u133 plus 2.0 microarray probe sets  (Thermo Fisher)

Journal: PLoS ONE

Article Title: Cell Cycle Gene Networks Are Associated with Melanoma Prognosis

doi: 10.1371/journal.pone.0034247

Figure Lengend Snippet: Gene signatures from multiple microarray studies of melanomas from patients.

Article Snippet: These analyses suggested that Affymetrix Human Genome U133 plus 2.0 microarray probe set pairs that were highly correlated in data from A375 cells were in general not highly correlated in data using the same microarray platform from MCF-7 cells and vice versa , suggesting that cross-hybridisation between Affymetrix probe sets was not the most significant driver of the clustering we observed across the A375 dataset.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Cell Cycle Gene Networks Are Associated with Melanoma Prognosis

doi: 10.1371/journal.pone.0034247

Figure Lengend Snippet: All possible gene-gene correlations within gene sets defined by TRANSFAC and GO were calculated. The proportion of the gene pairs within each gene set that had Spearman's |ρ|≥0.5 was calculated separately for A375 siRNA microarray data (blue bars), a composite Affymetrix dataset from three primary melanoma studies (red bars), and a composite Affymetrix dataset from four metastatic melanoma studies (green bars). The x-axis represents TRANSFAC or GO gene sets. The y-axis represents the proportion of gene pairs from each gene set that had Spearman's |ρ|≥0.5 for the A375 data, primary tumour data, and metastatic tumour data, respectively.

Article Snippet: These analyses suggested that Affymetrix Human Genome U133 plus 2.0 microarray probe set pairs that were highly correlated in data from A375 cells were in general not highly correlated in data using the same microarray platform from MCF-7 cells and vice versa , suggesting that cross-hybridisation between Affymetrix probe sets was not the most significant driver of the clustering we observed across the A375 dataset.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Cell Cycle Gene Networks Are Associated with Melanoma Prognosis

doi: 10.1371/journal.pone.0034247

Figure Lengend Snippet: The x-axes represent GO annotations. GO annotations with related functions are coloured and grouped together: red (cell cycle related); sky blue (DNA repair related); green (RNA related); purple (transcription related); dark blue (metabolism related); yellow (protein related) and grey (miscellaneous). The left-most box (white) in each panel represents all RNAs on the microarray. The y-axes represents minus log base2 p value, based on a Cox proportional hazards model, to indicate the strength of association between RNA abundance and patient survival. The horizontal line (y = 4.32) represents a threshold for a significant association with survival (equivalent to p = 0.05, above this line is a significant association). Within each box the dark horizontal line represents the median, the coloured area of the box the interquartile range. Panels A and B include all RNAs on the microarrays that have the specified GO annotations. Panels C and D include the Bayesian network hub RNAs, for which the function of downstream gene network children is significantly enriched for the specified GO annotations. Panels A and C represent primary tumours while panels B and D represent metastatic tumours .

Article Snippet: These analyses suggested that Affymetrix Human Genome U133 plus 2.0 microarray probe set pairs that were highly correlated in data from A375 cells were in general not highly correlated in data using the same microarray platform from MCF-7 cells and vice versa , suggesting that cross-hybridisation between Affymetrix probe sets was not the most significant driver of the clustering we observed across the A375 dataset.

Techniques: Microarray