Journal: BMC Genomics

Article Title: The stable traits of melanoma genetics: an alternate approach to target discovery

doi: 10.1186/1471-2164-13-156

Figure Lengend Snippet: PCA analysis based on the complete transciptional data set visualizing the tridimentsional distribution of cell lines (CM, pink) compared to pair melanoma tumors (TM, yellow) (A) of the distribution of the samples according to the patient identity from which either TMs or CMs were derived (B) . (C) Venn diagram displaying the results of a Pearson's correlation analysis of gene expression between TMs and CMs (p-value cutoff < 0.05). (D) Self-organizing hierarchical tree based on the top 1,006 genes whose expression was most significantly (p-value < 0.01) correlated between TMs light green) and CMs (light pink); sample ID refers to the patients from which either a TM or CM was derived. Brackets underline autologous TM/CM pairs demonstrating a comparable expression pattern. (E) Top functional network generated by Ingenuity Pathway Analysis (IPA) www.ingenuity.com based on the 3,030 target genes. (F) Bar graph demonstrating the top biological functions of the 3,030 target genes according to IPA.

Article Snippet: Pearson correlation between chromosomal copy number data and gene expression data was performed within Partek software using the "Biologic Integration/Correlating Gene Expression and Copy Number" function.

Techniques: Derivative Assay, Gene Expression, Expressing, Functional Assay, Generated

Journal: BMC Genomics

Article Title: The stable traits of melanoma genetics: an alternate approach to target discovery

doi: 10.1186/1471-2164-13-156

Figure Lengend Snippet: (A) (Left panel) percent of transcripts whose expression correlates with its respective copy number in different sets of genes ranked in .1 decrements of correlation (y value) in expression between CMs and TMs; significant correlation between RNA expression and DNA copy number set at a Pearson's correlation cutoff p-value of < 0.05 . The number of genes included in each gene set is shown in the right panel. (B) Venn diagram displaying the number of transcripts among the complete genome whose expression is consistent between CMs and TMs and correlates with copy number. (C) Bar graph demonstrating the top biological functions of the 968 target genes analyzed with Ingenuity Pathway Analysis www.ingenuity.com . (D) Top: Chromosomal view of the location of the 968 target genes mapped to their location within the genome. Copy number states are shown per sample for amplifications (red), deletions (blue), and unchanged regions (green); Bottom: Histogram depicting the number of the 968 target genes per chromosome. (E) - Self organizing clustering of CMs and TMs based on the 968 delegate transcripts. Sample ID refers to the patients from whom either CMs or TMs were derived. A, B and C refer to TARA's classification as discussed in the text.

Article Snippet: Pearson correlation between chromosomal copy number data and gene expression data was performed within Partek software using the "Biologic Integration/Correlating Gene Expression and Copy Number" function.

Techniques: Expressing, RNA Expression, Derivative Assay