Induced Lysosomal Genes

1 Supplemental Table 2: Functional Classes of Induced Genes in HeLa/16E6 Cells

Plexin / Semaphorin / Integrin Class (p = 9.6E-5)

Fold Entrez Gene Gene Symbol Description Induced 6.1 3696 ITGB8 Integrin, beta 8 5.3 10512 SEMA3C Semaphorin 3C 3.4 3675 ITGA3 Integrin, alpha 3 3.4 754 PTTG1IP Pituitary tumor-transforming 1 interacting protein 2.5 7869 SEMA3B Semaphorin 3B 2.3 3693 ITGB5 Integrin, beta 5 2.2 6405 SEMA3F Semaphorin 3F

Electron Transport Activity Class (p = 4.9E-4)

Fold Entrez Gene Gene Symbol Description Induced 3.1 231 AKR1B1 Aldo-keto reductase family 1, member B1 (aldose reductase) 2.7 444 ASPH Aspartate beta-hydroxylase 2.5 1645 AKR1C1 Aldo-keto reductase family 1, member C1 2.5 51706 CYB5R1 Cytochrome b5 reductase 1 2.3 5034 P4HB Procollagen-proline, 2-oxoglutarate 4-dioxygenase, beta polypeptide 2.2 5351 PLOD1 Procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1 2.1 5066 PAM Peptidylglycine alpha-amidating monooxygenase 2.1 2745 GLRX Glutaredoxin (thioltransferase) 2.0 7296 TXNRD1 Thioredoxin reductase 1 2.0 5264 PHYH Phytanoyl-CoA hydroxylase (Refsum disease) 2.0 85015 MGC14793 Hypothetical protein MGC14793

Transporter Activity Class (p = 1.2E-3)

Fold Entrez Gene Gene Symbol Description Induced 5.2 9635 CLCA2 Chloride channel, calcium activated, family member 2 5.0 8714 ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 4.1 60598 KCNK15 Potassium channel, subfamily K, member 15 (TASK-5) 3.3 54881 TEX10 Testis expressed gene 10 3.1 231 AKR1B1 Aldo-keto reductase family 1, member B1 (aldose reductase) 2.7 Clone IMAGE:1338238 2.7 444 ASPH Aspartate beta-hydroxylase 2.6 9429 ABCG2 ATP-binding cassette, sub-family G (WHITE), member 2 2.5 1645 AKR1C1 Aldo-keto reductase family 1, member C1 2.5 51706 CYB5R1 Cytochrome b5 reductase 1 2.5 57088 PLSCR4 Phospholipid scramblase 4 2.5 GRIA3 Glutamate receptor, ionotrophic, AMPA 3 2.4 5002 SLC22A18 Solute carrier family 22 member 18, transcript variant 1 2.3 5034 P4HB Procollagen-proline, 2-oxoglutarate 4-dioxygenase, beta polypeptide 2.2 5351 PLOD1 Procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1 2.2 10762 NUP50 Nucleoporin 50 kDa 2.2 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide 2.1 57582 KCNT1 Potassium channel, subfamily T, member 1 2 2.1 ABCG1 ATP-binding cassette, sub-family G (WHITE), member 1 2.1 51000 SLC35B3 Solute carrier family 35, member B3 2.1 5066 PAM Peptidylglycine alpha-amidating monooxygenase 2.1 2745 GLRX Glutaredoxin (thioltransferase) 2.1 537 ATP6S1 ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1 2.1 Homo sapiens cDNA FLJ30906 fis, clone FEBRA2006055 2.0 57192 MCOLN1 Mucolipin 1 2.0 7296 TXNRD1 Thioredoxin reductase 1 2.0 6262 RYR2 Ryanodine receptor 2 (cardiac) 2.0 5264 PHYH Phytanoyl-CoA hydroxylase (Refsum disease) 2.0 85015 MGC14793 Hypothetical protein MGC14793

Endoplasmic Reticulum Class (p = 2.2E-3)

