elmsford, N.Y.)

Article Title: Impact of Prenatal Arsenate Exposure on Gene Expression in a Pure Population of Migratory Cranial Neural Crest Cells

doi: 10.1016/j.reprotox.2019.04.001

Figure Lengend Snippet: Clustered image maps (heat maps) illustrating all genes (A) and the top thirty genes (B) differentially expressed between prenatal saline- and arsenate-exposed cranial neural crest cells (CNCCs). Each row of the clustered image map represents a gene, and each column represents one array for treatment type examined [saline (S) or arsenate (A)]. The color saturation represents the level of gene expression. The three columns marked ‘S’ represent clusters of genes from the three independent sets of CNCCs prenatally-exposed to saline (control), that exhibit increased (red) and decreased (blue) expression. The three columns marked ‘A’ represent clusters of the same genes from the three independent sets of CNCCs prenatally-exposed to arsenate. Clustered are those genes that were either up regulated (red) or down regulated (blue) in arsenate-exposed CNCCs when compared to their relative expression in saline exposed CNCCs. GeneSpring GX software (v 11.0, Agilent Technologies) was used for hierarchical clustering analysis to create a condition tree representing all of the differentially expressed genes based on their expression profiles. Genes demonstrating a 1.5-fold or greater difference (p <0.05) in expression are included in the map.

Article Snippet: Scanning of GeneChip ® arrays, subsequent image processing using Affymetrix GCOS v1.2 software, Robust Multi-chip Average, with GC-content background correction (GC-RMA) pre-processing, and ‘per gene normalization’ with GeneSpring v7.2 (Silicon Genetics, Inc., Redwood City, CA) were performed as described earlier [ 29 ].

Techniques: Expressing, Software