Table I.

Enrichment study of DEGs between malignant melanoma tissue and normal nevus tissue.

A. Downregulated DEGs
Term and description	Count in gene set	P-value
GO:0030801~Positive regulation of cyclic nucleotide metabolic process	3	3.39×10−5
GO:0005980~Glycogen catabolic process	4	4.72×10−5
GO:0051343~Positive regulation of cyclic-nucleotide phosphodiesterase activity	3	1.12×10−4
GO:0001975~Response to amphetamine	4	1.56×10−4
GO:1901841~Regulation of high voltage-gated calcium channel activity	3	2.35×10−4
GO:1901844~Regulation of cell communication by electrical coupling involved in cardiac conduction	3	3.13×10−4
GO:0007190~Activation of adenylate cyclase activity	4	3.35×10−4
GO:0060316~Positive regulation of ryanodine-sensitive calcium-release channel activity	3	4.01×10−4
GO:0006936~Muscle contraction	5	4.75×10−4
GO:0043647~Inositol phosphate metabolic process	4	5.41×10−4
GO:0021762~Substantia nigra development	4	6.12×10−4
GO:0019233~Sensory perception of pain	4	7.28×10−4
GO:0060315~Negative regulation of ryanodine-sensitive calcium-release channel activity	3	7.31×10−4
GO:0032516~Positive regulation of phosphoprotein phosphatase activity	3	8.62×10−4
GO:0005513~Detection of Ca2+	3	1.00×10−3
GO:0010801~Negative regulation of peptidyl-threonine phosphorylation	3	1.00×10−3
GO:0051412~Response to corticosterone	3	1.67×10−3
GO:0010880~Regulation of release of sequestered Ca2+ into cytosol by sarcoplasmic reticulum	3	1.67×10−3
GO:0010881~Regulation of cardiac muscle contraction by regulation of the release of sequestered Ca2+	3	1.87×10−3
GO:0060314~Regulation of ryanodine-sensitive calcium-release channel activity	3	1.87×10−3
GO:0055117~Regulation of cardiac muscle contraction	3	2.28×10−3
GO:0035307~Positive regulation of protein dephosphorylation	3	2.28×10−3
GO:0031954~Positive regulation of protein autophosphorylation	3	2.28×10−3
GO:0051000~Positive regulation of nitric-oxide synthase activity	3	2.50×10−3
GO:0032465~Regulation of cytokinesis	3	2.50×10−3
GO:0043547~Positive regulation of GTPase activity	8	3.00×10−3
GO:0001822~Kidney development	4	3.11×10−3
GO:0043065~Positive regulation of apoptotic process	6	3.45×10−3
GO:0050999~Regulation of nitric-oxide synthase activity	3	3.49×10−3
GO:0010800~Positive regulation of peptidyl-threonine phosphorylation	3	3.76×10−3
GO:0043388~Positive regulation of DNA binding	3	4.04×10−3
GO:0022400~Regulation of rhodopsin-mediated signaling pathway	3	4.33×10−3
GO:0002027~Regulation of heart rate	3	5.59×10−3
GO:0071902~Positive regulation of protein serine/threonine kinase activity	3	6.27×10−3
GO:0007223~Wnt signaling pathway, calcium-modulating pathway	3	7.74×10−3
GO:0045893~Positive regulation of transcription, DNA-templated	7	7.81×10−3
GO:0034704~Calcium channel complex	3	2.75×10−3
GO:0030017~Sarcomere	3	6.61×10−3
GO:0005876~Spindle microtubule	3	8.36×10−3
GO:0043274~Phospholipase binding	4	2.72×10−5
GO:0031997~N-terminal myristoylation domain binding	3	3.24×10−5
GO:0072542~Protein phosphatase activator activity	3	1.61×10−4
GO:0030235~Nitric-oxide synthase regulator activity	3	2.99×10−4
GO:0008440~Inositol-1,4,5-trisphosphate 3-kinase activity	3	4.78×10−4
GO:0031996~Thioesterase binding	3	9.59×10−4
GO:0031432~Titin binding	3	9.59×10−4
GO:0043539~Protein serine/threonine kinase activator activity	3	1.60×10−3
GO:0015276~Ligand-gated ion channel activity	3	6.33×10−3
GO:0001105~RNA polymerase II transcription coactivator activity	3	6.68×10−3
GO:0019901~Protein kinase binding	6	8.04×10−3
hsa05010:Alzheimer's disease	6	9.66×10−4
hsa04915:Estrogen signaling pathway	5	1.07×10−3
hsa04922:Glucagon signaling pathway	5	1.07×10−3
hsa04916:Melanogenesis	5	1.11×10−3
hsa04020:Calcium signaling pathway	6	1.28×10−3
hsa04728:Dopaminergic synapse	5	2.75×10−3
hsa05214:Glioma	4	3.29×10−3
hsa05031:Amphetamine addiction	4	3.43×10−3
hsa04720:Long-term potentiation	4	3.43×10−3
hsa04744:Phototransduction	3	6.84×10−3
B, Upregulated DEGs
Term and description	Count in gene set	P-value
GO:0007155~Cell adhesion	13	1.02 ×10−4
GO:0007010~Cytoskeleton organization	7	1.01×10−3
GO:0001501~Skeletal system development	6	2.92×10−3
GO:0045944~Positive regulation of transcription from RNA polymerase II promoter	16	3.94×10−3
GO:0008584~Male gonad development	5	4.48×10−3
GO:0002576~Platelet degranulation	5	6.18×10−3
GO:0042475~Odontogenesis of dentin-containing teeth	4	6.96×10−3
GO:0090190~Positive regulation of branching involved in ureteric bud morphogenesis	3	7.87×10−3
GO:0050679~Positive regulation of epithelial cell proliferation	4	8.85×10−3
GO:0016020~Membrane	29	8.21×10−4
GO:0005886~Plasma membrane	45	8.97×10−4
GO:0005856~Cytoskeleton	10	1.05×10−3
GO:0031012~Extracellular matrix	8	4.34×10−3
GO:0005925~Focal adhesion	9	5.57×10−3
GO:0031093~Platelet α granule lumen	4	6.37×10−3
GO:0005576~Extracellular region	21	6.61×10−3
GO:0005913~Cell-cell adhesion junction	8	6.92×10−3
GO:0043034~Costamere	3	7.39×10−3
GO:0005887~Integral component of plasma membrane	19	7.89×10−3
GO:0003779~Actin binding	11	2.55×10−5
GO:0005200~Structural constituent of cytoskeleton	5	7.42×10−3
GO:0050839~Cell adhesion molecule binding	4	9.33×10−3
hsa04510:Focal adhesion	9	9.83×10−4
hsa04512:ECM-receptor interaction	6	1.72×10−3
hsa04151:PI3K-Akt signaling pathway	11	2.13×10−3
hsa05205:Proteoglycans in cancer	8	3.71×10−3
hsa05200:Pathways in cancer	11	5.44×10−3
hsa05206:MicroRNAs in cancer	9	7.47×10−3

GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes; MM, malignant melanoma.