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Table 1 Probe sets selected by SAM analysis (section 2.4).

From: Gene function in early mouse embryonic stem cell differentiation

key

Probe set id

Gene

Gene description

Function/process/component (GO)1

D6

1418133_at

Bcl3

B-cell leukemia/lymphoma 3

DNA binding; transcription factor activity; regulation of transcription, DNA-dependent; nucleus;

D6

1418025_at

Bhlhb2

basic helix-loop-helix domain containing, class B2

DNA binding; protein binding; nucleus; regulation of transcription, DNA-dependent; transcriptional repressor activity; negative regulation of transcription, DNA-dependent;

D6

1419076_a_at

Brca2

breast cancer 2

nucleic acid binding; protein binding; nucleus; cytoplasm; DNA repair; response to DNA damage stimulus; double-strand break repair via homologous recombination; synaptonemal complex; single-stranded DNA binding; DNA replication; chromatin remodeling; apoptosis; regulation of S phase of mitotic cell cycle; mitotic checkpoint; transcriptional activator activity; regulation of transcription;

D6

1416039_x_at

Cyr61

cysteine rich protein 61

regulation of cell growth; patterning of blood vessels; protein binding; insulin-like growth factor binding; extracellular; extracellular space; chemotaxis; cell adhesion; heparin binding; growth factor binding; sensory perception;

D6

1417394_at

Klf4

Kruppel-like factor 4 (gut)

nucleic acid binding; DNA binding; nucleus; regulation of transcription, DNA-dependent; zinc ion binding; transcription factor activity; transcriptional activator activity; transcriptional repressor activity; negative regulation of transcription, DNA-dependent;

D6

1417395_at

   

D6

1435458_at

Pim1

proviral integration site 1

protein kinase activity; protein serine/threonine kinase activity; protein-tyrosine kinase activity; ATP binding; nucleus; protein amino acid phosphorylation; cell growth and/or maintenance; kinase activity; transferase activity;

D6

1437100_x_at

Pim3

proviral integration site 3

protein kinase activity; protein serine/threonine kinase activity; ATP binding; protein amino acid phosphorylation; kinase activity; transferase activity;

D6

1451069_at

   

D6

1423078_a_at

Sc4mol

sterol-C4-methyl oxidase-like

C-4 methyl sterol oxidase activity; catalytic activity; endoplasmic reticulum; plasma membrane; fatty acid metabolism; metabolism; steroid metabolism; integral to membrane; sterol biosynthesis; oxidoreductase activity;

D6

1415823_at

Scd2

stearoyl-Coenzyme A desaturase 2

fatty acid biosynthesis; superoxide metabolism; lipid biosynthesis; stearoyl-CoA 9-desaturase activity; copper, zinc superoxide dismutase activity; iron ion binding; oxidoreductase activity; metal ion binding; oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water; endoplasmic reticulum; membrane; integral to membrane; endoplasmic reticulum

D6

1416576_at

Socs3

suppressor of cytokine signaling 3

regulation of cell growth; signal transduction; intracellular signaling cascade; regulation of protein amino acid phosphorylation; protein binding; negative regulation of insulin receptor signaling pathway;

D6

1455899_x_at

   

D6

1456212_x_at

   

D6

1450989_at

Tdgf1

teratocarcinoma-derived growth factor

activation of MAPK; extracellular; extracellular space; epidermal growth factor receptor signaling pathway; growth factor activity; positive regulation of cell proliferation; determination of anterior/posterior axis, embryo; extrinsic to plasma membrane;

D12

1460330_at

Anxa3

annexin A3

phospholipase inhibitor activity; calcium ion binding; calcium-dependent phospholipid binding; phospholipase A2 inhibitor activity;

D12

1449141_at

Fblim1

filamin binding LIM protein 1

protein binding; cytoskeleton; cell adhesion; zinc ion binding; regulation of cell shape;

D12

1427238_at

Fbxo15

F-box protein 15

protein binding; ubiquitin cycle; SCF ubiquitin ligase complex;

D12

1426858_at

Inhbb

inhibin beta-B

hormone activity; extracellular; growth factor activity; cell growth and/or maintenance; growth; ovarian follicle development; defense/immunity protein activity; cytokine activity; response to external stimulus; protein homodimerization activity; host cell surface receptor binding; positive regulation of follicle-stimulating hormone secretion; negative regulation of follicle-stimulating hormone secretion; negative regulation of hepatocyte growth factor biosynthesis;

D12

1451021_a_at

Klf5

Kruppel-like factor 5

nucleic acid binding; DNA binding; nucleus; regulation of transcription, DNA-dependent; zinc ion binding; angiogenesis; transcription factor activity; protein binding; microvillus biogenesis; positive regulation of transcription;

