SCZ 2018 - Brain_Substantia_nigra
sheng Qian
2021-2-6
Last updated: 2022-05-19
Checks: 5 2
Knit directory: cTWAS_analysis/
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library(reticulate)
use_python("/scratch/midway2/shengqian/miniconda3/envs/PythonForR/bin/python",required=T)Weight QC
#number of imputed weights
nrow(qclist_all)[1] 15170#number of imputed weights by chromosome
table(qclist_all$chr)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1400 1082 880 623 588 770 877 489 649 714 913 791 301 549 531 626
17 18 19 20 21 22
1040 214 1116 542 34 441 #number of imputed weights without missing variants
sum(qclist_all$nmiss==0)[1] 13605#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)[1] 0.8968INFO:numexpr.utils:Note: NumExpr detected 56 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.finish
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionCheck convergence of parameters
| Version | Author | Date |
|---|---|---|
| 2749be9 | sq-96 | 2022-05-12 |
gene snp
0.0065597 0.0003205 gene snp
9.522 10.339 [1] 105318[1] 6278 6309950 gene snp
0.003723 0.198505 [1] 0.005031 1.088938Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
1685 DPYSL3 5_86 0.7628 23.36 1.291e-04 4.157 1 1
619 BDNF 11_19 0.7481 22.63 1.203e-04 4.348 1 1
5949 VPS41 7_28 0.5915 25.12 8.533e-05 -4.509 2 2
2308 GON4L 1_76 0.5783 27.63 8.773e-05 4.084 1 1
3192 MDK 11_28 0.5743 45.88 1.437e-04 7.159 1 1
241 AKT3 1_128 0.5675 34.01 1.146e-04 -6.291 6 6
4280 PTK2B 8_27 0.5262 26.09 6.880e-05 4.730 2 3
905 CASP2 7_89 0.5094 21.33 5.255e-05 -3.889 1 1
564 B3GAT1 11_84 0.4936 31.39 9.343e-05 -4.516 6 10
5880 UQCRC2 16_19 0.4789 22.53 4.905e-05 4.716 1 1
1513 DBF4B 17_26 0.4679 21.91 4.589e-05 -3.890 2 2
3022 LRP8 1_33 0.4353 32.61 1.042e-04 -4.624 6 6
1361 CRTAP 3_24 0.4343 20.01 6.921e-05 3.929 2 2
1067 CECR2 22_2 0.4330 20.33 3.620e-05 3.928 1 1
5465 THAP8 19_25 0.4107 20.21 6.381e-05 3.847 2 2
523 ATP2B2 3_8 0.3965 32.48 4.850e-05 4.158 1 1
3861 PBXIP1 1_76 0.3474 24.41 2.797e-05 -4.591 1 1
919 CBWD1 9_1 0.3442 22.78 2.562e-05 3.736 1 1
380 APOPT1 14_54 0.3413 44.24 1.124e-04 7.429 6 9
5564 TMEM219 16_24 0.3359 45.65 4.891e-05 -7.020 1 1Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_intron num_sqtl
3192 MDK 11_28 0.5743 45.88 1.437e-04 7.159 1 1
1685 DPYSL3 5_86 0.7628 23.36 1.291e-04 4.157 1 1
619 BDNF 11_19 0.7481 22.63 1.203e-04 4.348 1 1
241 AKT3 1_128 0.5675 34.01 1.146e-04 -6.291 6 6
380 APOPT1 14_54 0.3413 44.24 1.124e-04 7.429 6 9
3022 LRP8 1_33 0.4353 32.61 1.042e-04 -4.624 6 6
564 B3GAT1 11_84 0.4936 31.39 9.343e-05 -4.516 6 10
2308 GON4L 1_76 0.5783 27.63 8.773e-05 4.084 1 1
5949 VPS41 7_28 0.5915 25.12 8.533e-05 -4.509 2 2
1361 CRTAP 3_24 0.4343 20.01 6.921e-05 3.929 2 2
4280 PTK2B 8_27 0.5262 26.09 6.880e-05 4.730 2 3
5465 THAP8 19_25 0.4107 20.21 6.381e-05 3.847 2 2
905 CASP2 7_89 0.5094 21.33 5.255e-05 -3.889 1 1
5880 UQCRC2 16_19 0.4789 22.53 4.905e-05 4.716 1 1
5564 TMEM219 16_24 0.3359 45.65 4.891e-05 -7.020 1 1
2166 FXR1 3_111 0.2203 42.91 4.863e-05 -6.873 4 4
523 ATP2B2 3_8 0.3965 32.48 4.850e-05 4.158 1 1
1513 DBF4B 17_26 0.4679 21.91 4.589e-05 -3.890 2 2
4024 PLCB2 15_14 0.3091 24.42 4.023e-05 4.470 3 4
3706 NT5C2 10_66 0.2890 46.96 3.989e-05 -8.541 8 11Comparing z scores and PIPs
[1] 0.01434 genename region_tag susie_pip mu2 PVE z num_intron
3948 PGBD1 6_22 2.685e-02 155.68 6.492e-07 -13.087 2
1537 DDR1 6_25 5.752e-02 100.79 6.737e-06 11.175 3
2118 FLOT1 6_24 2.330e-02 77.49 1.883e-06 -10.944 5
692 BTN3A2 6_20 5.101e-02 88.48 2.308e-06 -10.665 4
574 BAG6 6_26 2.117e-05 160.21 9.162e-13 -10.247 5
984 CCHCR1 6_25 9.344e-03 62.23 1.192e-07 -9.378 5
2347 GPSM3 6_26 1.690e-06 118.03 3.202e-15 -9.377 1
6126 ZKSCAN3 6_22 1.027e-02 55.20 6.722e-08 -9.321 3
3706 NT5C2 10_66 2.890e-01 46.96 3.989e-05 -8.541 8
