MOESM4 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa

Additional file 4. Transcriptomics-based annotation support for genes in the plant cell wall degradation network (PCWDN) of N. crassa. The first sheet contains information on the transcriptomics-based annotation support for each gene in the PCWDN. The second sheet contains a table with the list of RNA-seq libraries for N. crassa WT strain grown in different conditions along with their GEO [101] accession numbers and references for the profiling data. The third sheet contains a table with the expression of genes in different conditions, separately, for replicate RNA-seq libraries. The fourth sheet contains a table with the average expression (Mean FPKM) of genes in each condition across replicate RNA-seq libraries. The fifth sheet contains a table with information on differential expression of genes in each condition compared to the No Carbon control. The sixth sheet contains a table with information on differential expression of genes in each condition compared to the sucrose control. The set of differentially expressed genes was computed using the Cuffdiff package [103]. The seventh and eighth sheets contain genes in the up-regulons and down-regulons, respectively, of N. crassa in seven conditions: Avicel, Xylan, Xyloglucan, Mannan, Mixed-Linkage Glucan, Pectin and Starch. NoC no carbon, CB cellobiose, XG xyloglucan, MLG mixed-linkage glucan, OPP orange peel powder.