BMC Genomics 2009, 10:442 http://www.biomedcentral.com/1471-2164/10/442 Table 4: Ingenuity Pathways Analysis: Top Bio Functions - Diseases and Disorders Category Cancer Hematological Disease Immunological Disease P-value* Molecules 1.12E-04 to 3.06E-02 RPL22, EPS8, LIF, NME2, SFPQ, CDKN2C, SSH1, PTEN, LIMK1, SERPINB2, SOD2, CASP9, CTSS, POSTN, NEDD4L, BIRC3, EPB41L1, CACNA1G, SOX4, YWHAE, RRAD, FGFR1, L1CAM, MBD2, NFKB2, JUNB, SIP1, ADI1, OGG1, NDN, CCND2, RAPGEF2, BTG2, PRKACA, RUNX1, CYLD, LRIG1, MME, BRD2, ICAM1, GEM, RGS3, BMP2, KLF10, MMP14, MCC, HAX1, SAT1, FKBP1A, EXT1, SEPT9, NFKB1, RPLP0 (includes EG:6175), COMP, EIF4EBP1, PGF, RASSF1, NFKBIA, ANGPTL4, EDN1, FOXO3, TAOK2 (includes EG:9344), MEG3 (includes EG:55384), B4GALT5, MMP1 (includes EG:4312), MUC1, CALR, SRC, PXN, RELB, APAF1, PPP1R15A (includes EG:23645), CEBPB, CLCF1, IGF2R, AFF1, NOV, PLAU 1.12E-04 to 3.06E-02 LIF, ICAM1, MCC, SFPQ, NFKB1, SERPINB2, PTEN, EIF4EBP1, CASP9, NFKBIA, HLA-C, SRC, RELB, ELL, MAN2A1, NFKB2, JUNB, CEBPB, CLCF1, AFF1, CCND2, BTG2, PRKACA, CYLD, PLAU, RUNX1, LRIG1 1.12E-04 to 3.06E-02 ICAM1, LIF, BGN, MMP14, BMP2, RELB, CDKN2C, NFKB2, JUNB, NFKB1, RPLP0 (includes EG:6175), CLCF1, PTEN, SOD2, CASP9, CCND2, NFKBIA, BTG2, FOXO3, RUNX1, CYLD, LRIG1, BIRC3, HLA-C Renal and Urological Disease 3.57E-04 to 3.06E-02 SRC, RASSF1, SOD2, EDN1, POSTN, NUPR1, PLAU, LRIG1, SIP1, PTEN Skeletal and Muscular Disorders 6.71E-04 to 3.06E-02 MME, LIF, ICAM1, BMP2, MMP14, EXT1, TNFAIP3, C18ORF10, IDE, NFKB1, PTEN, NR4A3, CASP9, SOD2, NFKBIA, EDN1, CTSS, FOXO3, RPS3, MAPKAPK2, MMP1 (includes EG:4312), HLA-C, SRC, NOX4, PPIF, MITF, BGN, APAF1, L1CAM, NFKB2, CEBPB, NDN, DCTN2, CLIC2, NUP62, PLAU, RUNX1, ATP2B4, C20ORF43, MCTP2 *Fischer's exact test was used to calculate a p-value determining the probability that each biological function and/or disease assigned to that data set is due to chance alone. N° 78 27 24 10 40 types also display molecular alterations. Lymphocytes from patients show reduced proliferation and impaired translational rates irrespective of the nature of the muta- tion [22]. An abnormal proliferation rate has been found also in fibroblasts from patients with mutations in RPS19. Additionally, both lymphocytes and fibroblasts are char- acterised by impaired pre-rRNA processing with accumu- lation of 21S species. Fibroblasts show abnormal nucleoli, which have irregular shape and disorganised dense fibril- lar centers, the compartments where early pre-ribosome maturation takes place [11]. To characterise the molecular abnormalities in DBA non- haematopoietic cells, we evaluated gene expression pro- files of fibroblasts isolated from DBA patients carrying mutations in RPS19. Patients 1 and 2 carried mutations leading to amino acid substitutions (p.Arg62Trp and p.Arg101His), the mutation in patient 3 (c.1-1G>A) impairs the correct splicing of the first intron and abro- gates the ATG start codon, whereas the mutation in patient 4 (c.del58G) causes a frameshift of the open read- ing frame with insertion of a premature stop codon. Regardless of the heterogeneity of the mutational types, we did not observe any significant difference when mis- sense cases were compared to the other mutations, although this may be due to the limited number of patient samples of each mutational class in our study. Gene expression profiling has been previously performed on bone marrow CD34+ cells isolated from three DBA patients with mutations in RPS19 and in remission from the disease (i.e. without any treatment for at least 10 years), compared with healthy controls [23], and on CD4+ peripheral blood mononuclear cells from two DBA patients with unknown mutations compared with two acquired aplastic anaemia patients [24]. Our study dem- onstrates for the first time a global alteration of several biological processes in non-haematopoietic DBA cells. In agreement with previous studies [23,24], we identified a cluster of 22 ribosomal protein genes down-regulated in DBA patients relative to controls. Patients exhibit signifi- cant down-regulation of genes encoding proteins impor- tant for translation, including several eukaryotic translation initiation factors (EIF3, EIF2, EIF4E), EIF3 and EIF4 interacting proteins (EIF3S6IP and EIF4EBP1) and the eukaryotic elongation factor 1 δ (EEF1D). This may be caused either by the co-regulated transcription of RP genes or by their coordinated post-transcriptional regulation. Most interestingly, among down-regulated genes we iden- tified a large cluster of aminoacyl-tRNA synthetases (QARS, EPRS, SARS, GARS, LARS, WARS). Aminoacyl- tRNA synthetases (ARS) catalyse the aminoacylation of their cognate tRNAs and thus are key enzymes to maintain the fidelity of protein synthesis. In mammals, additional Page 6 of 12 (page number not for citation purposes)