Supplemental Table 1. Primer Sequences for qPCR
DSC2 Forward: CTG ACC CTC GCG ATC TTAA TAT TT
DSC2 Reverse: GCA TCT AGT TTG GAG GGA ACA TG
DSC3 Forward: CCT GGC AAT AGA CAA AGA TGA TAG ATC
DSC3 Reverse: CTT GAA GTA TTT CTG GTG GAT TAT CAT TTT
ADCY1 Forward: CCT GCC AGG GAA GGT TCA TA
ADCY1 Reverse: CGT AAC CCG GTT CTA CCT CGT A
PDE4D Forward: GGT CAT TGA CAT CGT ACT TGC AA
PDE4D Reverse: TTA TCA AGA AGA AGA ACT CCA GAG CTT
ERO1L Forward: TGC TTC TGC CAG GGT AGT GGT TA
ERO1L Reverse: TGG GAA AAG CCT GTA GTT ATT AAA TCT
PPF1BP1 Forward: CTC CGT GGA CTT GGC AGA ATA T
PPF1BP1 Reverse: TCT AGA ACC ATG AGC CCA CCAT
TNIK Forward: GAC CTC ATC AAG AAC ACA AAA GGT AA
TNIK Reverse: TCA GCC CCC GTA AGA TTT CC
IRF5 Reverse: CTT CGA GAT CTT CTT CTG CTT TGG
IRF5 Forward: GCT ACA GGC ACC ACC TGT ACAG
HEBP2 Forward: CCC CAG CCC GGA AGT TA
HEBP2 Reverse: CCC GTC TGG ATG GCT GAAT
CR1 Forward: CAC ATG TGA AGT GAA ATC CTG TGA
CR1 Reverse: AGC TGG AGA TTT ACT GGA AAT AGCA
IRF5 Probe Set 3023264 FORWARD: 5’-ACT ACC AGT TGC TCC CAT GC
IRF5 Probe Set 3023264 REVERSE: 5’-ATT CCA CAC CCT TGC TTC AG
TNIK Forward: CGACACCCGCATGAGGAC
TNIK Forward: CGAATCAAAACGGGAATCCA
ERO1L Forward: TTA TCT AAG ATG GTT TCT GAG TGA A
ERO1L Reverse: CGC TAG TTT GAG AGA CTT AGA ACA
GLS Probe Set 2520346 Forward: TGT TTG GAT GAA ATT TGT G
GLS Probe Set 2520346 Reverse: CAA AAT GTA GGC ATA CTG GAA AA
Supplemental Table 2. Primer Sequences for Sequencing
Rs10488630 FORWARD: 5’-CCA ATA AAT CTG CAG GTC AGG
Rs10488630 REVERSE: 5’-AGGGAAGTGGTTCATTCTGC
Rs4728142 FORWARD: 5’- AGGCCATGTGAAGACAGAGC
Rs4728142 REVERSE: 5’-GCTTTGAAGTTTCTGGCACA
Rs10954214 ad rs10954213 Forward: CCAAGAACCTGGAGCAGAAA
Rs10954214 and rs10954213 Reverse: CACCTCGGGGGACAATATAA
Supplemental Table 3.
There were 222 genes with statistically significant Glucose Deprivation (GD) x Exon interaction
effects on expression after Bonferroni correction. The gene symbol, gene title, chromosome
(Chr), and p-value following Bonferroni correction is shown in the table below. Functional over-
representation analysis was performed on the set of genes, and the results are shown in
Supplemental Table 4.
