Download Supplementary table 2: Description of the gene pathways

Supplementary Table 2: Description of the gene pathways significantly altered in figures
13 and 14.
1. Muscle_Myosin
2. GLUCO
3. Glycolysis_and_Gluconeogenesis
4. Bile_acid_biosynthesis
5. ROS
6. Cdc25
7. GlycolysisPathway
8. Nos1
9. Eif2
10. FOSB
11. Mef2d
12. Ndk_Dynamin
13. Androgen_genes
14. Peng_GLUT_UP
15. Glycolysis
16. Glycogen_Metabolism
17. Peng_Leucine_UP
18. Carbon_Fixation
19. ST_Interferon_Gamma
20. ST_Type_I_Interferon
21. TCA
Genes related to muscle myosin
Genes involved in glucose processing
Genes involved in glycolysis and gluconeogenesis
Genes involved in bile acid biosynthesis
Reactive oxidative species related genes
The protein phosphatase Cdc25 is phosphorylated
by Chk1 and activates Cdc2 to stimulate eukaryotic
cells into M phase.
Glycolysis is an evolutionarily conserved pathway
by which one glucose molecule is converted to two
pyruvate molecules for a gain of 2 ATP.
Glutamate stimulates NMDA-mediated calcium
influx, which promotes nitric oxide synthesis from
arginine by neuronal nitric oxide synthase,
activating guanylate cyclase.
Eukaryotic initiation factor 2 (EIF2) initiates
translation by transferring Met-tRNA to the 40S
ribosome in a GTP-dependent process.
FOSB gene expression and drug abuse
Mef2 transcription factors promote calciuminduced apoptosis in T cells and are regulated by
MAP kinases and histone deacetylases.
Synaptic vesicle endocytosis is coordinated by
dephosphins, which are coordinately
dephosphorylated on calmodulin- and calcineurinmodulated calcium influx.
Genes annotated in NetAffx as androgen related
Genes upregulated in response to glutamine
starvation
Glycolysis related genes
Genes involved in glycogen metabolism
Genes upregulated in response to leucine
starvation
Genes related to carbon fixation in photosynthetic
organisms
The interferon gamma pathway resembles the JAKSTAT pathway and activates STAT transcription
factors.
Type I interferon is an antiviral cytokine that
induces a JAK-STAT type pathway leading to
ISGF3 activation and a cellular antiviral response.
Tricarboxylic acid related genes
1
22. Arf
23. Cbl
24. Ctla4
25. Fxr
26. Ifna
27. Intrinsic
28. Leptin
29. Pgc1a
30. Rarrxr
31. Calcineurin
32. Caspase
33. Sodd
34. Keratinocyte
35. VIP
Cyclin-dependent kinase inhibitor 2A is a tumor
suppressor that induces G1 arrest and can activate
the p53 pathway, leading to G2/M arrest.
Activated EGF receptors undergo endocytosis into
clathrin-coated vesicles, where they are recycled to
the membrane or ubiquitinated by Cbl.
T cell activation requires interaction with an
antigen-MHC-I complex on an antigen-presenting
cell (APC), as well as CD28 interaction with the
APC's CD80 or 86.
The nuclear receptor transcription factors FXR and
LXR are activated by cholesterol metabolites and
regulate cholesterol homeostasis.
Interferon alpha, active in the immune response,
binds to the IFN receptor and activates Jak1 and
Tyk2, which phosphorylate Stat1 and Stat2.
The intrinsic prothrombin activation pathway is
activated by traumatized blood vessels and induces
clot formation.
Leptin is a peptide secreted by adipose tissue that,
in skeletal muscle, promotes fatty acid oxidation,
decreases cells' lipid content, and promotes insulin
sensitivity.
PCG-1a is expressed in skeletal muscle, heart
muscle, and brown fat, and is a coactivator for
receptors such as glucocorticoid receptor and
thyroid hormone receptor.
RXR and RAR suppress transcription in the
absence of ligand and, on binding trans- or 9-cisretinoic acid, are ubiquitinated to allow
transcription to proceed.
Increased intracellular calcium activates the
phosphatase calcineurin in differentiating
keratinocytes.
Caspases are cysteine proteases active in apoptosis;
caspase-8 and 9 cleave and activate other caspases,
while 3, 6, and 7 cleave cellular targets.
Some members of the tumor necrosis factor
receptor family have cytoplasmic death domains
that promote apoptosis when active and are
repressed by silencers called SODDs.
Keratinocyte differentiation, which models the
differentiation of epidermal cells, requires the four
main MAP kinase pathways.
Apoptosis of activated T cells is inhibited by
vasoactive intestinal peptide (VIP) and its relative
2
36. Proteasome
37. Akap13
38. GPCRs_Class_C_Metabotropic_
Glutamate_Pheromone
39. Par1
40. Pentose_Phosphate
41. Glycolysis
42. Mef2d
43. Eryth
44. Prostaglandin_and_Leukotriene_
Metabolism
45. Androgen_genes
46. Cell_Adhesion_Molecule_
Activity
47. Nos1
48. GABA
49. Inflam
50. Reductive_Carboxylate_Cycle_
CO2_Fixation
51. Proteasome
PACAP.
Ubiquitinated proteins are targeted for proteolytic
degradation by the proteasome, where they are
unfolded and degraded to small peptides in an
ATP-dependent process.
A-kinase anchor protein 13 (AKAP13) localizes
protein kinase A holoenzyme and is a nucleotide
exchange factor for Rho/Rac.
