WGCNA: Identify DCGs (Differential Coexpressed Genes) based on the...

In DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

Description

A method to pick out DCGs from microarray data based on 'Weighted Gene Coexpression Network Analysis' (WGCNA) (Mason, MJ. Et al. 2009; van Nas et al. 2009 ).

Usage

WGCNA(exprs.1, exprs.2, power = 12, variant = "WGCNA")

Arguments

exprs.1	a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.
exprs.2	a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.
power	the thresholding parameter, an integer >1.
variant	if the variant is 'WGCNA' the original version is evoked; if it is 'DCp', the length-normalized Euclidean distance is adopted to replace the connectivity difference measure.

Details

The 'weighted gene coexpression network analysis' (WGCNA) weights links with correlation coefficients and compares the sums of the correlation coefficients of a gene (Mason, et al., 2009; van Nas, et al., 2009). Correlation coefficients are firstly softly thresholded by a 'power'.

Value

WGCNA

score of 'WGCNA' to identify DCGs

Author(s)

Bao-Hong Liu, Hui Yu

References

Mason, M.J., et al. (2009) Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells, BMC Genomics, 10, 327.

van Nas, A., Guhathakurta, D., Wang, S.S., Yehya, N., Horvath, S., Zhang, B., Ingram-Drake, L., Chaudhuri, G., Schadt, E.E., Drake, T.A., Arnold, A.P. and Lusis, A.J. (2009) Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks, Endocrinology, 150, 1235-1249.

Examples

data(exprs)
WGCNA(exprs[1:100,1:16],exprs[1:100,17:63],power=12,variant='WGCNA')

Example output

       AACS       FSTL1       ELMO2     CREB3L1       RPS11       PNMA1 
0.032491573 0.340345290 0.003607475 0.106060297 0.487543899 0.688860893 
       MMP2      SAMD4A     SMARCD3       A4GNT      PKNOX2       RALYL 
0.055532587 0.306929359 0.143748972 0.421625128 0.296036651 0.164518603 
       ZHX3       ERCC5       GPR98       RXFP3       APBB2       BBOX1 
0.083832350 0.112679144 0.073334981 0.066650504 0.008716904 0.024313279 
    PRO0478         XDH        EDN1       MTERF         AEN        CLK4 
0.399647460 0.356304624 0.008536358 0.020476887 0.172706050 0.064379101 
      KCNG1       CXCR4       DECR1       SALL1       PTPRR       CADM4 
0.029348125 0.037726173 0.142339497 0.192265472 0.017252518 0.253869309 
      IRAK1       CFHR5      TMSB10       CXCL3       LMAN1        CHD8 
0.310181364 0.129817868 0.435033351 0.072471863 0.327807434 0.786545837 
      SUMO1       GP1BA      OR7A10        DDB1     CHRNA10       STYK1 
0.535912883 0.076253872 0.057791157 0.047250211 0.266437916 0.025677555 
      MYO9B        CCNI        MMP7       EP300      CRNKL1     C9orf45 
0.240185468 0.040275941 0.068641074 0.453033899 0.455865429 0.077939731 
       XAB2        RTN1        HIC2       TBX10       CENPQ         UTY 
0.700706213 0.083996659 0.075069922 0.013703652 0.144338051 0.025968217 
      OR2W1       KCNA6      ATP5G2        ZEB1         ERG        FAT4 
0.221261970 0.010344958 0.044776060 0.317287703 0.260191021 0.276681666 
       PARN        SOD2       CYTH1      ADAM5P        CHD9       STK16 
0.685927044 0.137672950 0.037275193 0.233734384 0.178130469 0.144813112 
      PDE1C      SEMA4D      AGPAT1        TOB2       BANK1      MAP3K3 
0.174172649 0.150983942 0.524095428 0.320666481 0.070302341 0.206953214 
        MAX        GRM2      OSBPL8       PROSC       NR4A2        RICS 
0.064727567 0.142152824 0.619112319 0.011615626 0.130812813 0.030023983 
        PIR        PPCS        IPO9       LONP1         EVC      CXCL13 
0.068985938 0.545802591 0.600311463 0.148346756 0.031150027 0.746594291 
      FFAR3       SCYL3    KIAA1199       SORL1       NAT10        CHD1 
0.287071471 0.009680740 0.001102983 0.194798923 0.461902193 0.375919224 
       SYN3        DMC1     SLC22A2    SERPINF1    C20orf27      OR7A17 
0.170271991 0.146553939 0.006574458 0.065901303 0.095633301 0.289318753 
    RPS6KA5        HMX1      DHRS11         LHB 
0.537222145 0.225287530 0.204918591 0.186244528 

DCGL documentation built on May 1, 2019, 8:38 p.m.