Research Article

Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes

Table 1

Top 10 hub genes ordered by the degree of connectivity.

Gene identifierDegree of connectivityGene moduleGene nameDescription

AT1G271203327TurquoiseAT1G27120 (GALT4)Galactosyltransferase family protein
AT5G528202853BlueNOTCHLESS (NLE)WD-40 repeat family protein/notchless protein
AT5G560902348BrownCYTOCHROME C OXIDASE 15 (COX15)Encodes a homolog of COX15
AT2G431002134YellowISOPROPYLMALATE ISOMERASE 2 (IPMI2)Isopropylmalate isomerase 2
AT1G710101958GreenFORMS APLOID AND BINUCLEATE CELLS 1C (FAB1C)Encodes a protein that is predicted to act as a phosphatidylinositol-3P 5-kinase but lacks a FYVE domain
AT2G29890806RedVILLIN 1 (VLN1)Encodes a ubiquitously expressed villin-like protein
AT2G45600569BlackAT2G45600Alpha/beta-hydrolases superfamily protein
AT1G72400321MagentaAT1G72400Hypothetical protein
AT3G53980311PinkAT3G53980Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
AT5G65350243PurpleHISTONE 3 11 (HTR11)Histone 3 11
AT5G27560182Green-yellowAT5G27560DUF1995 domain protein, putative (DUF1995)
AT5G54855170TanAT5G54855Pollen Ole e 1 allergen and extensin family protein
AT1G75630156SalmonVACUOLAR H+-PUMPING ATPASE 16 KDA PROTEOLIPID SUBUNIT 4 (AVA-P4)Vacuolar H+-pumping ATPase 16 kD proteolipid (ava-p) mRNA
AT1G74450107CyanAT1G74450BPS1-like protein (DUF793)
AT2G23940107Midnight-blueAT2G23940Transmembrane protein (DUF788)
AT1G3046082Light-cyanCLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 30 (CPSF30)Encodes AtCPSF30, the 30-KDa subunit of cleavage and polyadenylation specificity factor
AT1G0604074Grey60SALT TOLERANCE (STO)B-box zinc finger family protein that encodes a salt tolerance protein
AT2G1156058Light-greenAT2G11560Mutator-like transposase/similar to MURA transposase of maize
AT3G5505050Dark-greenD-CLADE TYPE 2C PROTEIN PHOSPHATASE 4 (PP2C.D4)Protein phosphatase 2C family protein
ATCG0107048Dark-redNAD(P)H-QUINONE OXIDOREDUCTASE SUBUNIT 4L (NDHE)NADH dehydrogenase ND4L
AT3G2595048Royal-blueAT3G25950TRAM, LAG1, and CLN8 (TLC) lipid-sensing domain containing protein
AT1G6541039Dark-turquoiseATP-BINDING CASSETTE I13 (ABCI13)Encodes a member of NAP subfamily of transporters
AT5G0231038Light-yellowPROTEOLYSIS 6 (PRT6)Encodes a component of the N-end rule pathway that targets protein degradation
AT3G6113037Dark-greyGALACTURONOSYLTRANSFERASE 1 (GAUT1)Encodes a protein with putative galacturonosyltransferase activity
AT3G5335034Dark-orangeROP INTERACTIVE PARTNER 3 (RIP3)Encodes a microtubule-binding protein
AT5G4349034OrangeAT5G43490Myb-like protein X