Download Supplementary Table 5

R. A. Stone, et al.
Supplementary Table 5
Retinal Gene Profiling of Spectacle Lens Wear
page 1
Supplementary Table 5. Top Five Retinal/RPE Networks Generated by
Ingenuity, for 6 Hours or 3 Days of Minus Lens Wear
ID Molecules in Network (listed by gene symbol) *
Number of
Top Functions
Focus
of Network
Molecules
6 hours, minus lens wear
1
A2M ↓, ADNP ↓, BDNF↓, CAMKK1 ↓, CCAR1 ↓, CETN2 ↑,
DDB2 ↓, FBXW2 ↓, GFM1 ↓, GRID1 ↓, GRID2 ↓, GRIN2A ↓,
GRM5 ↓, HLA-DRB1 ↑, HNRNPA0 ↑, IRF2 ↓, JAK1 ↓,
KALRN ↓, KLF6 ↑, MAGI2 ↓, MAPKAPK2 ↑, MED10 ↑,
MED23 ↓, MTNR1A ↓, MYPN ↓, NEB ↓, NOS2 ↓, NUP153 ↓,
POLR2E ↑, RB1CC1 ↓, SHANK2 ↓, SMURF2 ↓, STAT1 ↓,
TPR ↓, VIP ↓
2
AKAP9 ↓, ANK2 ↓, ANK3↓, BCAR3 ↓, CACNG7, CASK ↓,
DDX24 ↓, EPB41L2 ↓, EPB41L3 ↓, EPHA7 ↓, EPHB6 ↓, GRIA3
↓, GRIA4 ↓, GRIK2 ↓, GRIP1 ↓, HECW1 ↓, HOOK1 ↓, ITPR1 ↓,
KIF5B ↓, KL ↑, MLLT4 ↓, NF1 ↓, NRXN2, SCN1A ↓, SCN1B,
SCN3A, SPTAN1 ↓, SPTBN1 ↓, SPTBN4, STARD13 ↓, TRAF3
↓, TRAF3IP1, USP7 ↓, USP9X ↓, ZMYND8 ↓
29
3
CAMKK1, CCDC88A, CEP250, CKAP5, CLASP1, CLASP2,
CLIP1, CLIP2, CRB3, DOCK7 (includes EG:85440), EPB41L2,
FAM190B, GAPVD1, HECTD1, HNRNPA2B1, KIF1B, LMO7,
MAPRE3, MPP5, MPP7, OFD1, PAFAH1B1, PARD3, PNN,
PPIG, SAV1, SFRS4, SFRS12, SHPRH, STK4, TARBP1
(includes EG:6894), TBC1D4, USP8, YWHAG, YWHAH
23
4
APC ↓, ARC, ASRGL1 ↓, C21ORF66 ↓, CACNG2 , CAPZA2,
CDH1, DCBLD2 ↓, DICER1 ↓, DLG4, DSCAM ↓, FAM171A1 ↓,
FMR1, FZD7, GRIA3 ↓, GRIK2 ↓, GRIN1 , GRIN2D, IQSEC1 ↓,
KALRN ↓, KCNA3, KCNA4 ↓, LIN7B, NLGN1 ↓, NLGN4X ↓,
NRXN1, PLCB4 ↓, SHANK2 ↓, SIPA1L1, SNTG1 ↓, SPTBN1 ↓,
TFAP2A, TFF3, TTC3 ↓, WNT7A
19
5
ACOX1, ANKRD11 ↓, APTX, BAZ2B ↓, BICD1, CEP290 ↓,
CEP350 ↓, CLOCK ↓, CORO2A, CRY2, CTBP2, DHX36 ↓,
DNM1L ↓, ESRRG , GSK3B, HES1 ↑, HEY2, HIVEP1 ↓, MKL1,
MKL2 ↓, MTA3, NCOA3 ↓, NCOR1 ↓, NIN ↓, NPAS2 ↓, NR1H2,
NR1H3 ↑, NRIP1 ↓, PER2, RPGR (includes EG:6103) ↓,
RPGRIP1, SPEN (includes EG:23013) ↓, TBL1X, TBL1XR1 ↓,
TIMELESS
35
Cell Signaling,
Small Molecule
Biochemistry,
Nervous System
Development and
Function
Neurological
Disease, Cell-ToCell Signaling and
Interaction,
Nervous System
Development and
Function
Cell Cycle,
Embryonic
Development, Hair
and Skin
Development and
Function
Nervous System
Development and
Function, Cell-ToCell Signaling and
Interaction,
Cellular Assembly
and Organization
19
Gene Expression,
Behavior, Nervous
System
Development and
Function
35
Gene Expression,
Cellular Growth
and Proliferation,
Organismal Injury
and Abnormalities
35
Cell Death,
Cellular Growth