4651 RP5-874C20.8 6_22 9.524e-03 45.29 8.981e-08 -8.313 4
3090 MAD1L1 7_3 1.916e-01 62.14 2.905e-05 8.215 4
463 AS3MT 10_66 2.347e-01 44.47 2.347e-05 8.051 3
6270 ZSCAN16 6_22 1.249e-02 52.38 1.093e-07 7.468 3
380 APOPT1 14_54 3.413e-01 44.24 1.124e-04 7.429 6
3192 MDK 11_28 5.743e-01 45.88 1.437e-04 7.159 1
209 AIF1 6_26 6.555e-03 59.25 4.835e-08 -7.131 5
5564 TMEM219 16_24 3.359e-01 45.65 4.891e-05 -7.020 1
1581 DGKZ 11_28 1.388e-01 43.55 7.970e-06 -6.964 1
2643 INO80E 16_24 1.831e-01 44.02 1.567e-05 -6.917 4
2166 FXR1 3_111 2.203e-01 42.91 4.863e-05 -6.873 4
num_sqtl
3948 2
1537 3
2118 5
692 4
574 7
984 8
2347 1
6126 3
3706 11
4651 5
3090 6
463 3
6270 3
380 9
3192 1
209 5
5564 1
1581 2
2643 5
2166 4GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 8Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
Term
1 positive regulation of neuron projection development (GO:0010976)
2 positive regulation of cell projection organization (GO:0031346)
3 regulation of neuron projection development (GO:0010975)
4 negative regulation of neuron apoptotic process (GO:0043524)
5 regulation of neuron apoptotic process (GO:0043523)
6 negative regulation of neuron death (GO:1901215)
7 positive regulation of vascular endothelial cell proliferation (GO:1905564)
8 regulation of vascular endothelial cell proliferation (GO:1905562)
9 negative regulation of apoptotic process (GO:0043066)
10 regulation of leukocyte chemotaxis (GO:0002688)
11 regulation of macrophage chemotaxis (GO:0010758)
12 negative regulation of ossification (GO:0030279)
13 regulation of actin cytoskeleton reorganization (GO:2000249)
14 positive regulation of cell-substrate adhesion (GO:0010811)
15 positive regulation of endothelial cell proliferation (GO:0001938)
16 regulation of cell migration (GO:0030334)
17 positive regulation of endothelial cell migration (GO:0010595)
18 regulation of actin cytoskeleton organization (GO:0032956)
19 positive regulation of epithelial cell proliferation (GO:0050679)
20 regulation of cell adhesion (GO:0030155)
21 enzyme linked receptor protein signaling pathway (GO:0007167)
22 regulation of cell differentiation (GO:0045595)
23 positive regulation of neutrophil extravasation (GO:2000391)
24 late endosome to lysosome transport (GO:1902774)
25 regulation of inflammatory response to wounding (GO:0106014)
26 regulation of inositol trisphosphate biosynthetic process (GO:0032960)
27 endothelin receptor signaling pathway (GO:0086100)
28 negative regulation of regulatory T cell differentiation (GO:0045590)
29 activation of Janus kinase activity (GO:0042976)
30 positive regulation of non-membrane spanning protein tyrosine kinase activity (GO:1903997)
31 negative regulation of cardiac muscle cell apoptotic process (GO:0010667)
32 leukocyte chemotaxis involved in inflammatory response (GO:0002232)
33 regulation of hepatocyte proliferation (GO:2000345)
34 positive regulation of receptor binding (GO:1900122)
35 regulation of neutrophil extravasation (GO:2000389)
36 regulation of inositol phosphate biosynthetic process (GO:0010919)
37 marginal zone B cell differentiation (GO:0002315)
38 regulation of bone remodeling (GO:0046850)
39 nucleobase catabolic process (GO:0046113)
40 regulation of non-membrane spanning protein tyrosine kinase activity (GO:1903995)
41 negative regulation of striated muscle cell apoptotic process (GO:0010664)
42 positive regulation of oligodendrocyte differentiation (GO:0048714)
43 pyrimidine nucleobase catabolic process (GO:0006208)
44 regulation of collateral sprouting (GO:0048670)
45 endosomal vesicle fusion (GO:0034058)
46 positive regulation of cell motility (GO:2000147)
47 apoptotic process (GO:0006915)
48 bone resorption (GO:0045453)
49 ionotropic glutamate receptor signaling pathway (GO:0035235)
