Computation of Median(logFC_m)

GEO ArrayExpress

Selection of studies

Key words: Nf1 MPNST neurofibromatosis neurofibroma

E-MEXP-353

E-TABM-69

GSE41747

GSE66743

(Affymetrix)

(Agilent)

(Affymetrix)

(ABI)

GSE41747 (Affymetrix)

MAIN OUTPUTS

Normalization Retrieval of R and G values from MA matrix

Probe numberj log2(Expression)ij Adjustment of batch effect

Preprocessing

Adjustment of batch effect

(Probe number in Table 1 & Table A in Results B in S1 Appendix)

1st Filter: s < quantile 0.2 Grouping of samples by phenotypes (NF and MPNST ) 2nd Filter: ANOVA FDR < 0.05 Differential expression

Final probe numberj (Probe number in Table 1 & Table A in Results B in S1 Appendix)

logFCij

pvalij

Bij

(logFCij in S1 Table)

Translation of probe names to ENSEMBL gene ID’s

ENSGENEij

(Probe number in Table 1 & Table A in Results B in S1 Appendix)

Additional computations

logFC_mij

MADij

(logFC_mij in S1 Table)

Calculation of score of ith gene in jth experiment

Score computation

Calculation of human score of ith gene

sij (S1 Table) human si

mouse si

Comparison of human si and mouse si Calculation of score of ith gene

Calculation of the median of human logFC of ith gene

Computation of Median(logFC)

human logFCi

mouse logFCi

Comparison of human logFCi and mouse logFCi Calculation of logFC of ith gene

Calculation of the median of human logFC_m of ith gene

Computation of Median(logFC_m)

si (Table A in S2 Table)

logFCi

human logFC_mi

(Table A in S2 Table)

mouse logFC_mi

Comparison of human logFC_mi and mouse logFC_mi Calculation of logFC_m of ith gene

3rd Filter: si sign ≠ logFCi sign and si sign ≠ logFC_mi sign

logFC_mi (Table A in S2 Table)

MPNST vs. NF gene list (Table A in S2 Table)

4th Filter: if score

i > 0 => scorei > quantile 0.9 if scorei < 0 => scorei < quantile 0.1 /logFCi/ > 0.99

MPNST vs. NF gene signature (Table A in S2 Table, bold-highlighted)