Gene
Symbol
Gene Title
bonferroni
(pvalue(Glucose *
Exon ID))
Chr
KIF2C
kinesin family member 2C
0.00
1
C2orf28
chromosome 2 open reading frame 28
0.00
2
GLS
glutaminase
SMC4 structural maintenance of
chromosomes 4-like 1 (yeast)
interleukin enhancer binding factor 3, 90kDa
0.00
2
0.00
0.00
3
19
0.00
9
0.00
2
PFAS
outer dense fiber of sperm tails 2
phenylalanine-tRNA synthetase-like, beta
subunit
phosphoribosylformylglycinamidine synthase
(FGAR amidotransferase)
0.00
17
KDELC1
KDEL (Lys-Asp-Glu-Leu) containing 1
0.00
13
ATRN
0.00
20
MCM4
attractin
MCM4 minichromosome maintenance
deficient 4 (S. cerevisiae)
0.00
8
SFXN2
sideroflexin 2
0.00
10
ARID1A
AT rich interactive domain 1A (SWI- like)
ubiquitin-conjugating enzyme E2G 1 (UBC7
homolog, C. elegans)
0.00
1
0.00
1
0.00
3
ASPM
ATPase, Ca++ transporting, type 2C, member 1
asp (abnormal spindle)-like, microcephaly
associated (Drosophila)
0.00
1
CDK5RAP2
CDK5 regulatory subunit associated protein 2
0.00
9
PTHLH
RANBP5
parathyroid hormone-like hormone
RAN binding protein 5
0.00
0.00
12
13
SMC4L1
ILF3
ODF2
FARSLB
UBE2G1
ATP2C1
FC
1.5
5
1.2
9
1.3
5
1.6
8
1.3
1.1
9
1.4
1.2
3
1.4
4
1.2
9
1.4
6
1.5
2
1.2
3
1.3
1
1.3
4
1.8
7
1.3
2
1.1
9
1.3
TREX1
three prime repair exonuclease 1
0.00
3
SEPT9
septin 9
0.00
17
TMEM1
transmembrane protein 1
staufen, RNA binding protein, homolog 2
(Drosophila)
AU RNA binding protein
0.00
21
0.00
0.00
8
9
0.00
20
0.00
17
0.00
4
MYB
CGI-09 protein
chromodomain helicase DNA binding protein
3
coenzyme Q2 homolog, prenyltransferase
(yeast)
v-myb myeloblastosis viral oncogene homolog
(avian)
0.00
6
RERE
arginine-glutamic acid dipeptide (RE) repeats
0.00
1
AKAP8
A kinase (PRKA) anchor protein 8
0.00
19
KIAA0690
KIAA0690
0.00
10
KIAA2010
0.00
14
TRPM7
COL19A1
KIAA2010
transient receptor potential cation channel,
subfamily M, member 7
collagen, type XIX, alpha 1
0.00
0.00
15
6
WDSOF1
WD repeats and SOF1 domain containing
0.00
8
GLCCI1
glucocorticoid induced transcript 1
0.00
7
RAD1
RAD1 homolog (S. pombe)
0.00
5
LOC402521
0.00
THRAP2
hypothetical LOC402521
thyroid hormone receptor associated protein
2
0.00
12
KLHL9
kelch-like 9 (Drosophila)
0.00
9
C1orf22
chromosome 1 open reading frame 22
0.00
1
STAU2
AUH
CGI-09
CHD3
COQ2
8
0.9
9
0.9
3
1.2
3
1.3
4
1.1
1.3
1
1.2
7
1.5
1
2.0
5
1.0
8
1.2
4
1.3
1
1.3
4
1.3
4
1.4
1.2
4
1.1
8
1.5
8
1.3
4
1.5
1
1.3
5
1.6
6
KIF13B
kinesin family member 13B
0.00
8
BCS1L
BCS1-like (yeast)
0.00
2
UBP1
upstream binding protein 1 (LBP-1a)
0.00
3
LMNB1
lamin B1
phosphoinositide-3-kinase, regulatory subunit
2 (p85 beta)
0.00
5
0.00
19
0.00
4
0.00
11
ADAM10
SCC-112 protein
HMT1 hnRNP methyltransferase-like 3 (S.