50 regulation of receptor binding (GO:1900120)
51 adrenal gland development (GO:0030325)
52 nerve growth factor signaling pathway (GO:0038180)
53 regulation of macrophage migration (GO:1905521)
54 regulation of epithelial cell apoptotic process (GO:1904035)
55 positive regulation of signal transduction (GO:0009967)
56 cellular response to interleukin-2 (GO:0071352)
57 positive regulation of cellular extravasation (GO:0002693)
58 regulation of cardiac muscle cell apoptotic process (GO:0010665)
59 positive regulation of keratinocyte proliferation (GO:0010838)
60 interleukin-2-mediated signaling pathway (GO:0038110)
61 cellular component assembly (GO:0022607)
62 positive regulation of cell migration (GO:0030335)
63 actin crosslink formation (GO:0051764)
64 regulation of sequestering of calcium ion (GO:0051282)
65 pyrimidine nucleobase metabolic process (GO:0006206)
66 regulation of leukocyte cell-cell adhesion (GO:1903037)
67 mitochondrial genome maintenance (GO:0000002)
68 positive regulation of neuron migration (GO:2001224)
69 negative regulation of cellular senescence (GO:2000773)
70 regulation of leukocyte adhesion to vascular endothelial cell (GO:1904994)
71 mature B cell differentiation involved in immune response (GO:0002313)
72 negative regulation of myotube differentiation (GO:0010832)
73 negative regulation of potassium ion transport (GO:0043267)
74 negative regulation of bone mineralization (GO:0030502)
75 negative regulation of T cell differentiation (GO:0045581)
76 positive regulation of macrophage chemotaxis (GO:0010759)
77 neurotrophin TRK receptor signaling pathway (GO:0048011)
78 peptidyl-tyrosine autophosphorylation (GO:0038083)
79 oogenesis (GO:0048477)
80 positive regulation of leukocyte adhesion to vascular endothelial cell (GO:1904996)
81 regulation of establishment of cell polarity (GO:2000114)
82 negative regulation of cell aging (GO:0090344)
83 pyrimidine-containing compound catabolic process (GO:0072529)
84 positive regulation of smooth muscle cell migration (GO:0014911)
85 positive regulation of cartilage development (GO:0061036)
86 positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)
87 positive regulation of synaptic transmission, glutamatergic (GO:0051968)
88 positive regulation of excitatory postsynaptic potential (GO:2000463)
89 regulation of cartilage development (GO:0061035)
90 positive regulation of glial cell differentiation (GO:0045687)
91 response to axon injury (GO:0048678)
92 positive regulation of lymphocyte chemotaxis (GO:0140131)
93 regulation of establishment or maintenance of cell polarity (GO:0032878)
94 positive regulation of neutrophil chemotaxis (GO:0090023)
95 negative regulation of striated muscle cell differentiation (GO:0051154)
96 regulation of oligodendrocyte differentiation (GO:0048713)
97 positive regulation of macrophage migration (GO:1905523)
98 regulation of granulocyte chemotaxis (GO:0071622)
99 regulation of tissue remodeling (GO:0034103)
100 positive regulation of lymphocyte differentiation (GO:0045621)
101 negative regulation of response to wounding (GO:1903035)
102 extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)
103 long-term synaptic potentiation (GO:0060291)
104 neurotrophin signaling pathway (GO:0038179)
105 positive regulation of neural precursor cell proliferation (GO:2000179)
106 negative regulation of biomineral tissue development (GO:0070168)
107 positive regulation of neutrophil migration (GO:1902624)
108 cellular response to nerve growth factor stimulus (GO:1990090)
109 positive regulation of granulocyte chemotaxis (GO:0071624)
110 negative regulation of myeloid cell differentiation (GO:0045638)
111 positive regulation of protein phosphorylation (GO:0001934)
112 regulation of calcium ion transmembrane transport (GO:1903169)
