of note 14. 7%, 12. 2% and 12. 2% of transcripts differen tially expressed are involved in carbohydrate metabolism, lipid metabolism and the biosynthesis of secondary Sorafenib Tosylate FDA metabolites respectively. Around 21% of differentially expressed transcripts have no homolog, however by far the largest class of probe sets that had significantly altered expression in our analysis were unclassified with a homolog. This result led us to use other bioinfor matics strategies to annotate the probe sets on the genome array. To further refine the functional classification and annota tion of metabolic probe sets on the Medicago genome array we used PathExpress. Using this database we were able to identify Inhibitors,Modulators,Libraries statistically significant over represen Inhibitors,Modulators,Libraries tation of metabolic pathways in the embryogenic and non embryogenic cultures as shown in Table 2.

Five met abolic pathways are significantly over represented Inhibitors,Modulators,Libraries in the embryogenic cultures. They are Sphingolipid Ascorbate and aldarate metabolism. Biosynthesis of 12. 14 and 16 membered macrolides. We also annotated the array by comparing the data set with the Arabidopsis Gene Family Information database maintained by the Arabidopsis Information Resource. As of April 2007 the database contained 996 gene families and 8,331 genes. Using Blast, we were able to classify Inhibitors,Modulators,Libraries 3,159 Medicago probe sets into these families. Forty one and ten of the over expressed probe sets from the embryogenic and non embryogenic cultures respec tively were classified in the gene families. Two cytochrome P450 families were significantly over represented in the non embryogenic line Jemalong.

Finally, transcription factors on the Genome array were pre dicted by homology relationship based on the Database of Arabidopsis Transcription Factors. This analysis showed that 2,323 probe sets on the Genome array have sequence homology to described plant TFs. Twenty one predicted TFs were up regulated in the embryogenic Inhibitors,Modulators,Libraries line 2HA cultures and six TFs were up regulated in the non embryogenic Jemalong cultures. The families represented in the embryogenic cul tures selleck chemicals Rapamycin are the basic helix loop helix, zinc finger domain TFs C2C2 co like and C2C2 DOF, response regu lators, GRAS domain containing TFs, MADS box TFs and MYB DNA binding domain TFs. The TF families represented in the non embryogenic cultures are APETALA 2 and ethylene responsive element binding proteins, auxin responsive protein indoleacetic acid induced pro tein and ETHYLENE INSENSITIVE 3. With the exception of bHLH and zinc finger containing TFs, the TF gene families are plant specific. We confirmed the expression of several TFs betweens the cultures of two lines using qRT PCR.