cerevisiae)
a disintegrin and metalloproteinase domain
10
0.00
15
DATF1
death associated transcription factor 1
0.00
20
LYCAT
lysocardiolipin acyltransferase
0.00
2
CGI-119
0.00
12
GTF3C1
CDCA2
CGI-119 protein
general transcription factor IIIC, polypeptide
1, alpha 220kDa
cell division cycle associated 2
0.00
0.00
16
8
CTSO
cathepsin O
0.00
4
RPN2
ribophorin II
0.00
20
WDR33
WD repeat domain 33
0.00
2
PPIL2
peptidylprolyl isomerase (cyclophilin)-like 2
0.00
22
ZNF258
0.00
1
0.00
19
M11S1
zinc finger protein 258
aldehyde dehydrogenase 16 family, member
A1
membrane component, chromosome 11,
surface marker 1
0.00
11
TBC1D1
TBC1 (tre-2
0.00
4
ATXN1
ataxin 1
0.00
6
PIK3R2
SCC-112
HRMT1L3
ALDH16A1
1.2
2
1.1
9
1.2
5
1.3
6
1.0
5
1.3
2
1.4
4
1.2
6
1.1
8
1.3
4
1.4
7
1.2
1.7
1.5
3
1.2
9
1.2
4
1.2
6
1.0
9
1.1
7
1.1
8
1.2
6
1.1
6
PRKAG2
protein kinase, AMP-activated, gamma 2 noncatalytic subunit
0.00
7
0.00
6
0.00
12
ALDH5A1
F-box protein 30
Mdm2, transformed 3T3 cell double minute 2,
p53 binding protein (mouse)
aldehyde dehydrogenase 5 family, member A1
(succinate-semialdehyde dehydrogenase)
0.00
6
SHCBP1
SHC SH2-domain binding protein 1
0.00
16
H2AFX
H2A histone family, member X
0.00
11
TMEM48
transmembrane protein 48
0.00
1
CDW92
CDW92 antigen
0.00
9
SCARB2
0.00
4
GlyBP
scavenger receptor class B, member 2
glycine-, glutamate-,
thienylcyclohexylpiperidine-binding protein
0.00
1
TRIM24
tripartite motif-containing 24
0.00
7
USP50
ubiquitin specific protease 50
0.00
15
RAD23B
0.00
9
RUNX1
RAD23 homolog B (S. cerevisiae)
runt-related transcription factor 1 (acute
myeloid leukemia 1; aml1 oncogene)
0.00
21
DONSON
downstream neighbor of SON
0.00
21
DERP6
S-phase 2 protein
0.00
17
C13orf18
0.00
13
0.00
8
DDOST
chromosome 13 open reading frame 18
1-acylglycerol-3-phosphate O-acyltransferase
5 (lysophosphatidic acid acyltransferase,
epsilon)
dolichyl-diphosphooligosaccharide-protein
glycosyltransferase
0.00
1
SMARCA2
SWI
0.00
9
CCNA2
cyclin A2
0.00
4
FBXO30
MDM2
AGPAT5
1.1
4
1.3
9
1.2
4
1.4
6
1.7
6
1.2
7
1.7
4
1.3
8
1.6
3
1.1
5
1.2
2
1.2
2
1.2
1
1.1
7
1.1
7
1.1
1
1.2
8
1.3
6
1.1
3
1.3
9
1.5
9
PLXNC1
plexin C1
0.00
12
MIB1
mindbomb homolog 1 (Drosophila)
0.00
18
ALMS1
Alstrom syndrome 1
0.00
2
TOP1
topoisomerase (DNA) I
LanC lantibiotic synthetase component C-like
2 (bacterial)
0.00
20
0.00
7
0.00
2
0.00
9
SLC30A1
HCV NS3-transactivated protein 1
SMC5 structural maintenance of
chromosomes 5-like 1 (yeast)
solute carrier family 30 (zinc transporter),
member 1
0.00
1
WSB1
WD repeat and SOCS box-containing 1
0.00
17
EXOC7
0.00
17
SLC25A10
exocyst complex component 7
solute carrier family 25 (mitochondrial carrier;
dicarboxylate transporter), member 10
0.00
17
C10orf137
chromosome 10 open reading frame 137
0.00
10
MBNL3
muscleblind-like 3 (Drosophila)
source of immunodominant MHC-associated
peptides
chromosome 1 open reading frame 73
0.00
X
0.00
0.00
3
1
0.00
18
SPEN
thioredoxin-like 1
spen homolog, transcriptional regulator
(Drosophila)
0.00
1
SLBP
stem-loop (histone) binding protein
0.00
4
ANXA11
annexin A11
0.00
10
WDR77
0.00
1
NUDT21
WD repeat domain 77