113 regulation of mononuclear cell migration (GO:0071675)
114 regulation of neural precursor cell proliferation (GO:2000177)
115 positive regulation of morphogenesis of an epithelium (GO:1905332)
116 negative regulation of programmed cell death (GO:0043069)
117 lymphocyte activation involved in immune response (GO:0002285)
118 regulation of keratinocyte proliferation (GO:0010837)
119 endocrine system development (GO:0035270)
120 regulation of proteolysis involved in cellular protein catabolic process (GO:1903050)
121 negative regulation of ion transport (GO:0043271)
122 regulation of myotube differentiation (GO:0010830)
123 regulation of neutrophil chemotaxis (GO:0090022)
124 peripheral nervous system development (GO:0007422)
125 phosphorylation (GO:0016310)
126 regulation of regulatory T cell differentiation (GO:0045589)
127 glial cell development (GO:0021782)
128 positive regulation of filopodium assembly (GO:0051491)
129 regulation of chondrocyte differentiation (GO:0032330)
130 transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)
131 modulation of excitatory postsynaptic potential (GO:0098815)
132 positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)
133 T cell activation involved in immune response (GO:0002286)
134 positive regulation of response to wounding (GO:1903036)
135 positive regulation of synapse assembly (GO:0051965)
136 regulation of neuron migration (GO:2001222)
137 positive regulation of leukocyte migration (GO:0002687)
138 positive regulation of lipid kinase activity (GO:0090218)
139 regulation of cellular senescence (GO:2000772)
140 positive regulation of leukocyte cell-cell adhesion (GO:1903039)
141 regulation of potassium ion transport (GO:0043266)
142 activation of phospholipase C activity (GO:0007202)
143 regulation of cell migration involved in sprouting angiogenesis (GO:0090049)
144 regulation of NMDA receptor activity (GO:2000310)
145 nervous system development (GO:0007399)
146 actin filament bundle assembly (GO:0051017)
147 actin filament bundle organization (GO:0061572)
148 positive regulation of receptor signaling pathway via JAK-STAT (GO:0046427)
149 regulation of protein localization to cell surface (GO:2000008)
150 female gamete generation (GO:0007292)
151 positive regulation of interleukin-12 production (GO:0032735)
152 regulation of trans-synaptic signaling (GO:0099177)
153 regulation of phosphatidylinositol 3-kinase activity (GO:0043551)
154 positive regulation of cell population proliferation (GO:0008284)
155 positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)
156 regulation of ossification (GO:0030278)
157 negative regulation of epithelial cell apoptotic process (GO:1904036)
158 glutamate receptor signaling pathway (GO:0007215)
159 regulation of apoptotic signaling pathway (GO:2001233)
160 regulation of T cell differentiation (GO:0045580)
161 protein phosphorylation (GO:0006468)
162 regulation of filopodium assembly (GO:0051489)
163 positive regulation of protein tyrosine kinase activity (GO:0061098)
164 regulation of ubiquitin-dependent protein catabolic process (GO:2000058)
165 positive regulation of epithelial to mesenchymal transition (GO:0010718)
166 positive regulation of axonogenesis (GO:0050772)
167 positive regulation of phospholipase C activity (GO:0010863)
168 cellular response to retinoic acid (GO:0071300)
169 positive regulation of T cell differentiation (GO:0045582)
170 positive regulation of cell-matrix adhesion (GO:0001954)
171 positive regulation of nervous system development (GO:0051962)
172 positive regulation of chemotaxis (GO:0050921)
173 regulation of synaptic transmission, glutamatergic (GO:0051966)
174 regulation of cellular protein localization (GO:1903827)
175 epidermal growth factor receptor signaling pathway (GO:0007173)
