Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space

Figure 2

The semantic space. (a) The whole semantic space. (b) Magnified view of specific regions of the semantic space. On magnified views, title of each landmark gene set is presented near it. (a) LIAN_MYELOID_DIFF_GRANULE: granule constituents expressed during mouse promyelocytic cell line cell differentiation; METHOTREXATE_PROBCELL_DN: downregulated in pro B cells FL5 12 following treatment with methotrexate; JNK_UP: upregulated by expression of constitutively active JNK in 3T3 cells; CAMPTOTHECIN_PROBCELL_DN: downregulated in pro B cells FL5 12 following treatment with camptothecin; ADIP_DIFF_CLUSTER2: strongly upregulated at 2 hours during differentiation of 3T3 L1 fibroblasts into adipocytes cluster 2. (b) PDGF_ES_UP: upregulated by PDGF in mouse embryonic stem cells via microarray coupled gene trap mutagenesis; CPR_NULL_LIVER_DN: downregulated in mouse liver tissue from mice in which NADPH cytochrome P450 reductase CPR was specifically deleted in the liver by cre lox recombination versus lox only controls; CPR_NULL_LIVER_UP: upregulated in mouse liver tissue from mice in which NADPH cytochrome P450 reductase CPR was specifically deleted in the liver by cre lox recombination versus lox only controls. (c) MOUSE_TISSUE_TESTIS: genes expressed specifically in mouse testis tissue; HIPPOCAMPUS_DEVELOPMENT_PRENATAL: highly expressed in prenatal mouse hippocampus cluster 1; GENOTOXINS_24HRS_DISCR: group of genes whose regulation pattern significantly discriminates between direct cisplatin methyl methanesulfonate mitomycin C and indirect taxol hydroxyurea etoposide genotoxins 24 hours following treatment of mouse lymphocytes TK 3 7 2C; IDX_TSA_DN_CLUSTER6: strongly downregulated at 2 hours during differentiation of 3T3 L1 fibroblasts into adipocytes with IDX insulin dexamethasone and isobutyl xanthine versus fibroblasts treated with IDX TSA to prevent differentiation cluster 6. (d) TPA_SKIN_DN: downregulated in murine dorsal skin cells 6 hours after treatment with the phorbol ester carcinogen TPA; ABBUD_LIF_DN: genes downregulated by LIF treatment 10 ng mL overnight in AtT20 cells; LEE_MYC_UP: genes upregulated in hepatoma tissue of Myc transgenic mice; AGED_MOUSE_HYPOTH_UP: upregulated in the hypothalamus of BALB c mice aged 22 months compared to young 2-month controls; NOVA2_KO_SPLICING: genes that are alternatively spliced in the neocortex of mice deficient in the neuron specific splicing factor Nova2 compared to wild type controls.