Gene Page: TRAPPC4
Summary ?
| GeneID | 51399 |
| Symbol | TRAPPC4 |
| Synonyms | CGI-104|HSPC172|PTD009|SBDN|SYNBINDIN|TRS23 |
| Description | trafficking protein particle complex 4 |
| Reference | MIM:610971|HGNC:HGNC:19943|Ensembl:ENSG00000196655|HPRD:18220|Vega:OTTHUMG00000166351 |
| Gene type | protein-coding |
| Map location | 11q23.3 |
| Pascal p-value | 0.01 |
| Sherlock p-value | 0.93 |
| Fetal beta | 0.743 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Nishioka_2013 | Genome-wide DNA methylation analysis | The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. | 1 |
| GSMA_I | Genome scan meta-analysis | Psr: 0.006 | |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 3 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg22307649 | 11 | 118889171 | TRAPPC4 | -0.025 | 0.26 | DMG:Nishioka_2013 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs58709307 | 11 | 118877563 | TRAPPC4 | ENSG00000196655.5 | 1.109E-6 | 0.01 | -12290 | gtex_brain_ba24 |
| rs11606357 | 11 | 118878222 | TRAPPC4 | ENSG00000196655.5 | 1.066E-6 | 0.01 | -11631 | gtex_brain_ba24 |
| rs7120445 | 11 | 118879285 | TRAPPC4 | ENSG00000196655.5 | 1.731E-6 | 0.01 | -10568 | gtex_brain_ba24 |
| rs11825284 | 11 | 118880012 | TRAPPC4 | ENSG00000196655.5 | 1.73E-6 | 0.01 | -9841 | gtex_brain_ba24 |
| rs11607569 | 11 | 118880668 | TRAPPC4 | ENSG00000196655.5 | 2.099E-6 | 0.01 | -9185 | gtex_brain_ba24 |
| rs60065241 | 11 | 118883491 | TRAPPC4 | ENSG00000196655.5 | 3.019E-6 | 0.01 | -6362 | gtex_brain_ba24 |
| rs10111 | 11 | 118886117 | TRAPPC4 | ENSG00000196655.5 | 1.614E-6 | 0.01 | -3736 | gtex_brain_ba24 |
| rs7131534 | 11 | 118886656 | TRAPPC4 | ENSG00000196655.5 | 1.728E-6 | 0.01 | -3197 | gtex_brain_ba24 |
| rs7121270 | 11 | 118887568 | TRAPPC4 | ENSG00000196655.5 | 4.057E-6 | 0.01 | -2285 | gtex_brain_ba24 |
| rs7105187 | 11 | 118887581 | TRAPPC4 | ENSG00000196655.5 | 2.729E-6 | 0.01 | -2272 | gtex_brain_ba24 |
| rs11217124 | 11 | 118889132 | TRAPPC4 | ENSG00000196655.5 | 4.002E-6 | 0.01 | -721 | gtex_brain_ba24 |
| rs11217125 | 11 | 118889185 | TRAPPC4 | ENSG00000196655.5 | 2.692E-6 | 0.01 | -668 | gtex_brain_ba24 |
| rs4938621 | 11 | 118892277 | TRAPPC4 | ENSG00000196655.5 | 1.072E-6 | 0.01 | 2424 | gtex_brain_ba24 |
| rs117289748 | 11 | 118892757 | TRAPPC4 | ENSG00000196655.5 | 2.448E-6 | 0.01 | 2904 | gtex_brain_ba24 |
| rs143660533 | 11 | 118892759 | TRAPPC4 | ENSG00000196655.5 | 2.448E-6 | 0.01 | 2906 | gtex_brain_ba24 |
| rs61179449 | 11 | 118892835 | TRAPPC4 | ENSG00000196655.5 | 1.072E-6 | 0.01 | 2982 | gtex_brain_ba24 |
| rs58955701 | 11 | 118892872 | TRAPPC4 | ENSG00000196655.5 | 1.072E-6 | 0.01 | 3019 | gtex_brain_ba24 |