176 regulation of synapse assembly (GO:0051963)
177 positive regulation of cell-cell adhesion (GO:0022409)
178 positive regulation of blood vessel endothelial cell migration (GO:0043536)
179 cellular response to mechanical stimulus (GO:0071260)
180 negative regulation of cell projection organization (GO:0031345)
181 cellular defense response (GO:0006968)
182 positive regulation of actin filament polymerization (GO:0030838)
183 positive regulation of cell morphogenesis involved in differentiation (GO:0010770)
184 negative regulation of cellular process (GO:0048523)
185 intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)
186 regulation of substrate adhesion-dependent cell spreading (GO:1900024)
187 regulation of interleukin-12 production (GO:0032655)
188 regulation of release of sequestered calcium ion into cytosol (GO:0051279)
189 sprouting angiogenesis (GO:0002040)
190 positive regulation of developmental growth (GO:0048639)
191 plasma membrane bounded cell projection morphogenesis (GO:0120039)
192 positive regulation of leukocyte chemotaxis (GO:0002690)
193 regulation of blood vessel endothelial cell migration (GO:0043535)
194 chemokine-mediated signaling pathway (GO:0070098)
195 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)
196 peptidyl-tyrosine modification (GO:0018212)
197 positive regulation of cell junction assembly (GO:1901890)
198 regulation of bone mineralization (GO:0030500)
199 positive regulation of protein binding (GO:0032092)
200 regulation of neurotransmitter receptor activity (GO:0099601)
201 negative regulation of neuron projection development (GO:0010977)
202 Notch signaling pathway (GO:0007219)
203 cellular response to chemokine (GO:1990869)
204 positive regulation of cellular process (GO:0048522)
205 negative regulation of response to stimulus (GO:0048585)
206 response to retinoic acid (GO:0032526)
207 regulation of cell-matrix adhesion (GO:0001952)
208 mitotic G1 DNA damage checkpoint signaling (GO:0031571)
209 ERBB signaling pathway (GO:0038127)
210 cellular response to nutrient levels (GO:0031669)
211 vascular endothelial growth factor receptor signaling pathway (GO:0048010)
212 regulation of myeloid cell differentiation (GO:0045637)
213 synapse assembly (GO:0007416)
214 positive regulation of protein polymerization (GO:0032273)
215 peptidyl-tyrosine phosphorylation (GO:0018108)
216 gland development (GO:0048732)
217 extrinsic apoptotic signaling pathway (GO:0097191)
218 negative regulation of cell adhesion (GO:0007162)
219 regulation of actin filament polymerization (GO:0030833)
220 positive regulation of synaptic transmission (GO:0050806)
221 positive regulation of JNK cascade (GO:0046330)
222 DNA damage response, signal transduction by p53 class mediator (GO:0030330)
223 positive regulation of T cell activation (GO:0050870)
224 integrin-mediated signaling pathway (GO:0007229)
225 regulation of epithelial to mesenchymal transition (GO:0010717)
226 negative regulation of apoptotic signaling pathway (GO:2001234)
227 regulation of neuron differentiation (GO:0045664)
228 positive regulation of cell adhesion (GO:0045785)
229 activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)
230 positive regulation of cytoskeleton organization (GO:0051495)
231 positive regulation of plasma membrane bounded cell projection assembly (GO:0120034)
232 regulation of apoptotic process (GO:0042981)
233 regulation of cation channel activity (GO:2001257)
234 positive regulation of inflammatory response (GO:0050729)
235 regulation of endothelial cell migration (GO:0010594)
236 positive regulation of supramolecular fiber organization (GO:1902905)
237 T cell activation (GO:0042110)
238 regulation of peptidyl-tyrosine phosphorylation (GO:0050730)
239 regulation of endothelial cell proliferation (GO:0001936)