nudix (nucleoside diphosphate linked moiety
X)-type motif 21
0.00
16
ZBTB40
CRR9
zinc finger and BTB domain containing 40
cisplatin resistance related protein CRR9p
0.00
0.00
1
5
LANCL2
NS3TP1
SMC5L1
SIMP
C1orf73
TXNL1
1.2
1.2
9
1.3
9
1.3
5
1.7
1.2
5
1.3
2
1.6
5
0.8
6
1.2
3
1.2
2
1.4
3
1.4
2
1.2
3
1.6
1.1
1
1.2
1
1.1
7
0.9
3
1.4
6
1.3
5
1.1
8
1.4
TOP2A
topoisomerase (DNA) II alpha 170kDa
0.00
17
PCTK2
0.00
12
0.00
14
0.00
7
0.00
21
CASP4
PCTAIRE protein kinase 2
bromodomain adjacent to zinc finger domain,
1A
MCM7 minichromosome maintenance
deficient 7 (S. cerevisiae)
1-acylglycerol-3-phosphate O-acyltransferase
3
caspase 4, apoptosis-related cysteine
protease
0.00
11
CAS1
O-acetyltransferase
0.00
7
E2F7
E2F transcription factor 7
0.00
12
CSRP2BP
0.00
20
0.00
6
PPRC1
CSRP2 binding protein
mitogen-activated protein kinase kinase
kinase 5
peroxisome proliferative activated receptor,
gamma, coactivator-related 1
0.00
10
ELL2
elongation factor, RNA polymerase II, 2
0.00
5
CHAF1B
0.00
21
ANLN
chromatin assembly factor 1, subunit B (p60)
anillin, actin binding protein (scraps homolog,
Drosophila)
0.00
7
THADA
thyroid adenoma associated
0.00
2
VCPIP1
valosin containing protein (p97)
0.00
8
NUP214
nucleoporin 214kDa
steroid sulfatase (microsomal), arylsulfatase C,
isozyme S
0.00
9
0.01
X
tubulin-specific chaperone d
CD44 antigen (homing function and Indian
blood group system)
BRF1 homolog, subunit of RNA polymerase III
transcription initiation factor IIIB (S. cerevisiae)
0.01
17
0.01
11
0.01
14
BAZ1A
MCM7
AGPAT3
MAP3K5
STS
TBCD
CD44
BRF1
7
1.9
3
1.2
5
1.2
7
1.4
5
1.1
2
1.0
8
1.6
1
1.4
7
1.3
8
1.3
1
1.3
3
1.3
4
1.3
9
1.7
1
1.4
4
1.2
8
1.2
2
1.5
1.1
7
1.1
1.0
9
0.01
0.01
3
2
SLC4A5
cyclin L1
hypothetical protein BC014022
solute carrier family 4, sodium bicarbonate
cotransporter, member 5
0.01
2
ZNF289
zinc finger protein 289, ID1 regulated
0.01
11
HIPK2
homeodomain interacting protein kinase 2
0.01
7
PCTP
phosphatidylcholine transfer protein
0.01
17
DYM
dymeclin
0.01
18
NKTR
natural killer-tumor recognition sequence
0.01
3
FBXO33
F-box protein 33
0.01
14
APRIN
androgen-induced proliferation inhibitor
0.01
13
BAG1
BCL2-associated athanogene
0.01
9
HIC1
C14orf101
hypermethylated in cancer 1
chromosome 14 open reading frame 101
0.01
0.01
17
14
DEPDC1B
C3orf23
DEP domain containing 1B
chromosome 3 open reading frame 23
0.01
0.01
5
3
ATAD2
ATPase family, AAA domain containing 2
ubiquitination factor E4B (UFD2 homolog,
yeast)
0.01
8
0.01
1
forkhead box M1
proteasome (prosome, macropain) 26S
subunit, non-ATPase, 1
0.01
12
0.01
2
melanoma antigen family F, 1
HIR histone cell cycle regulation defective
homolog A (S. cerevisiae)
BTAF1 RNA polymerase II, B-TFIID
transcription factor-associated, 170kDa (Mot1
homolog, S. cerevisiae)
leucyl-tRNA synthetase
0.01
3
0.01
22
1.0
8
1.2
1.1
6
1.1
5
1.0
9
1.2
5
1.0
7
1.3
1
1.3
1
1.5
1
1.0
8
1.2
1
1.3
1.5
2
1.4
1.6
5
1.1
6
1.5
2
1.3
8
1.1
5
1.2
3
0.01
0.01
10
5
1.1
5
1.1
CCNL1
LOC116143
UBE4B
FOXM1
PSMD1
MAGEF1
HIRA
BTAF1
LARS
ECT2
epithelial cell transforming sequence 2
oncogene
0.01
3
AQR
aquarius homolog (mouse)
