Background
Methods
Subjects
MRI of brain
RNA and array processing
Analysis of predicted DAS
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Yijklm represents the mth observation on the ith Group, jth Batch, kth MarkerID, lth SampleID.
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μ is the common effect for the whole experiment.
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ϵijklm represents the random error present in the mth observation on the ith Group, jth Batch, kth MarkerID, lth SampleID. The errors ϵijklm are assumed to be normally and independently distributed with mean 0 and standard deviation δ for all measurements.
Hierarchical clustering and principal component analyses
Functional pathways associated with DAS in ASD
Results
Participants’ characteristics
TD | ASD | ASD Normal TCV | ASD Enlarged TCV | |
---|---|---|---|---|
n
| ||||
Subjects | 20 | 30 | 20 | 10 |
Age (years) | ||||
Mean ± SD | 3.0 ± 0.3 | 2.9 ± 0.4 | 3.0 ± 0.5 | 3.1 ± 0.2 |
Gender | ||||
Male, n (%) | 20 (100%) | 30 (100%) | 20 (100%) | 10 (100%) |
Race, n (%) | ||||
White | 14 (70%) | 15 (50%) | 11(55%) | 4 (40%) |
Black | 0 (0%) | 3 (10%) | 2 (10%) | 1 (10%) |
Asian | 0 (0%) | 1 (3%) | 1 (5%) | 0 (0%) |
Other | 0 (0%) | 1 (3%) | 1 (5%) | 0 (0%) |
Mixed | 3 (15%) | 2 (7%) | 1(5%) | 1 (10%) |
Unknown | 3 (15%) | 8 (27%) | 4 (20%) | 4 (40%) |
TCV (cm3) | ||||
Mean ± SD | 994.8 ± 65.0 | 1049.7 ± 87.4 | 997.7 ± 51.0 | 1153.7 ± 33.6 |
ADOS Severity Score | ||||
Mean ± SD | NA | 8.0 ± 1.7 | 8.3 ± 1.7 | 7.4 ± 1.6 |
Developmental quotient (DQ) | ||||
Mean ± SD | 106.6 ± 14.0 | 60.2 ± 22.7 | 61.4 ± 20.9 | 57.7 ± 27.0 |
Verbal quotient (VQ) | ||||
Mean ± SD | 109.5 ± 15.6 | 53.6 ± 28.2 | 54.4 ± 25.9 | 52.1 ± 33.8 |
Nonverbal quotient (NVQ) | ||||
Mean ± SD | 103.6 ± 14.6 | 66.7 ± 19.9 | 68.4 ± 18.9 | 63.3 ± 22.5 |
DAS/DEU in ASD groups compared to TD
Gene symbol | Gene title | FDR P(DAS) |
---|---|---|
CDK13 | Cyclin-dependent kinase 13 | 5.50E-05 |
USP48 | Ubiquitin specific peptidase 48 | 1.11E-03 |
SFPQ | Splicing factor proline/glutamine-rich | 1.11E-03 |
FXR1 | Fragile X mental retardation, autosomal homolog 1 | 1.11E-03 |
C19orf6 | Chromosome 19 open reading frame 6 | 1.85E-03 |
CAT | Catalase | 1.85E-03 |
ZNF330 | Zinc finger protein 330 | 1.85E-03 |
C19orf2 | Chromosome 19 open reading frame 2 | 1.85E-03 |
TARS2 | Threonyl-tRNA synthetase 2, mitochondrial (putative) | 3.66E-03 |
LRPPRC | Leucine-rich PPR-motif containing | 3.86E-03 |
PIK3C3 | Phosphoinositide-3-kinase, class 3 | 4.65E-03 |
CLTB | Clathrin, light chain B | 5.13E-03 |
SOD2 | Superoxide dismutase 2, mitochondrial | 6.11E-03 |
OS9 | Osteosarcoma amplified 9, endoplasmic reticulum lectin | 6.11E-03 |
ACPT | Acid phosphatase, testicular | 6.71E-03 |
PPP2R2A | Protein phosphatase 2, regulatory subunit B, alpha | 1.05E-02 |
C14orf159 | Chromosome 14 open reading frame 159 | 1.05E-02 |
FGR | Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog | 1.09E-02 |
GSN | Gelsolin | 1.09E-02 |
EAPP | E2F-associated phosphoprotein | 1.22E-02 |
PIP4K2A | Phosphatidylinositol-5-phosphate 4-kinase, type II, alpha | 1.24E-02 |
TADA3 | Transcriptional adaptor 3 | 1.65E-02 |
PRSS36 | Protease, serine, 36 | 2.17E-02 |
HELQ | Helicase, POLQ-like | 2.17E-02 |