The group of G-protein coupled receptors that are
structurally/functionally related to the metabotropic
glutamate receptors
Activated extracellular thrombin cleaves and
activates the G-protein coupled receptors PAR1 and
PAR4, which activate platelets.
Pentose Phosphate Pathway
Glycolysis is an evolutionarily conserved pathway
by which one glucose molecule is converted to two
pyruvate molecules for a gain of 2 ATP.
Mef2 transcription factors promote calciuminduced apoptosis in T cells and are regulated by
MAP kinases and histone deacetylases.
Erythropoietin selectively stimulates erythrocyte
differentiation from CFU-GEMM cells in bone
marrow.
Genes related to prostaglandin and leukotriene
metabolism
Genes annotated in NetAffx as androgen related
Obsolete by GO - mediates the adhesion of the cell
to other cells or to the extracellular matrix.
Glutamate stimulates NMDA-mediates calcium
influx, which promotes nitric oxide synthesis from
arginine by neuronal nitric oxide synthase,
activating guanylate cyclase.
Gamma-aminobutyric acid (GABA) is an inhibitory
neurotransmitter whose receptor is regulated by
Plic-1, gephyrin, and GABARAP, which promote
receptor clustering.
Interleukins and TNF serve as signals to coordinate
the inflammatory response, in which macrophages
recruit and activate neutrophils, fibroblasts, and T
cells.
Reductive carboxylate cycle CO2 fixation related
genes
Ubiquitinated proteins are targeted for proteolytic
degradation by the proteasome, where they are
unfolded and degraded to small peptides in an
3
52. p35_Alzheimers
53. GLUCO
54. FBW7
55. Arginine_and_Proline_
Metabolism
56. Tert
57. Eif2
58. IL12
59. Pgc1a
60. Human_CD34_Enriched_
Transcription_Factors
61. HDAC
62. Glycolosis_and_Gluconeogenesis
63. G2
64. PS1
65. CR CAM
66. Spry
67. Mitr
ATP-dependent process.
p35, a neuron-specific activator of cyclindependent kinase 5, is cleaved to p25 in
Alzheimer's disease and promotes
hyperphosphorylated tau formation and apoptosis.
Genes involved in glucose processing
Cyclin E interacts with cell cycle checkpoint kinase
cdk2 to allow transcription of genes required for S
phase, including transcription of additional cyclin
E.
Genes involved in arginie and proline metabolism
hTERC, the RNA subunit of telomerase, and
hTERT, the catalytic protein subunit, are required
for telomerase activity and are overexpressed in
many cancers.
Eukaryotic initiation factor 2 (EIF2) initiates
translation by transferring Met-tRNA to the 40S
ribosome in a GTP-dependent process.
IL12 and Stat4 Dependent Signaling Pathway in
Th1 Development
PCG-1a is expressed in skeletal muscle, heart
muscle, and brown fat, and is a coactivator for
receptors such as glucocorticoid receptor and
thyroid hormone receptor.
Human CD34 enriched transcription factors related
genes
Myocyte enhancer factor MEF2 activates
transcription of genes required for muscle cell
differentiation and is inhibited by histone
deacetylases.
Genes involved in glycolysis and gluconeogenesis
Activated Cdc2-cyclin B kinase regulates the G2/M
transition; DNA damage stimulates the DNAPK/ATM/ATR kinases, which inactivate Cdc2.
Presenilin is required for gamma-secretase activity
to activate Notch signaling; presenilin also inhibits
beta-catenin in the Wnt/Frizzled pathway.
PNAS 2002: Cancer related genes involved in cell
adhesion and metalloproteinases
Four members of the Sprouty protein family block
proliferative EGF signals by binding Grb-2,
preventing Ras and MAP kinase activation.
The MyoD/MEF2 transcription factors induce
muscle cell differentiation and are repressed by the
4
68. Ctla4
69. Bile_acid_biosynthesis
70. MalateX
71. Ndk_Dynamin
72. p53
73. Type_III_secretion_system
74. ATP_synthesis
75. ROS
76. TCA
77. VIP
78. Cdc25
79. RB
80. Arf
transcriptional repressor MITR.
T cell activation requires interaction with an
antigen-MHC-I complex on an antigen-presenting
cell (APC), as well as CD28 interaction with the
APC's CD80 or 86.
Genes involved in bile acid biosynthesis
The tricarboxylate transfer pathway shuttles acetyl
groups of acetyl-CoA between mitochondria and
the cytoplasm.
Synaptic vesicle endocytosis is coordinated by
dephosphins, which are coordinately
dephosphorylated on calmodulin- and calcineurinmodulated calcium influx.
p53 induces cell cycle arrest or apoptosis under
conditions of DNA damage.
Type III secretion system related genes
Genes involved in ATP synthesis
Reactive oxidative species related genes
Tricarboxylic acid related genes
Apoptosis of activated T cells is inhibited by
vasoactive intestinal peptide (VIP) and its relative
PACAP.
The protein phosphatase Cdc25 is phosphorylated
by Chk1 and activates Cdc2 to stimulate eukaryotic
cells into M phase.
The ATM protein kinase recognizes DNA damage
and blocks cell cycle progression by
phosphorylating chk1 and p53, which normally
inhibits Rb to allow G1/S transitions.
Cyclin-dependent kinase inhibitor 2A is a tumor
suppressor that induces G1 arrest and can activate
the p53 pathway, leading to G2/M arrest.
5