0.01
15
ZNF318
zinc finger protein 318
0.01
6
TYMS
thymidylate synthetase
0.01
18
CASC5
cancer susceptibility candidate 5
0.01
15
DDX46
DEAD (Asp-Glu-Ala-Asp) box polypeptide 46
0.01
5
TH1L
0.01
20
HNRPDL
TH1-like (Drosophila)
heterogeneous nuclear ribonucleoprotein Dlike
0.01
4
ADCY1
adenylate cyclase 1 (brain)
0.02
7
FAM82A
family with sequence similarity 82, member A
0.02
2
LOC439991
DPYSL2
0.02
0.02
10
8
COCH
similar to D-PCa-2 protein
dihydropyrimidinase-like 2
coagulation factor C homolog, cochlin
(Limulus polyphemus)
0.02
14
SH3KBP1
SH3-domain kinase binding protein 1
0.02
X
GTSE1
G-2 and S-phase expressed 1
0.02
22
SEC23IP
SEC23 interacting protein
0.02
10
HRB
UBE3C
HIV-1 Rev binding protein
ubiquitin protein ligase E3C
0.02
0.02
2
7
MTMR10
myotubularin related protein 10
0.02
15
TARSL1
threonyl-tRNA synthetase-like 1
0.02
1
RREB1
ras responsive element binding protein 1
0.02
6
FADS1
fatty acid desaturase 1
0.02
11
8
1.6
3
1.4
1
1.1
7
1.4
3
2.0
6
1.6
3
1.2
6
1.2
2
1.3
4
1.3
3
0.9
8
1.3
1.2
9
1.0
7
1.4
6
1.2
7
1.1
4
1.2
1.2
8
1.0
8
1.0
4
0.6
6
SAMD9
sterile alpha motif domain containing 9
0.02
7
RANBP2
RAN binding protein 2
0.02
2
LOC441093
LOC441093
0.02
5
IDE
insulin-degrading enzyme
0.02
10
TTL
tubulin tyrosine ligase
0.02
2
CLSPN
claspin homolog (Xenopus laevis)
0.02
1
LOC159090
similar to hypothetical protein MGC17347
0.02
X
FANCD2
Fanconi anemia, complementation group D2
0.02
3
FSIP2
fibrous sheath interacting protein 2
UDP-GalNAc:betaGlcNAc beta 1,3galactosaminyltransferase, polypeptide 2
carbohydrate (N-acetylglucosamine-6-O)
sulfotransferase 2
0.02
2
0.03
1
0.03
3
0.03
11
CPSF2
tetratricopeptide repeat domain 12
cleavage and polyadenylation specific factor 2,
100kDa
0.03
14
RTN4
reticulon 4
0.03
2
STAG1
stromal antigen 1
0.03
3
DPF1
D4, zinc and double PHD fingers family 1
0.03
19
PB1
0.03
3
CYP20A1
polybromo 1
cytochrome P450, family 20, subfamily A,
polypeptide 1
0.03
2
DAZL
deleted in azoospermia-like
0.03
3
C9orf40
chromosome 9 open reading frame 40
0.03
9
APITD1
UBE2J1
apoptosis-inducing, TAF9-like domain 1
ubiquitin-conjugating enzyme E2, J1 (UBC6
0.03
0.03
1
6
B3GALNT2
CHST2
TTC12
1.2
6
1.4
4
1.7
7
1.4
1
1.2
9
1.7
4
1.3
1
1.5
9
1.4
3
1.2
1
1.1
5
1.5
2
1.3
1
1.1
1
1.5
2
1.1
3
1.4
3
1.6
1
1.3
5
1.1
4
1.2
1
1.3
FUBP1
homolog, yeast)
far upstream element (FUSE) binding protein
1
0.03
1
TA-PP2C
T-cell activation protein phosphatase 2C
0.03
12
PIPOX
pipecolic acid oxidase
0.03
17
CLTC
0.03
17
0.03
X
PLCG2
clathrin, heavy polypeptide (Hc)
Alport syndrome, mental retardation, midface
hypoplasia and elliptocytosis chromosomal
region, gene 1
phospholipase C, gamma 2
(phosphatidylinositol-specific)
0.04
16
EP300
E1A binding protein p300
0.04
22
TMEM30A
FLJ14681
transmembrane protein 30A
hypothetical protein FLJ14681
0.04
0.04
6
2
KIAA1280
KIAA1280 protein
0.04
X
RINT-1
Rad50-interacting protein 1
0.04
7
TMEM33
transmembrane protein 33
0.04
4
KIAA1961
KIAA1961 gene
0.04
5
GANAB
glucosidase, alpha; neutral AB
0.04
11
FLJ20257
hypothetical protein FLJ20257
0.04
7
ZBTB4
0.04
17
PLRG1
MAML1