EMD | Emerin | 2.47E-02 |
C1orf175 | Chromosome 1 open reading frame 175 | 2.77E-02 |
AEBP2 | AE binding protein 2 | 2.86E-02 |
R3HDM1 | R3H domain containing 1 | 2.96E-02 |
SRPK1 | Serine/arginine-rich splicing factor kinase 1 | 3.29E-02 |
LEF1 | Lymphoid enhancer-binding factor 1 | 3.29E-02 |
MPHOSPH10 | M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprote | 3.29E-02 |
PRDX1 | Peroxiredoxin 1 | 3.29E-02 |
MPP1 | Membrane protein, palmitoylated 1, 55kDa | 3.29E-02 |
CNOT2 | CCR4-NOT transcription complex, subunit 2 | 3.53E-02 |
GOLGA7 | Golgin A7 | 3.53E-02 |
WDR67 | WD repeat domain 67 | 3.61E-02 |
AAMP | Angio-associated, migratory cell protein | 4.10E-02 |
KLHL9 | Kelch-like 9 (Drosophila) | 4.24E-02 |
CC2D1A | Coiled-coil and C2 domain containing 1A | 4.49E-02 |
STAT4 | Signal transducer and activator of transcription 4 | 4.49E-02 |
DHX29 | DEAH (Asp-Glu-Ala-His) box polypeptide 29 | 4.51E-02 |
MGST3 | Microsomal glutathione S-transferase 3 | 4.51E-02 |
TEPP | Testis, prostate, and placenta expressed | 4.51E-02 |
UTRN | Utrophin | 4.51E-02 |
PUM2 | Pumilio homolog 2 (Drosophila) | 4.51E-02 |
CHID1 | Chitinase domain containing 1 | 4.51E-02 |
GFER | Growth factor, augmenter of liver regeneration | 4.51E-02 |
RPGR | Retinitis pigmentosa GTPase regulator | 4.51E-02 |
SUCLA2 | Succinate-CoA ligase, ADP-forming, beta subunit | 4.72E-02 |
ZNF512B | Zinc finger protein 512B | 4.72E-02 |
MORN2 | MORN repeat containing 2 | 4.72E-02 |
DNAJC17 | DnaJ (Hsp40) homolog, subfamily C, member 17 | 4.88E-02 |
FGD3 | FYVE, RhoGEF and PH domain containing 3 | 4.88E-02 |
Gene symbol | Gene title | FDR P(DAS) |
---|---|---|
TMEM204 | Transmembrane protein 204 | 2.26E-05 |
SRSF2IP | Splicing factor, arginine/serine-rich 2-interacting protein | 7.17E-05 |
PPP1R10 | Protein phosphatase 1, regulatory (inhibitor) subunit 10 | 4.19E-04 |
ATXN7L3B | Ataxin 7-like 3B | 1.52E-03 |
HPS1 | Hermansky-Pudlak syndrome 1 | 1.90E-03 |
ANKRD44 | Ankyrin repeat domain 44 | 4.46E-03 |
EXOG | Endo/exonuclease (5'-3'), endonuclease G-like | 5.11E-03 |
ZNF493 | Zinc finger protein 493 | 1.51E-02 |
DHX29 | DEAH (Asp-Glu-Ala-His) box polypeptide 29 | 1.57E-02 |
HOOK2 | Hook homolog 2 (Drosophila) | 2.02E-02 |
IL12RB2 | Interleukin 12 receptor, beta 2 | 2.14E-02 |
BAT3 | HLA-B associated transcript 3 | 2.53E-02 |
DVL3 | Dishevelled, dsh homolog 3 (Drosophila) | 2.53E-02 |
RAB7A | RAB7A, member RAS oncogene family | 2.53E-02 |
TNFRSF14 | Tumor necrosis factor receptor superfamily, member 14 | 2.53E-02 |
PPIP5K2 | Diphosphoinositol pentakisphosphate kinase 2 | 2.67E-02 |
NDST1 | N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 | 3.26E-02 |
DPH2 | DPH2 homolog (S. cerevisiae) | 3.71E-02 |
PDP1 | Pyruvate dehyrogenase phosphatase catalytic subunit 1 | 3.71E-02 |
TGFB1I1 | Transforming growth factor beta 1 induced transcript 1 | 4.14E-02 |
UBA6 | Ubiquitin-like modifier activating enzyme 6 | 4.41E-02 |
SLC38A5 | Solute carrier family 38, member 5 | 4.42E-02 |
PLCD3 | Phospholipase C, delta 3 | 4.45E-02 |
COL15A1 | Collagen, type XV, alpha 1 | 4.47E-02 |
KDELR3 | KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein | 4.47E-02 |
BIRC3 | Baculoviral IAP repeat-containing 3 | 4.47E-02 |
ALOX15 | Arachidonate 15-lipoxygenase | 4.47E-02 |