Figure 3. False discoveries explain the majority of novel imprinted genes.

(A) Schematic of experimental design and mock (negative control) comparisons. The red arrows indicate mock comparisons, green arrows indicate same-sex reciprocal comparisons, while blue arrows indicate mixed-sex reciprocal comparisons. (B) Number of SNPs/genes that exceed threshold used by [16], [17] in reciprocally crossed and mock PFC samples. (C) Agreement on known and novel imprinted genes detected in the two reciprocal comparisons shown in 2B. (D) Number of genes exceeding the threshold used in [16], [17] in a mock cross between E17.5 brains from embryos of the same sex (males) is not significantly different from mock comparison of opposite sexes. (E) Relationship between read depth and sensitivity (number of transcripts reaching significance). Aligned reads from the same cross (1+3 and 2+4) were selected at random in equal proportions for each sample (see Materials and Methods). Average values for 100 sampling iterations (+/− standard error) are shown. (F) Proportion of novel imprinted genes estimated to be false-positives as a function of input read depth adjusted by random sampling (see Materials and Methods). Average values for 100 sampling iterations (+/− standard error) are shown.