zinc finger and BTB domain containing 4
pleiotropic regulator 1 (PRL1 homolog,
Arabidopsis)
mastermind-like 1 (Drosophila)
0.04
0.04
4
5
C6orf167
chromosome 6 open reading frame 167
0.04
6
ZNF664
zinc finger protein 664
0.05
12
ANKRD13C
TEF
ankyrin repeat domain 13C
thyrotrophic embryonic factor
0.05
0.05
1
22
AMMECR1
7
1.3
2
0.9
9
0.7
7
1.3
2
1.1
4
1.1
5
1.2
5
1.2
9
1.2
1.1
7
1.2
6
1.2
2
1.1
8
1.3
2
1.2
1
1.0
2
1.2
2
1
1.5
1
1.0
8
1.2
7
1.0
KLHL2
0.05
4
0.05
0.05
1
15
POLA2
kelch-like 2, Mayven (Drosophila)
protein O-linked mannose beta1,2-Nacetylglucosaminyltransferase
FLJ43276 protein
polymerase (DNA directed), alpha 2 (70kD
subunit)
0.05
11
NCOA7
nuclear receptor coactivator 7
0.05
6
POMGNT1
FLJ43276
8
1.2
8
1.0
8
1.4
1.4
1
1.3
1
Supplementary Figures 1-4. Significant Glucose Deprivation x Diagnosis x Exon interaction
effect on transcripts expression. For each gene, the top graph depicts transcript expression for
different exons during glucose deprivation and the bottom graph depicts transcript expression for
different exons under normal glucose conditions. The probe set number is shown on the x-axis,
and the average group expression on the y-axis.
Supplementary Figure 1. A.) There was a significant Glucose Deprivation x Diagnosis x Exon
Interaction effect on FBXW5 expression. B.) The probe set with the most significant Diagnosis
X Glucose interaction was probeset 3230531 (p = 0.007) and is depicted by dot plot. In control
subjects there was a significant increase in probe set expression following glucose deprivation (p
= 0.002). In contrast, in subjects with schizophrenia there was a trend toward a decrease in probe
set expression following glucose deprivation (p = 0.08).
A.)
B.)
Supplementary Figure 2. A.) There was a significant Glucose Deprivation X Diagnosis X Exon
Interaction Effect on PPARGC1B expression. B.) The probeset with the most significant
Diagnosis X Glucose interaction was probeset 2835214 (p = 0.006). Posthoc analysis revealed a
significant increase in probeset expression in subjects with schizophrenia following glucose
deprivation (p = 0.02).
A.)
B.)
Supplementary Figure 3. A.) There was a significant Glucose Deprivation X Diagnosis X Exon
Interaction Effect on PPP4R1 expression. B.) The probeset with the most significant Diagnosis X
Glucose interaction was probeset (p = 0.002). Posthoc analysis revealed a significant increase in
probeset expression in normal controls (p = 0.009) and a significant decrease in probeset
expression in subjects with schizophrenia (p = 0.02) in the glucose deprived condition compared
to the normal glucose condition.
Supplementary Figure 4. A.) There was a significant Glucose Deprivation x Diagnosis x Exon
Interaction Effect on KIAA1404 expression. B.) The probeset with the most significant
Diagnosis X Glucose interaction was probeset 3908875 (p = 0.002). There was a significant
increase in probeset expression in subjects with schizophrenia after glucose deprivation (p =
0.004) while in controls there was a significant decrease in probeset expression after glucose
deprivation. (p = 0.04).
A.)
B.)