Fold Entrez Gene Gene Symbol Description Induced 4.0 285362 SUMF1 Sulfatase modifying factor 1 3.0 3303 HSPA1A Heat shock 70kD protein 1A 2.8 23385 NCSTN Nicastrin 2.7 444 ASPH Aspartate beta-hydroxylase 2.5 7869 SEMA3B Semaphorin 3B 2.5 6319 SCD Stearoyl-CoA desaturase (delta-9-desaturase) 2.5 1543 CYP1A1 Cytochrome P450, family 1, subfamily A, polypeptide 1 2.4 BAC clone RP11-613E4 from 7 2.3 5034 P4HB Procollagen-proline, 2-oxoglutarate 4-dioxygenase, beta polypeptide 2.2 2052 EPHX1 Epoxide hydrolase 1, microsomal (xenobiotic) 2.2 5351 PLOD1 Procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1 2.2 4043 LRPAP1 Low density lipoprotein receptor-related protein associated protein 1 2.1 224 ALDH3A2 Aldehyde dehydrogenase 3 family, member A2 2.1 9619 ABCG1 ATP-binding cassette, sub-family G (WHITE), member 1 2.1 10550 ARL6IP5 ADP-ribosylation-like factor 6 interacting protein 5

Calcium Binding Class (p = 2.4E-3)

Fold Entrez Gene Gene Symbol Description Induced 7.2 3906 LALBA Lactalbumin, alpha 4.0 285362 SUMF1 Sulfatase modifying factor 1 3.5 6840 SVIL Supervillin 3.4 3675 ITGA3 Integrin, alpha 3 2.7 444 ASPH Aspartate beta-hydroxylase 2.5 57088 PLSCR4 Phospholipid scramblase 4 2.4 92737 cDNA DKFZp761G02121 (from clone DKFZp761G02121) 2.4 BAC clone RP11-613E4 from 7 2.4 414 cDNA FLJ11410 fis, clone HEMBA1000852 2.2 301 ANXA1 Annexin A1 2.2 4043 LRPAP1 Low density lipoprotein receptor-related protein associated protein 1 2.1 1953 MEGF6 Multiple EGF-like-domains 6 2.1 57582 KCNT1 Potassium channel, subfamily T, member 1 2.1 6281 S100A10 S100 calcium binding protein A10 2.1 4636 MYL5 Myosin, light polypeptide 5, regulatory 2.0 57192 MCOLN1 Mucolipin 1 3 2.0 667 DST Dystonin 2.0 307 ANXA4 Annexin A4 2.0 6262 RYR2 Ryanodine receptor 2 (cardiac)

Protease Class (5.2E-3)

Fold Entrez Gene Gene Symbol Description Induced 8.1 1675 DF D component of complement (adipsin) 3.6 629 BF Complement factor B, properdin 3.1 1509 CTSD Cathepsin D (lysosomal aspartyl protease) 2.8 6768 ST14 Suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin) 2.6 8754 ADAM9 A disintegrin and metalloproteinase domain 9 (meltrin gamma) 2.6 1508 CTSB Cathepsin B 2.4 6590 SLPI Secretory leukocyte protease inhibitor (antileukoproteinase) 2.3 1200 CLN2 Ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease) 2.2 5972 REN Renin 2.1 5654 PRSS11 Protease, serine, 11 (IGF binding) 2.0 85015 MGC14793 Hypothetical protein MGC14793

Oxidoreductase Activity Class (p = 6.6E-3)

Fold Entrez Gene Gene Symbol Description Induced 3.1 231 AKR1B1 Aldo-keto reductase family 1, member B1 (aldose reductase) 2.7 444 ASPH Aspartate beta-hydroxylase 2.5 1645 AKR1C1 Aldo-keto reductase family 1, member C1 2.5 6319 SCD Stearoyl-CoA desaturase (delta-9-desaturase) 2.5 1543 CYP1A1 Cytochrome P450, family 1, subfamily A, polypeptide 1 2.3 2495 FTH1 Ferritin, heavy polypeptide 1 2.3 51449 PCYOX1 Prenylcysteine oxidase 1 2.2 5351 PLOD1 Procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1 2.1 224 ALDH3A2 Aldehyde dehydrogenase 3 family, member A2 2.1 5066 PAM Peptidylglycine alpha-amidating monooxygenase 2.0 7296 TXNRD1 Thioredoxin reductase 1 2.0 5264 PHYH Phytanoyl-CoA hydroxylase (Refsum disease)

Complement Pathway Class (p = 6.8E-3)

Fold Entrez Gene Gene Symbol Description Induced 8.1 1675 DF D component of complement (adipsin) 3.6 629 BF Complement factor B, properdin 2.5 718 C3 Complement component 3 2.1 1191 CLU Clusterin