3 days, minus lens wear
1
2
AMD1 ↓, ASCC3 ↓, ATP2A2 ↓, CREM ↓, CXCL14 ↓, DGCR6 ↑,
DIO2↓, DUSP4 ↓, EDF1 ↑, EGR1 ↓, FOSL2 ↓, GCLC ↓, IKBKAP
↑, IP6K2 ↓, JAZF1 ↓, JUN ↑, KCNIP4 , LAMP2 ↓, MAP3K7 ↓,
MXI1 ↓, NDRG1 ↓, PDE3A ↓, PLK2 ↑, PPP2R2A ↓, PSEN2 ↓,
PTGS2 ↓, SIK1 ↓, SRI ↓, STRADA ↓, TAB2 ↓, TAB3 ↓, TBL1X
↓, TIRAP ↑, TRIP4 ↑, UBE2J1 ↓
BCL2 ↓, BDNF ↓, C19ORF50 ↑, CCDC53 ↓, CCNL2 ↑, CHN2 ↓,
COL2A1 ↑, CRY1 ↓, FBF1 ↑, FBXO33 ↓, GAD2 ↓, HNRNPH3 ↓,
R. A. Stone, et al.
Supplementary Table 5
Retinal Gene Profiling of Spectacle Lens Wear
3
4
5
HSP90AB1 ↑, IFT20 ↑, KPNA1 ↓, KSR1 ↓, MAP2K2 ↑, MYH4 ↑,
NAE1 ↑, NAPB ↓, NPAS2 ↓, PDCD5 ↓, SLC16A7 ↓, SNAP25 ↓,
SNAP91 ↓, SRPK2 ↓, STX2 ↓, STXBP5 ↓, TP53BP2 ↓, TPM3 ↑,
UTP6 ↓, UTP14A ↑, WDR33 ↑, WTAP ↓, YWHAB ↓
ACTL6A ↓, ACTR6 ↓, ASH2L ↑, BTAF1 ↓, CTNNBIP1 ↓, DDB1
↑, DKC1 ↑, EP300 ↓, EXOC8 ↑, GDI2 ↓, HNRNPU ↓, INO80D ↑,
KAT2A ↑, MED1 ↑, NEIL1 ↑, NFYB ↓, NSFL1C ↑, PELO ↑,
POLB ↓, RAB8A ↓, RAD52 ↑, RNF4 ↓, RUVBL1 ↑, SFRS12 ↓,
TADA1 ↓, TADA2A ↑, TAF7 ↑, TAF11 ↑, TARBP1 (includes
EG:6894) ↓, TBP ↓, WDR5 ↑, WDR26 ↓, WDTC1 ↑, WRN
(includes EG:7486) ↑, XPA ↑
ACTA1 ↑, ADAM9 ↓, ARHGDIB ↑, BICD1 ↑, DCX ↓, FYN ↓,
GABRG2 ↓, GIT2 ↓, HNRNPAB ↑, ICMT ↑, LGALS8 ↓,
MAPK8IP3 ↓, PACSIN2 ↓, PRKAB2 ↑, PTK2 ↓, PTPN4 ↓,
PTPRA ↑, RAB14 ↓, RBBP4 ↑, RHOA↓, SCNN1A ↓, SEMA7A
↑, SH3PXD2A ↓, SHC3 ↓, SMARCB1 ↑, SNX9 (includes
EG:51429) ↓, SORBS1 ↓, SPEN (includes EG:23013) ↑,
SYNJ1 ↓, TJP1 ↓, USP9X ↓, WASF3 ↓, WASL (includes
EG:8976) ↓, WNK2 ↓, WWP1 ↓
C16ORF80 ↑, CCDC76 ↓, CCDC82 ↓, CDK5RAP3 (includes
EG:80279), COMMD9 ↓, E2F4, ECD ↓, FAIM2 ↑, FAS, FIG4 ↓,
HNF4A, ISOC1 ↓, KLHDC3 ↑, MRPL37 ↑, PEMT ↑, PEX3,
PEX16 ↑, PGM3 ↑, PRKAB1, SMAD3, TIMM17A (includes
EG:10440) ↑, UFM1 ↓, VHL, VIPAR ↑
page 2
and Proliferation,
Cell Morphology
35
DNA Replication,
Recombination,
and Repair, Gene
Expression, Amino
Acid Metabolism
35
Cellular Assembly
and Organization,
Cell-To-Cell
Signaling and
Interaction,
Cellular Movement
16
Cellular Assembly
and Organization,
Cell Death,
Carbohydrate
Metabolism
* Molecules differentially expressed by transcriptome profiling are identified in bold font within
each network; these molecules are termed “focus molecules” by Ingenuity. The molecules in
non-bold font are inserted by Ingenuity from its database to create networks but were not
identified as differentially expressed by the retina/RPE profiling. Arrows indicate the direction of
differential expression of each gene in the lens wearing eye relative to its contralateral control
eye.