Table S1. Ontology: examples of the functional categories of the known in the subtracted cDNA library

TESS Category Description Nucleic acid metabolism/Transcription 21.C5 Sox4: SRY-box containing gene 4 Has diverse roles in vertebrate neural differentiation Member of the SRY-related HMG-box family of transcription factors; may have a role in the 28.G5 Sox11, SRY-box containing gene 11 developing nervous system 32.F8 Lhx2, LIM homeobox 2 The encoded protein may function as a transcriptional regulator. 19.H3 Nr2f1, Nuclear receptor subfamily 2, group F, member 1 Nuclear receptor involved in organogenesis 0.G2 Sp5, Trans-acting transcription factor 5 Role in regulation of transcription 27.B12 Bach2, BTB and CNC homology 2 Has important roles in coordinating transcriptional activation and repression 19.E3 Foxp2: Forkhead box P2 Transcriptional repressor that has an important role in specification and differentiation. 22.H2 Pb1-pending: Polybromo 1 May have a role in protein-protein interactions involved in gene silencing May be a trans-acting factor involved in the development and maintenance of the mammalian 12.C4 Neurod6;Neurogenic differentiation 6 central nervous system 6.G4 Gabpa, GA repeat binding protein, alpha Probably involved in activation of cytochrome oxidase expression Sirtuin are known to regulate epigenetic gene silencing and suppress recombination of 19.C6 Sirt1: Sirtuin 1 rDNA 20.B4 Rad21, RAD21 homolog (S. pombe) Role in sister chromatid cohesion in mitotic cells This protein has also been reported to be involved in the final ligation step in DNA end-joining 29.E3 Hmgb2, High mobility group box 2 processes of DNA double-strand break repairs and V(D)J recombination Implicated in a number of cellular processes involving alteration of RNA secondary structure, 30.E8 Ddx21;DEAD box polypeptide 21 such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. 7.E5 Brunol4, Bruno-like 4 Implicated in regulation of alternative splicing

Cell cycle/Proliferation 6.B10 Ccnb1, Cyclin B1 This gene is a regulatory protein involved in 21.C12 Lek1;Leucine, glutamic acid, lysine family 1 protein The protein is a component of the nuclear matrix during the G2 phase of interphase The protein encoded by this gene is a transforming protein that is related to Rho-specific 21.G9 Ect2,Ect2 oncogene exchange factors and yeast cell-cycle regulators.

Development Involved in embryonic cental nervous system development, modulator of LINE retroposon 14.F12 Sox21;SRY-box containing gene 21 promoter activity 24.F7 Foxg1 Forkhead box G1 It may have a role in the development of the brain and telencephalon Contains a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and 8.G10 Dlx2: Distal-less homeobox 2 limbs of the developing fruit fly. 6.B4 Dlx5, Distal-less homeobox 5 The DLX proteins are postulated to play a role in forebrain and craniofacial development. 16.F11 Neurog2, Neurogenin 2 Involved in neurogenesis 27.A12 Abr, Active BCR-related gene Abr and Bcr have important complementary roles during vestibular morphogenesis 18.D6 Qk, Quaking Quaking is essential for blood vessel development during embryonic development. May be involved in the control of cell-type determination within the developing central nervous 9.G12 Nhlh2, Nescient helix loop helix 2 system The developmentally regulated expression of Twisted gastrulation reveals a role for bone 32.A6 Twsg1, Twisted gastrulation homolog 1 morphogenetic proteins in the control of T-cell development

Protein metabolism 20.D12 Mest, Mesoderm specific transcript Predicted hydrolase or acyltransferase 20.B2 Ube2d2: Ubiquitin-conjugating enzyme E2D 2 This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Adamts5, A disintegrin-like and metalloprotease (reprolysin The enzyme encoded by this gene contains two C-terminal TS motifs and functions as an 28.E9 type) with thrombospondin type 1 motif, 5 aggrecanase, to cleave aggrecan, a major proteoglycan of cartilage. 6.C8 Nbea;Neurobeachin May mediate protein-protein interactions 16.G8 Ngly1;N-glycanase 1 This enzyme has been implicated in proteasomal degradation 23.G5 Cct2: Chaperonin subunit 2 (beta) This protein assists the folding of proteins upon ATP hydrolysis

Signal transduction Gnai3;Guanine nucleotide binding protein, alpha inhibiting 25.E10 Involved as modulators or transducers in various transmembrane signaling systems. 3 24.G12 Akap9: A kinase (PRKA) anchor protein (yotiao) 9 Interacts with numerous signaling proteins from multiple signal transduction pathways. It has been implicated in nuclear signaling events that control neuronal growth, differentiation 12.E3 Camk4: Calcium/calmodulin-dependent protein kinase IV and plasticity. 31.G5 Fyn proto-oncogene Involved in signal transduction related to cytoskeletal organization. 30.F9 GRIK1, Glutamate receptor, ionotropic, kainate 1 It may have a role in synaptic plasticity; important for learning and memory ROCK1 is a protein serine/threonine kinase that is activated when bound to the GTP-bound 22.B12 Rock1: Rho-associated coiled-coil forming kinase 1 form of Rho PTPs are known to be signaling molecules that regulate a variety of cellular processes, 18.D9 Ptprd: Protein tyrosine phosphatase, receptor type, D including cell growth, differentiation, the mitotic cycle and oncogenic transformation.

Cell-cell signaling/Cell adhesion 13.H12 Cdh2,Cadherin 2 Cadherins are calcium dependent cell adhesion proteins The protein is likely to be involved in integrin signaling through its LIM-domain-mediated 13.A8 Lims1l, LIM and senescent cell antigen-like domains 1-like interaction with integrin-linked kinase; found in focal adhesion plaques 32.D4 Gja1 Gap junction membrane channel protein alpha 1 Is a member of the connexin gene family and a component of gap junctions. Cdon: Cell adhesion molecule-related/down-regulated by 20.D2 It is a component of a cell surface receptor that positively regulates myogenesis in vitro. oncogenes 31.D5 Pcdh18, Protocadherin 18 Cadherins are calcium-dependent cell adhesion proteins 28.F7 Arhe Ras homolog gene family, member E It regulates the actin cytoskeleton and cell adhesion

Cell organization and biogenesis 28.G4 H3f3b H3 histone, family 3B Responsible for the nucleosome structure of the chromosomal fiber in eukaryotes This protein establishes mitochondrial morphology through a role in distributing mitochondrial 21.A3 Dnm1l;Dynamin 1-like tubules throughout the cytoplasm. 16.H1 Vim: Vimentin Represent a well-characterized cytoskeletal element.

Metabolism 22.E9 Hadha;Hydroxyacyl-Coenzyme A dehydrogenase Catalyzes two steps of the fatty acid beta-oxidation cycle. May be functional in fatty acid metabolism; member of the enoyl-CoA hydratase/ isomerase 12.A4 Echdc1: Enoyl Coenzyme A hydratase domain containing 1 family

Response to external stimulus Prothymosin alpha may mediate immune function by conferring resistance to certain 29.D8 Ptma: Prothymosin alpha opportunistic infections. 26.H2 Peli1 Pellino 1 Phosducin-like protein and phosphoducin have been shown to regulate G-protein signaling by 29.E2 Pdcl: Phosducin-like binding to the beta-gamma subunits of G proteins.

Cell death 25.C9 Gas2, Growth arrest specific 2 May have a role in apoptosis, by acting as a cell death substrate for caspases