240 positive regulation of peptidyl-serine phosphorylation (GO:0033138)
241 positive regulation of epithelial cell migration (GO:0010634)
242 protein maturation (GO:0051604)
243 positive regulation of defense response (GO:0031349)
244 regulation of peptidyl-serine phosphorylation (GO:0033135)
245 positive regulation of stress-activated MAPK cascade (GO:0032874)
Overlap Adjusted.P.value Genes
1 4/88 7.562e-06 BDNF;MDK;DPYSL3;PTK2B
2 4/117 1.197e-05 BDNF;MDK;DPYSL3;PTK2B
3 4/165 3.179e-05 BDNF;MDK;DPYSL3;PTK2B
4 3/71 1.855e-04 BDNF;MDK;PTK2B
5 3/98 3.274e-04 BDNF;MDK;PTK2B
6 3/98 3.274e-04 BDNF;MDK;PTK2B
7 2/13 4.872e-04 MDK;AKT3
8 2/18 7.468e-04 MDK;AKT3
9 4/485 7.468e-04 BDNF;MDK;CASP2;PTK2B
10 2/19 7.468e-04 MDK;PTK2B
11 2/22 9.165e-04 MDK;PTK2B
12 2/24 1.003e-03 MDK;PTK2B
13 2/37 2.229e-03 MDK;PTK2B
14 2/70 7.457e-03 MDK;PTK2B
15 2/77 8.421e-03 MDK;AKT3
16 3/408 8.554e-03 MDK;DPYSL3;PTK2B
17 2/86 9.264e-03 AKT3;PTK2B
18 2/91 9.793e-03 MDK;PTK2B
19 2/123 1.689e-02 MDK;AKT3
20 2/133 1.874e-02 MDK;PTK2B
21 2/140 1.975e-02 BDNF;PTK2B
22 2/156 2.144e-02 BDNF;MDK
23 1/5 2.144e-02 MDK
24 1/5 2.144e-02 VPS41
25 1/5 2.144e-02 MDK
26 1/5 2.144e-02 PTK2B
27 1/5 2.144e-02 PTK2B
28 1/5 2.144e-02 MDK
29 1/6 2.144e-02 PTK2B
30 1/6 2.144e-02 BDNF
31 1/6 2.144e-02 MDK
32 1/6 2.144e-02 MDK
33 1/6 2.144e-02 MDK
34 1/6 2.144e-02 BDNF
35 1/6 2.144e-02 MDK
36 1/7 2.189e-02 PTK2B
37 1/7 2.189e-02 PTK2B
38 1/7 2.189e-02 MDK
39 1/7 2.189e-02 DPYSL3
40 1/7 2.189e-02 BDNF
41 1/8 2.216e-02 MDK
42 1/8 2.216e-02 MDK
43 1/8 2.216e-02 DPYSL3
44 1/8 2.216e-02 BDNF
45 1/8 2.216e-02 VPS41
46 2/221 2.216e-02 MDK;PTK2B
47 2/231 2.225e-02 CASP2;PTK2B
48 1/9 2.225e-02 PTK2B
49 1/10 2.225e-02 PTK2B
50 1/10 2.225e-02 BDNF
51 1/10 2.225e-02 MDK
52 1/10 2.225e-02 BDNF
53 1/10 2.225e-02 PTK2B
54 1/10 2.225e-02 MDK
55 2/252 2.225e-02 BDNF;PTK2B
56 1/11 2.225e-02 PTK2B
57 1/11 2.225e-02 MDK
58 1/11 2.225e-02 MDK
59 1/11 2.225e-02 MDK
60 1/11 2.225e-02 PTK2B
61 2/261 2.225e-02 DPYSL3;PTK2B
62 2/269 2.225e-02 MDK;PTK2B
63 1/12 2.225e-02 DPYSL3
64 1/12 2.225e-02 PTK2B
65 1/12 2.225e-02 DPYSL3
66 1/12 2.225e-02 MDK
67 1/12 2.225e-02 AKT3
68 1/13 2.225e-02 MDK
69 1/13 2.225e-02 AKT3
70 1/13 2.225e-02 MDK
71 1/13 2.225e-02 PTK2B
72 1/13 2.225e-02 BDNF
73 1/13 2.225e-02 PTK2B
74 1/14 2.301e-02 PTK2B
75 1/14 2.301e-02 MDK
76 1/14 2.301e-02 MDK
77 1/15 2.402e-02 BDNF
78 1/15 2.402e-02 PTK2B
79 1/16 2.416e-02 MDK
80 1/16 2.416e-02 MDK
81 1/16 2.416e-02 PTK2B
82 1/17 2.416e-02 AKT3
83 1/17 2.416e-02 DPYSL3
84 1/17 2.416e-02 MDK
85 1/18 2.416e-02 MDK
86 1/18 2.416e-02 AKT3
87 1/18 2.416e-02 PTK2B
88 1/18 2.416e-02 PTK2B
89 1/18 2.416e-02 MDK
90 1/18 2.416e-02 MDK
91 1/18 2.416e-02 DPYSL3
92 1/18 2.416e-02 PTK2B
93 1/18 2.416e-02 PTK2B
94 1/19 2.445e-02 MDK
95 1/19 2.445e-02 BDNF
96 1/19 2.445e-02 MDK
97 1/19 2.445e-02 MDK
98 1/20 2.494e-02 MDK
99 1/20 2.494e-02 MDK
100 1/20 2.494e-02 MDK
101 1/21 2.494e-02 MDK
102 1/21 2.494e-02 CASP2
103 1/21 2.494e-02 PTK2B
104 1/21 2.494e-02 BDNF
105 1/22 2.494e-02 MDK
106 1/22 2.494e-02 PTK2B
107 1/22 2.494e-02 MDK
108 1/22 2.494e-02 BDNF
109 1/22 2.494e-02 MDK
110 1/22 2.494e-02 PTK2B
111 2/371 2.494e-02 BDNF;PTK2B
112 1/23 2.494e-02 PTK2B
113 1/23 2.494e-02 MDK
114 1/23 2.494e-02 MDK
115 1/23 2.494e-02 MDK
116 2/381 2.512e-02 CASP2;PTK2B
117 1/24 2.512e-02 MDK
118 1/24 2.512e-02 MDK
119 1/24 2.512e-02 MDK
120 1/25 2.512e-02 PTK2B
121 1/25 2.512e-02 PTK2B
122 1/25 2.512e-02 BDNF
123 1/25 2.512e-02 MDK
124 1/25 2.512e-02 BDNF
125 2/400 2.512e-02 AKT3;PTK2B
126 1/26 2.512e-02 MDK
127 1/26 2.512e-02 MDK
128 1/26 2.512e-02 DPYSL3
129 1/26 2.512e-02 MDK
130 2/404 2.532e-02 BDNF;PTK2B
131 1/27 2.565e-02 PTK2B
132 1/28 2.565e-02 PTK2B
133 1/28 2.565e-02 MDK
134 1/28 2.565e-02 MDK
135 1/28 2.565e-02 BDNF
136 1/28 2.565e-02 MDK
137 1/29 2.637e-02 MDK
