Skip to main content

Table 1 Modules of co-expressed genes and their intramodular hubs

From: Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis

Module

Number of genes

Module-trait relationships (p < 0.1 and correlation > ± 0.5)

Intramodular hubs (top 10 Kwithin values)

Turquoise

944

EMT and metastasis

Slit3, Lrfn3, Gm29100, Ankfn1, Cxcl14, H2-DMb1, Unc5c, Loxl1, Nid2, Prrx2

Blue

721

Tumor, progression, and metastasis

Sec13, Cmas, Kmt2a, Sco1, Manf, Mrpl55, Golt1b, Thoc3, Cdc34, Cox10

Yellow

509

EMT and metastasis

Prelid1, Snx3, Ppip5k1, Kremen1, Ttyh2, Pla2g12a, Ost4, Kat8, Snd1, Mvb12b

Red

295

Tumor, progression, and EMT

Abhd10, Lrch3, Robo1, Ubl4a, Prim2, Hmces, 4933423P22Rik, Slc2a4, Dlg1, Pdzd11

Black

293

Progression and metastasis

Prex1, Map2k4, Eepd1, Psma3, Fam131c, Cc2d1b, Prkx, Mbtps1, Tpk1, Neto2

Magenta

149

EMT and metastasis

Dnajc8, Cars2, Pank4, Edem1, Sap30, Mutyh, Usp28, Adi1, Zbtb16, Gbe1

Purple

130

Tumor

Gpat4, Pithd1, Pex14, A430005L14Rik, Dgat2, Mtfr1l, Psmb2, Rps6, Brf2, Coprs

Green yellow

122

EMT and metastasis

Gyg, Hgsnat, Rnf41, Psen2, Mapkapk3, BC031181, Vat1, Gab2, Traf4, Supt16

Tan

119

EMT

Kif4, Sra1, Tmem38a, Aco2, Coq10b, Klhl15, Mapre1, Mark4, 1500011B03Rik, Mttp

Salmon

118

EMT

Pcdhb18, Scube3, Pkib, Mid2, Gpa33, Bicd1, Gfra1, Col9a1, Ssc5d, Ctnnal1

Midnight blue

109

EMT and metastasis

Trabd2b, Ccdc88c, Mdm1, Bace2, M6pr, Pla2g7, Ube2t, Cdh5, Agl, Flt1

Light cyan

85

Progression and metastasis

N4bp1, Mks1, Irak1bp1, Wdr41, Keap1, Tgfbrap1, Extl2, Commd3, Osbpl9, Gba2

Pink

178

Progression

Arhgap12, Mad2l1bp, Nfkbil1, Zfp397, Plpp1, Mgat1, Bag3, Zfp653, Surf4, Cog1

Brown

519

No relationship

Yme1l1, Psmc6, Ranbp2, Nol8, Fam208b, Ap4e1, Prpf4b, Uba6, Ckap5, Bod1l

  1. Hubs were defined as the top 10 ranked genes in each module based on Kwithin values. Module-trait relationships were considered to be significant if the p value < 0.1 and the correlation ≥ 0.5