MOESM1 of Anti-inflammatory activities of Ganoderma lucidum (Lingzhi) and San-Miao-San supplements in MRL/lpr mice for the treatment of systemic lupus erythematosus

Additional file 1. Ethical approval document of animal experiments

UMU sample set characteristics.

<p>UMU sample set characteristics.</p

Genes of interest.

<p>Genes of interest.</p

Description of genomic events.

a<p>nTot = nA + nB, where nA and nB represent calculated copy numbers for the separate alleles at a given probe.</p

Frequency of genomic events among UMU samples.

<p>Frequency (%) is represented on the y-axis and genomic position on the x-axis. The permutation derived event frequency cutoff (used to establish regions with significantly recurring events among the UMU samples) is illustrated by the red line.</p

Frequency of homozygous deletion at chr9.p21, among UMU samples.

<p>The samples are split into two groups, based on their genotype at the EGFR variant rs1015793. HD frequency among samples homozygous for the major allele is plotted on the upper half of the upper panel (grey bars), and the HD frequency among samples homozygous for the rare allele plus heterozygous samples is plotted on the lower half of the upper panel (grey bars). The frequency difference between the groups is illustrated with overlaying red and green bars. The event frequency cutoff is illustrated by the horizontal red lines. The dark grey, vertical lines represent CDKN2A and CDKN2B. The lower panel illustrates the p-values (−log10 transformed) at each genomic site, with the horizontal red line illustrating the permutation derived p-value cutoff (0.0085).</p

EGFR gene structure.

<p>Schematic diagram of the EGFR gene structure, marking all gene variants included in the study and their internal LD structure. Pairs of risk variants (red) and surrogate markers used in the UMU data (blue) are marked with dashed rectangles.</p

Tumor ploidy.

<p>ASCAT calculated tumor ploidy for 81 UMU samples (<b>a</b>) and 285 TCGA samples (<b>b</b>). Samples with ploidy >2.8 were classified as tetraploid-like and samples with ploidy < = 2.8 as diploid-like.</p

Risk gene variants.

<p><i>LD(r∧2)</i> HapMap linkage disequilibrium (r2) data between used surrogate marker and original risk variant, <i>n</i> number, <i>major</i> samples homozygous for the major allele, <i>rare+hz</i> samples homozygous for the rare allele plus heterozygous samples.</p

ASCAT-profiles.

<p>Whole genome ASCAT-profiles from two samples in the UMU dataset; one diploid (<b>a</b>) and one tetraploid (<b>b</b>). Green represents the allele with the lower copy number, and red represents the allele with the higher copy number (the colors are slightly offsetted to avoid overlap, red downwards and green upwards).</p