138 1/30 2.708e-02 PTK2B
139 1/31 2.738e-02 AKT3
140 1/31 2.738e-02 MDK
141 1/31 2.738e-02 PTK2B
142 1/32 2.755e-02 BDNF
143 1/32 2.755e-02 AKT3
144 1/32 2.755e-02 PTK2B
145 2/447 2.755e-02 BDNF;MDK
146 1/33 2.757e-02 DPYSL3
147 1/33 2.757e-02 DPYSL3
148 1/33 2.757e-02 PTK2B
149 1/33 2.757e-02 BDNF
150 1/34 2.803e-02 MDK
151 1/34 2.803e-02 MDK
152 1/35 2.847e-02 BDNF
153 1/35 2.847e-02 PTK2B
154 2/474 2.872e-02 MDK;PTK2B
155 1/36 2.872e-02 MDK
156 1/36 2.872e-02 MDK
157 1/37 2.913e-02 MDK
158 1/37 2.913e-02 PTK2B
159 1/38 2.973e-02 BDNF
160 1/39 3.026e-02 MDK
161 2/496 3.026e-02 AKT3;PTK2B
162 1/41 3.147e-02 DPYSL3
163 1/42 3.162e-02 BDNF
164 1/42 3.162e-02 PTK2B
165 1/42 3.162e-02 MDK
166 1/43 3.162e-02 BDNF
167 1/43 3.162e-02 BDNF
168 1/43 3.162e-02 PTK2B
169 1/43 3.162e-02 MDK
170 1/44 3.216e-02 PTK2B
171 1/45 3.250e-02 BDNF
172 1/45 3.250e-02 MDK
173 1/46 3.284e-02 PTK2B
174 1/46 3.284e-02 BDNF
175 1/47 3.298e-02 PTK2B
176 1/47 3.298e-02 BDNF
177 1/47 3.298e-02 MDK
178 1/48 3.343e-02 AKT3
179 1/49 3.343e-02 CASP2
180 1/49 3.343e-02 DPYSL3
181 1/49 3.343e-02 PTK2B
182 1/49 3.343e-02 PTK2B
183 1/50 3.378e-02 MDK
184 2/566 3.378e-02 MDK;PTK2B
185 1/51 3.378e-02 CASP2
186 1/51 3.378e-02 MDK
187 1/51 3.378e-02 MDK
188 1/52 3.378e-02 PTK2B
189 1/52 3.378e-02 PTK2B
190 1/52 3.378e-02 BDNF
191 1/52 3.378e-02 BDNF
192 1/54 3.489e-02 MDK
193 1/55 3.534e-02 AKT3
194 1/56 3.543e-02 PTK2B
195 1/56 3.543e-02 CASP2
196 1/56 3.543e-02 PTK2B
197 1/57 3.569e-02 BDNF
198 1/57 3.569e-02 PTK2B
199 1/58 3.577e-02 BDNF
200 1/58 3.577e-02 PTK2B
201 1/58 3.577e-02 DPYSL3
202 1/60 3.662e-02 MDK
203 1/60 3.662e-02 PTK2B
204 2/625 3.687e-02 MDK;PTK2B
205 1/61 3.687e-02 AKT3
206 1/62 3.728e-02 PTK2B
207 1/65 3.869e-02 PTK2B
208 1/65 3.869e-02 CASP2
209 1/66 3.890e-02 PTK2B
210 1/66 3.890e-02 VPS41
211 1/67 3.930e-02 PTK2B
212 1/68 3.969e-02 PTK2B
213 1/69 3.971e-02 BDNF
214 1/69 3.971e-02 PTK2B
215 1/69 3.971e-02 PTK2B
216 1/71 4.065e-02 MDK
217 1/72 4.084e-02 CASP2
218 1/73 4.084e-02 MDK
219 1/73 4.084e-02 PTK2B
220 1/73 4.084e-02 PTK2B
221 1/73 4.084e-02 PTK2B
222 1/74 4.120e-02 CASP2
223 1/75 4.138e-02 MDK
224 1/75 4.138e-02 PTK2B
225 1/76 4.174e-02 MDK
226 1/78 4.263e-02 BDNF
227 1/79 4.298e-02 BDNF
228 1/80 4.333e-02 MDK
229 1/81 4.367e-02 CASP2
230 1/82 4.401e-02 PTK2B
231 1/83 4.434e-02 DPYSL3
232 2/742 4.475e-02 CASP2;PTK2B
233 1/89 4.669e-02 PTK2B
234 1/89 4.669e-02 MDK
235 1/89 4.669e-02 PTK2B
236 1/91 4.743e-02 PTK2B
237 1/92 4.743e-02 MDK
238 1/92 4.743e-02 PTK2B
239 1/92 4.743e-02 AKT3
240 1/93 4.774e-02 BDNF
241 1/94 4.805e-02 PTK2B
242 1/97 4.935e-02 CASP2
243 1/98 4.944e-02 MDK
244 1/98 4.944e-02 BDNF
245 1/99 4.973e-02 PTK2B
[1] "GO_Cellular_Component_2021"
Term Overlap
1 NMDA selective glutamate receptor complex (GO:0017146) 1/8
2 apical dendrite (GO:0097440) 1/10
3 dendrite (GO:0030425) 2/270
Adjusted.P.value Genes
1 0.04337 PTK2B
2 0.04337 PTK2B
3 0.04337 BDNF;PTK2B
[1] "GO_Molecular_Function_2021"
Term
1 growth factor activity (GO:0008083)
2 dihydropyrimidinase activity (GO:0004157)
3 NMDA glutamate receptor activity (GO:0004972)
4 cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)
5 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)
6 filamin binding (GO:0031005)
7 cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)
8 death receptor binding (GO:0005123)
9 cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)
10 receptor ligand activity (GO:0048018)
11 ionotropic glutamate receptor activity (GO:0004970)
12 protein serine/threonine kinase activity (GO:0004674)
13 calmodulin-dependent protein kinase activity (GO:0004683)
14 non-membrane spanning protein tyrosine kinase activity (GO:0004715)
15 SH3 domain binding (GO:0017124)
16 ligand-gated cation channel activity (GO:0099094)
Overlap Adjusted.P.value Genes