| rs7127188 | 11 | 118893023 | TRAPPC4 | ENSG00000196655.5 | 1.072E-6 | 0.01 | 3170 | gtex_brain_ba24 |
| rs111230411 | 11 | 118893134 | TRAPPC4 | ENSG00000196655.5 | 2.362E-6 | 0.01 | 3281 | gtex_brain_ba24 |
| rs199590107 | 11 | 118893671 | TRAPPC4 | ENSG00000196655.5 | 3.747E-6 | 0.01 | 3818 | gtex_brain_ba24 |
| rs111322300 | 11 | 118893878 | TRAPPC4 | ENSG00000196655.5 | 2.448E-6 | 0.01 | 4025 | gtex_brain_ba24 |
| rs569 | 11 | 118894287 | TRAPPC4 | ENSG00000196655.5 | 2.448E-6 | 0.01 | 4434 | gtex_brain_ba24 |
| rs11006 | 11 | 118895202 | TRAPPC4 | ENSG00000196655.5 | 2.448E-6 | 0.01 | 5349 | gtex_brain_ba24 |
| rs8192696 | 11 | 118895686 | TRAPPC4 | ENSG00000196655.5 | 1.043E-6 | 0.01 | 5833 | gtex_brain_ba24 |
| rs61506726 | 11 | 118831335 | TRAPPC4 | ENSG00000196655.5 | 1.051E-6 | 0 | -58518 | gtex_brain_putamen_basal |
| rs10892315 | 11 | 118831727 | TRAPPC4 | ENSG00000196655.5 | 2.339E-6 | 0 | -58126 | gtex_brain_putamen_basal |
| rs10892317 | 11 | 118832035 | TRAPPC4 | ENSG00000196655.5 | 2.339E-6 | 0 | -57818 | gtex_brain_putamen_basal |
| rs113975105 | 11 | 118836606 | TRAPPC4 | ENSG00000196655.5 | 2.351E-6 | 0 | -53247 | gtex_brain_putamen_basal |
| rs75067211 | 11 | 118854372 | TRAPPC4 | ENSG00000196655.5 | 3.713E-6 | 0 | -35481 | gtex_brain_putamen_basal |
| rs3887652 | 11 | 118856582 | TRAPPC4 | ENSG00000196655.5 | 3.172E-6 | 0 | -33271 | gtex_brain_putamen_basal |
| rs4938618 | 11 | 118867803 | TRAPPC4 | ENSG00000196655.5 | 3.172E-6 | 0 | -22050 | gtex_brain_putamen_basal |
| rs4445645 | 11 | 118868750 | TRAPPC4 | ENSG00000196655.5 | 1.793E-9 | 0 | -21103 | gtex_brain_putamen_basal |
| rs3737504 | 11 | 118869460 | TRAPPC4 | ENSG00000196655.5 | 1.308E-7 | 0 | -20393 | gtex_brain_putamen_basal |
| rs11822103 | 11 | 118869539 | TRAPPC4 | ENSG00000196655.5 | 3.172E-6 | 0 | -20314 | gtex_brain_putamen_basal |
| rs6589713 | 11 | 118872404 | TRAPPC4 | ENSG00000196655.5 | 1.169E-6 | 0 | -17449 | gtex_brain_putamen_basal |
| rs4558175 | 11 | 118872581 | TRAPPC4 | ENSG00000196655.5 | 2.347E-7 | 0 | -17272 | gtex_brain_putamen_basal |
| rs4573680 | 11 | 118872741 | TRAPPC4 | ENSG00000196655.5 | 7.509E-8 | 0 | -17112 | gtex_brain_putamen_basal |
| rs9645664 | 11 | 118873987 | TRAPPC4 | ENSG00000196655.5 | 1.494E-7 | 0 | -15866 | gtex_brain_putamen_basal |
| rs4936457 | 11 | 118875727 | TRAPPC4 | ENSG00000196655.5 | 3.863E-8 | 0 | -14126 | gtex_brain_putamen_basal |
| rs4936458 | 11 | 118875761 | TRAPPC4 | ENSG00000196655.5 | 3.868E-8 | 0 | -14092 | gtex_brain_putamen_basal |
| rs11403557 | 11 | 118875783 | TRAPPC4 | ENSG00000196655.5 | 5.406E-8 | 0 | -14070 | gtex_brain_putamen_basal |