D12

1418153_at

Lama1

laminin, alpha 1

morphogenesis of an epithelial sheet; receptor binding; structural molecule activity; extracellular matrix structural constituent; protein binding; extracellular matrix; basement membrane; basal lamina; laminin-1; cell adhesion; cell surface receptor linked signal transduction; histogenesis; regulation of cell adhesion; regulation of cell migration; regulation of embryonic development; establishment of epithelial cell polarity;

D12

1424719_a_at

Mapt

microtubule-associated protein tau

protein binding; cytoskeletal regulatory protein binding; cytoskeleton; microtubule associated complex; microtubule-based process; microtubule stabilization; microtubule; actin filament organization; microtubule-based movement;

D12

1449590_a_at

Mras

muscle and microspikes RAS

GTP binding; small GTPase mediated signal transduction; small monomeric GTPase activity; RAS small monomeric GTPase activity;

D12

1417760_at

Nr0b1

nuclear receptor subfamily 0, group B, member 1

DNA binding; transcription factor activity; steroid hormone receptor activity; receptor activity; ligand-dependent nuclear receptor activity; nucleus; cytoplasm; regulation of transcription, DNA-dependent; negative regulation of transcription; transcriptional repressor activity;

D12

1448612_at

Sfn

stratifin

regulation of progression through cell cycle; regulation of cyclin dependent protein kinase activity; protein domain specific binding; cytoplasm;

D12

1423505_at

Tagln

transgelin

muscle development; NOT cytoskeleton organization and biogenesis;

D12

1418756_at

Trh

thyrotropin releasing hormone

hormone activity; neuropeptide hormone activity; protein binding; extracellular; extracellular space; thyrotropin-releasing hormone activity; hormone mediated signaling;

D12

1450641_at

Vim

vimentin

structural molecule activity; intermediate filament; type III intermediate filament; intermediate filament-based process; oxygen transporter activity; oxygen transport;

U12

1427202_at

4833442J19Rik

RIKEN cDNA 4833442J19 gene

S-adenosylmethionine-dependent methyltransferase activity;nucleus;

U12

1416077_at

Adm

adrenomedullin

hormone activity; neuropeptide hormone activity; extracellular; extracellular space; neuropeptide signaling pathway;

U12

1449324_at

Ero1l/LOC434220

ERO1-like (S. cerevisiae)

endoplasmic reticulum; electron transport; protein folding; transport; membrane; oxidoreductase activity; integral to endoplasmic reticulum membrane;

U12

1421317_x_at

Myb

myeloblastosis oncogene

regulation of cell cycle; G1/S transition of mitotic cell cycle; DNA binding; transcription factor activity; nucleus; regulation of transcription, DNA-dependent; calcium ion transport; cell growth and/or maintenance; viral assembly;

U12

1425926_a_at

Otx2

orthodenticle homolog 2 (Drosophila)

DNA binding; transcription factor activity; protein binding; nucleus; regulation of transcription, DNA-dependent; regulation of transcription from Pol II promoter; development; central nervous system development; organogenesis; anterior/posterior pattern formation; dorsal/ventral pattern formation; transcription regulator activity; forebrain development; midbrain development; eye photoreceptor cell fate commitment; cell fate commitment;

U12

1418391_at

Phf21a

PHD finger protein 21A

transcription; regulation of transcription, DNA-dependent; DNA binding; protein binding; zinc ion binding

U12

1417288_at

Plekha2

pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2

phosphatidylinositol binding; nucleus; lipid binding; membrane;

U6

1448129_at

Arpc5

actin related protein 2/3 complex, subunit 5

structural constituent of cytoskeleton; cytoplasm; Arp2/3 protein complex; cell motility; actin filament organization; actin cytoskeleton; DNA binding; electron transport; heme binding; lamellipodium; regulation of actin filament polymerization; regulation of transcription;

U6

1434642_at

Dhrs8

dehydrogenase/reductase (SDR family) member 8

extracellular space; metabolism; oxidoreductase activity;

U6

1452670_at

Myl9

myosin, light polypeptide 9, regulatory

calcium ion binding; muscle myosin; regulation of muscle contraction; muscle development; structural constituent of muscle; myosin; motor activity;

U6

1426596_a_at

Smn1

survival motor neuron 1

nucleic acid binding; RNA binding; nucleus; cytoplasm; mRNA processing; spliceosome assembly;

U6

1423054_at

Wdr1

WD repeat domain 1

actin binding; cytoskeleton; perception of sound; actin cytoskeleton;

U6

1437591_a_at

   

U6

1450851_at

   
  1. Column 1 indicates probe set behaviour: D6, down-regulated at 6 h; D12, down-regulated at 12 h; U12, up-regulated at 12 h; U6, up-regulated at 6 h. Associated information was taken from NetAffx unless otherwise indicated.
  2. 1GO-terms in italics were manually derived from database entries linked from NetAffx using the assistance of a data mining method [64]