1 2/87 0.01236 BDNF;MDK
2 1/6 0.01479 DPYSL3
3 1/8 0.01479 PTK2B
4 1/10 0.01479 CASP2
5 1/10 0.01479 DPYSL3
6 1/11 0.01479 DPYSL3
7 1/13 0.01479 CASP2
8 1/15 0.01479 BDNF
9 1/15 0.01479 CASP2
10 2/307 0.01479 BDNF;MDK
11 1/17 0.01479 PTK2B
12 2/344 0.01542 AKT3;PTK2B
13 1/24 0.01765 PTK2B
14 1/35 0.02386 PTK2B
15 1/62 0.03926 DPYSL3
16 1/80 0.04734 PTK2BDisGeNET enrichment analysis for genes with PIP>0.5
Description FDR Ratio BgRatio
28 Profound Mental Retardation 0.002809 3/6 139/9703
36 Mental Retardation, Psychosocial 0.002809 3/6 139/9703
124 Mental deficiency 0.002809 3/6 139/9703
49 Status Epilepticus 0.009790 2/6 68/9703
73 Petit mal status 0.009790 2/6 67/9703
80 Grand Mal Status Epilepticus 0.009790 2/6 67/9703
86 Complex Partial Status Epilepticus 0.009790 2/6 67/9703
120 Status Epilepticus, Subclinical 0.009790 2/6 67/9703
121 Non-Convulsive Status Epilepticus 0.009790 2/6 67/9703
122 Simple Partial Status Epilepticus 0.009790 2/6 67/9703WebGestalt enrichment analysis for genes with PIP>0.5
Warning: replacing previous import 'lifecycle::last_warnings' by
'rlang::last_warnings' when loading 'hms'Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...Warning in oraEnrichment(interestGeneList, referenceGeneList, geneSet, minNum =
minNum, : No significant gene set is identified based on FDR 0.05!NULL
Sensitivity, specificity and precision for silver standard genes
#number of genes in known annotations
print(length(known_annotations))[1] 130#number of genes in known annotations with imputed expression
print(sum(known_annotations %in% ctwas_gene_res$genename))[1] 42#significance threshold for TWAS
print(sig_thresh)[1] 4.466#number of ctwas genes
length(ctwas_genes)[1] 0#number of TWAS genes
length(twas_genes)[1] 90#show novel genes (ctwas genes with not in TWAS genes)
ctwas_gene_res[ctwas_gene_res$genename %in% novel_genes,report_cols][1] genename region_tag susie_pip mu2 PVE z num_intron
[8] num_sqtl
<0 rows> (or 0-length row.names)#sensitivity / recall
print(sensitivity) ctwas TWAS
0.00000 0.07692 #specificity
print(specificity) ctwas TWAS
1.0000 0.9872 #precision / PPV
print(precision) ctwas TWAS
NaN 0.1111
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.4.0 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.3 tidyverse_1.3.1 tibble_3.1.7
[9] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0 cowplot_1.1.1
[13] ggplot2_3.3.5 dplyr_1.0.7 reticulate_1.25 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 doParallel_1.0.16 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 doRNG_1.8.2
[9] bslib_0.2.5.1 utf8_1.2.1 R6_2.5.0 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.2 ggrastr_1.0.1
[17] tidyselect_1.1.1 processx_3.5.2 curl_4.3.2 compiler_4.1.0
[21] git2r_0.28.0 rvest_1.0.0 cli_3.0.0 Cairo_1.5-15
[25] xml2_1.3.2 labeling_0.4.2 sass_0.4.0 scales_1.1.1
[29] callr_3.7.0 systemfonts_1.0.4 apcluster_1.4.9 digest_0.6.27
[33] rmarkdown_2.9 svglite_2.0.0 pkgconfig_2.0.3 htmltools_0.5.1.1
[37] dbplyr_2.1.1 highr_0.9 rlang_1.0.2 rstudioapi_0.13
[41] jquerylib_0.1.4 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[45] magrittr_2.0.1 Matrix_1.3-3 ggbeeswarm_0.6.0 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.0 stringi_1.6.2
[53] whisker_0.4 yaml_2.2.1 plyr_1.8.6 grid_4.1.0
[57] ggrepel_0.9.1 parallel_4.1.0 promises_1.2.0.1 crayon_1.4.1
[61] lattice_0.20-44 haven_2.4.1 hms_1.1.0 knitr_1.33
[65] ps_1.6.0 pillar_1.7.0 igraph_1.2.6 rjson_0.2.20
[69] rngtools_1.5 reshape2_1.4.4 codetools_0.2-18 reprex_2.0.0
[73] glue_1.4.2 evaluate_0.14 getPass_0.2-2 modelr_0.1.8
[77] data.table_1.14.0 png_0.1-7 vctrs_0.3.8 httpuv_1.6.1
[81] foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[85] xfun_0.24 broom_0.7.8 later_1.2.0 iterators_1.0.13
[89] beeswarm_0.4.0 ellipsis_0.3.2 here_1.0.1