Urzúa et al. BMC Genomics 2010, 11(Suppl 5):S1 http://www.biomedcentral.com/1471-2164/11/S5/S1 OTF and 20 NL correlated transcripts. Genes with the top correlation coefficients (R) and equivalent distribu- tion of positive and negative correlation are shown. R values of negatively correlated clones ranged -0.999 to -0.798, and +0.998 to +0.875 for the positively correlated ones. Similarly, R values for NL correlated genes ranged -0.986 to -0.845 and +0.999 to +0.756 [Additional file 1, 2, 3 “OTF&NL_correlated_transcripts.xls”]. Following exclusion of unknown clones and merging of repeats, the OTF/NL-145 clones list was reduced to 117 single Unigene IDs including 21 transcribed loci of known chromosomal location but unassigned biological func- tion. Thus, the final list actually consisted of 96 unique gene identities and was further decomposed in 2 sub- lists based on direction of correlation: 76 OTF(-) NL(+) genes and 20 OTF(+) NL(-) genes, where the minus sign indicates negative correlation and the plus sign indicates positive correlation. The genes in enriched functional categories (56 out of the 96) are shown in Additional file 4. Overall, the predominant functions were related to RNA-metabolism (i. e. RNA binding, mRNA processing, regulation of transcription, zinc ion binding) and protein folding and degradation. Eleven of the 56 genes have not been linked to a defined cellular or physiological process since they comprise recently identified genes for which GO terms were inferred from electronic annotation. Importantly, 15 genes are linked to normal or pathological ovarian processes, including Cited1 and Ece1 directly implicated in reproductive functions. Further links to reproduction involve the genes Aplp2, Dnaja1, Htt, Rps6kb1 and Spin1 which were part of the overall correlated 590 clones subset (see Discussion). In addition, as shown in Additional file 4, five genes have been described in normal or altered hematopoiesis, 5 genes are associated to neurological disorders, 3 genes are muscle-related and 3 genes are linked to non-ovarian endocrine function. Discussion Complex phenotypes are the outcome of many genes interacting with each other and with endogenous or exogenous factors. Mouse strains displaying phenotype variability allow interrogation on their molecular basis in a particular tissue or condition. In this report, the ovarian expression of roughly 400 genes (corresponding to 590 transcripts in Table 2) was significantly corre- lated to 4 of 5 mouse tumor and reproductive pheno- types assessed with a linear regression model. The predominant gene ontology (GO) terms were “regulation of transcription”, “RNA binding” and “RNA metabolism” accounting for 105 of all correlated genes. A minor, but significant group was “ubiquitin cycle” with 14 genes. Links to reproductive processes are described for Aplp2, Chuk, Dnaja1, Htt, Pten, Rps6kb1, Sf1, Spin1 and Tnc in Page 6 of 11 the GO directory. Rps6kb1 is involved in proliferation of granulosa cells in response to FSH [27]. Rps6kb1 and Chuk, in addition to Nfkb1, Map3k10, Flna, Kras, Rap1a, and Hspb1 belong to the MAP kinase signaling pathway which has been implicated in mammalian oocyte maturation and fertilization [28]. The correlation of Kras (K-Ras 2), commonly mutated in various human tumors, with litter size (LS) can be supported by its involvement in granulosa cell differentiation and ovula- tion [29]. In a study on Foxo3 mice, a mutant displaying early ovarian hyperplasia due to synchronous primordial follicle activation, 6 genes (Spin1, Slc45a3, Rspo2, Star, Trim71 and Gm196) present in our 400-genes list were postulated as fertility factors [30]. Star (steroidogenic acute regulatory) protein was positively correlated to OTF (see Figure 2). Star transports cholesterol into the mitochodria, a key process in steroid-hormone synthesis in all major steroidogenic tissues [20]. Additional genes related to steroid metabolism and present in the 400-list included Hmgcr (3-hydroxy-3-methylglutaryl-CoA reductase), the major regulatory step in cholesterol synthesis; Idi1 (isopentenyl-diphosphate delta isomerase) involved in conversion of mevalonate into activated iso- prene units, and Lss (lanosterol synthase) that catalyzes the cyclization of squalene-2,3-epoxide to lanosterol. A recent work has implicated metabolic products of lanos- terol in primordial folliculogenesis by regulation of oocyte meiosis and apoptosis [31]. Other indirectly ster- oid-related gene was Mbtps2, a membrane-embedded zinc metalloprotease which activates signaling proteins involved in transcription induced by steroids [32]. A large portion of the 590 list (24.6%, i.e. 145 clones) was found to be associated both to spontaneous ovarian tumor frequency (OTF) and number of litters (NL) as shown in Table 2. A link between OTF and NL agrees with an increased risk of ovarian tumorigenesis due to successive menstrual cycles in women. In contrast, con- ditions that interrupt cycles block ovulations and thus reduce risk [2]. Accordingly, a mouse strain displaying high NL has been subjected to a longer period without cycling than compared with a low NL strain. Successive pregnancies and lactation may be responsible of this effect. We detected a set of 76 mouse genes that were positively correlated to NL, i.e. elevated expression levels were observed in strains showing high NL. Thus, since a concomitant negative correlation was observed with ovarian tumor frequency (OTF), over-expression of these 76 genes set could be considered “protective”. By analogy, the 20 genes that were negatively correlated to NL, i.e. down-regulated in high NL mice, may have a role as “susceptibility” genes since they showed a parallel positive correlation with OTF. Importantly, high litter sizes (LS) involve multiple simultaneous ovulations but