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Table 6 Assessment of the accuracy in identifying differentially expressed genes in interface regions of C. japonica - G. max association

From: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

C.japonica read

Cj_Gmif_reads1

Cj_Gmif_reads2

G. max read

Gm_Cjif_reads1

Gm_Cjif_reads2

C. japonica contig

Cj_contigs_cg1

Cj_contigs_cg2

G. max contig

Gmax_275_Wm82.a2.v1.transcript

Gmax_275_Wm82.a2.v1.transcript

Mapping procedure

Separatelya

Mergedb

Separatelya

Mergedb

Differentially expressed genesc in C. japonica in G. max

number of contigs (%)d

number of contigs (%)d

3,819

3,819

10,806

10,806

(6.4)

(6.4)

(4.3)

(4.3)

17,653

17,656

17,653

17,526

(19.9)

(19.9)

(19.9)

(19.7)

  1. aIndicated reads were mapped onto C. japonica contig and G. max contig separately, and uniquely hit reads to each contig set was used to estimate gene expression level. bIndicated reads were mapped onto a merged contig set of C. japonica contig and G. max contig. If a given read hit to wrong contigs (C. japonica read to G. max contig, or vice versa) that read was excluded from the estimation of gene expression level. cDifferentially expressed genes detected by using TCC software [45] with the q-value <0.05. dPercentage of the number of differentially expressed genes to the total number of C. japonica or G. max contigs.