Table 2

Comparison of the functional annotation results from different methods for Melanoma
Molecules
Joint Analysis FA (HC) Separate Analysis FA (HC)
mRNA mRNA mRNA mRNA mRNA mRNA
&Prot &Prot +Prot +Prot
Biological terms &miRNA +miRNA
GO:0048066 pigmentation during development X (X) X (X) X (X) X (X) X (X) X (X)
GO:0043473 pigmentation X (X) X (X) X (X) X (X) X (X) X (X)
GO:0030318 melanocyte differentiation X (X) X (X) X (X) X (X) X (X) X (X)
GO:0050931 pigment cell differentiation X (X) X (X) X (X) X (X) X (X) X (X)
GO:0042438 melanin biosynthetic process X (X) X (X) X (X) - (X) - (-) - (-)
GO:0006582 melanin metabolic process - (-) X (X) X (-) - (-) - (-) - (-)
GO:0046148 pigment biosynthetic process - (-) - (X) - (-) - (-) - (-) - (-)
hsa04916:Melanogenesis - (-) X (-) X (-) - (-) - (-) - (-)
BP00193:Developmental processes - (-) X (-) - (-) - (-) X (X) - (-)
GO:0010033 response to organic substance - (-) X (-) - (-) - (-) - (-) - (-)
GO:0019233 sensory perception of pain - (-) X (-) - (-) - (-) - (-) - (-)
GO:0030029 actin filament-based process - (X) - (X) - (-) - (-) - (-) - (-)
GO:0030036 actin cytoskeleton organization - (X) - (X) - (-) - (-) - (-) - (-)
GO:0001501 skeletal system development - (-) - (-) - (-) - (-) X (X) - (-)

Comparison of the annotations done on the joint versus the separate analysis for the FA based method (indicated with FA). The table also contains the comparison with the alternative method hierarchical clustering and SAM (indicated by HC, the results are listed in parentheses in each cell and refer to the application of HC to the joint or separate analysis coherently with the FA annotation in the same cell). &indicate that the annotations are done on the corresponding molecules treated jointly and + indicates that annotation is done downstream of 3 independent analyses.

Liu et al.

Liu et al. BMC Systems Biology 2013 7:14   doi:10.1186/1752-0509-7-14

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