Pathway Aminoacyl-tRNA Biosynthesis Role of PKR in Interferon Induction and Antiviral Response Death Receptor Signaling RAR Activation 3.36E+00 2.84E+00 2.73E+00 2.31E+00 2.28E+00 Glycine, Serine and Threonine Metabolism 4.17E-02 PSAT1, PHGDH, GARS, CTH, SARS, SHMT2 BMC Genomics 2009, 10:442 http://www.biomedcentral.com/1471-2164/10/442 Table 2: Ingenuity Pathways Analysis: Top canonical pathways. -Log(P-value*) Ratio** Molecules 7.14E-02 LARS, WARS, GARS, SARS, QARS, EPRS 1.28E-01 CASP9, NFKBIA, NFKBIE (includes EG:4794), APAF1, NFKB2, NFKB1 1.08E-01 CASP9, NFKBIA, NFKBIE (includes EG:4794), APAF1, NFKB2, NFKB1, BIRC3 6.04E-02 SRC, PRMT2, RDH11, ADCY3, PRKACA, NFKB2, NFKB1, MAPKAPK2, RBP1, MMP1 (includes EG:4312), PTEN *Fischer's exact test was used to calculate a p-value determining the probability that each canonical pathway assigned to that data set is due to chance alone. **Number of genes from the dataset that map to the pathway divided by the total number of molecules that exist in the canonical pathway COMP, WARS and ZIC1 (down-regulated in DBA patients) was tested. All genes were found to be differen- tially expressed in patients relative to controls and data are statistically significant (figure 2a). The correlation between qRT-PCR and microarray data is 0.7 (figure 2b), which corresponds to the value obtained in similar stud- ies [20,21]. Figure 2c shows the comparison of fold changes from qRT-PCR and microarray analysis. Microar- ray data showed the same trend as qRT-PCR results for all the examined genes in each sample, as represented in fig- ure 3. These data overall indicate that the expression pat- terns detected by microarray analysis are in good agreement with those detected by qRT-PCR and validate our study. Discussion The most prominent feature in DBA is anaemia due to paucity of erythroid progenitors. However, other cellular Table 3: Ingenuity Pathways Analysis: Top Bio Functions - Molecular and Cellular Functions Category Protein Synthesis Cell Death P-value* Molecules 3.67E-07 to 3.06E-02 MME, RPL22, UBE2H (includes EG:7328), RPL27A, LIF, RPL29, MMP14, RPL31, RPL14, IDE, NFKB1, EIF4EBP1, CASP9, TRHDE, RPL18A, EDN1, CTSS, MRP63, EIF5, RPS3, RPL18, MMP1 (includes EG:4312), RPL13, SRC, RRBP1, PJA1, EIF3H, RPL3, RPL34, C9ORF3, RPS2, APAF1, CEBPB, DCTN2, RPS12, KIAA0368, RPL15, WARS, RPL28, USE1, SGSM3, IFT52, SMURF2, PLAU 1.78E-04 to 3.06E-02 LIF, ATXN1, NME2, CDKN2C, TMEM132A, ARG2, MSX2, RBP1, PTEN, SOD2, CASP9, CCNB1IP1, CTSS, PQBP1, SUB1, NUPR1, FOSL2, BIRC3, HLA-C, FBL, NOX4, RP5-886K2.1, NOVA1, YWHAE, SGCG, MITF, FGFR1, THRA, JUNB, NFKB2, NDN, ADI1, OGG1, CCND2, RAPGEF2, BTG2, PRKACA, RUNX1, CYLD, LRIG1, MME, BRD2, GABPB2, ICAM1, RGS3, MMP14, KLF10, BMP2, SAT1, EXT1, DUSP22, TNFAIP3, FKBP1A, FNTA, NFKB1, QARS, ASNS, RPLP0 (includes EG:6175), COMP, EIF4EBP1, PGF, RASSF1, ANGPTL4, NFKBIA, EDN1, FOXO3, ACTC1, MMP1 (includes EG:4312), ATN1, B4GALT5, MUC1, CALR, SRC, PXN, PRMT2, THG1L, PPIF, BGN, ELL, APAF1, PPP1R15A (includes EG:23645), CEBPB, CLCF1, IGF2R, PRG2 (includes EG:5553), NUP62, MAFB, CTH, PLAU, ATP2B4 Cellular Development 2.14E-04 to 3.06E-02 LIF, NME2, SFPQ, MSX2, EEF1D, LIMK1, PTEN, SERPINB2, NR4A3, CDON, POSTN, NUPR1, FOSL2, NOX4, NAB1, MITF, FGFR1, THRA, L1CAM, NFKB2, MBD2, JUNB, NDN, CCND2, BTG2, RUNX1, MAST2, MSC, ICAM1, NLGN1, MMP14, BMP2, KLF10, MCC, METTL8, TNFAIP3, EXT1, NFKB1, PGF, RASSF1, NFKBIA, EDN1, FOXO3, ATN1, MMP1 (includes EG:4312), SRC, NHEJ1, CALR, PXN, RELB, ELL, APAF1, IRAK3, CEBPB, IGF2R, CLCF1, AFF1, RBPJ, MAFB, PLAU Lipid Metabolism 2.41E-04 to 3.06E-02 MUC1, SRC, CASP9, EDN1, APAF1, PHGDH, FAR2, ABCA1, PTEN Molecular Transport 2.41E-04 to 3.06E-02 CACNA1G, CALR, SRC, YWHAE, ATXN1, NUP133, SAT1, APAF1, NUP50, ABCA1, CASP9, EDN1, SMG7, PHGDH, ATP2B4 *Fischer's exact test was used to calculate a p-value determining the probability that each biological function assigned to that data set is due to chance alone. N° 6 6 7 6 11 N° 44 90 60 9 15 Page 5 of 12 (page number not for citation purposes)