| rs58709307 | 11 | 118877563 | TRAPPC4 | ENSG00000196655.5 | 2.187E-10 | 0 | -12290 | gtex_brain_putamen_basal |
| rs11606357 | 11 | 118878222 | TRAPPC4 | ENSG00000196655.5 | 2.126E-10 | 0 | -11631 | gtex_brain_putamen_basal |
| rs7120445 | 11 | 118879285 | TRAPPC4 | ENSG00000196655.5 | 4.027E-11 | 0 | -10568 | gtex_brain_putamen_basal |
| rs73559119 | 11 | 118879824 | TRAPPC4 | ENSG00000196655.5 | 1.782E-8 | 0 | -10029 | gtex_brain_putamen_basal |
| rs11825284 | 11 | 118880012 | TRAPPC4 | ENSG00000196655.5 | 4.865E-11 | 0 | -9841 | gtex_brain_putamen_basal |
| rs11607569 | 11 | 118880668 | TRAPPC4 | ENSG00000196655.5 | 3.671E-9 | 0 | -9185 | gtex_brain_putamen_basal |
| rs73559126 | 11 | 118880727 | TRAPPC4 | ENSG00000196655.5 | 2.766E-6 | 0 | -9126 | gtex_brain_putamen_basal |
| rs11217122 | 11 | 118880740 | TRAPPC4 | ENSG00000196655.5 | 5.777E-10 | 0 | -9113 | gtex_brain_putamen_basal |
| rs60065241 | 11 | 118883491 | TRAPPC4 | ENSG00000196655.5 | 5.002E-10 | 0 | -6362 | gtex_brain_putamen_basal |
| rs11828415 | 11 | 118884323 | TRAPPC4 | ENSG00000196655.5 | 3.239E-7 | 0 | -5530 | gtex_brain_putamen_basal |
| rs11821562 | 11 | 118884370 | TRAPPC4 | ENSG00000196655.5 | 3.268E-7 | 0 | -5483 | gtex_brain_putamen_basal |
| rs61381062 | 11 | 118884708 | TRAPPC4 | ENSG00000196655.5 | 1.013E-7 | 0 | -5145 | gtex_brain_putamen_basal |
| rs58601794 | 11 | 118884726 | TRAPPC4 | ENSG00000196655.5 | 1.012E-7 | 0 | -5127 | gtex_brain_putamen_basal |
| rs59095933 | 11 | 118885161 | TRAPPC4 | ENSG00000196655.5 | 4.373E-7 | 0 | -4692 | gtex_brain_putamen_basal |
| rs59608621 | 11 | 118885163 | TRAPPC4 | ENSG00000196655.5 | 1.13E-7 | 0 | -4690 | gtex_brain_putamen_basal |
| rs10111 | 11 | 118886117 | TRAPPC4 | ENSG00000196655.5 | 1.998E-9 | 0 | -3736 | gtex_brain_putamen_basal |
| rs7131534 | 11 | 118886656 | TRAPPC4 | ENSG00000196655.5 | 4.256E-11 | 0 | -3197 | gtex_brain_putamen_basal |
| rs7121270 | 11 | 118887568 | TRAPPC4 | ENSG00000196655.5 | 1.552E-8 | 0 | -2285 | gtex_brain_putamen_basal |
| rs7105187 | 11 | 118887581 | TRAPPC4 | ENSG00000196655.5 | 4.41E-8 | 0 | -2272 | gtex_brain_putamen_basal |
| rs3916581 | 11 | 118887887 | TRAPPC4 | ENSG00000196655.5 | 4.184E-7 | 0 | -1966 | gtex_brain_putamen_basal |
| rs3916582 | 11 | 118887888 | TRAPPC4 | ENSG00000196655.5 | 4.25E-7 | 0 | -1965 | gtex_brain_putamen_basal |
| rs11602764 | 11 | 118888619 | TRAPPC4 | ENSG00000196655.5 | 1.001E-7 | 0 | -1234 | gtex_brain_putamen_basal |
| rs11820805 | 11 | 118888831 | TRAPPC4 | ENSG00000196655.5 | 1.001E-7 | 0 | -1022 | gtex_brain_putamen_basal |
| rs11217124 | 11 | 118889132 | TRAPPC4 | ENSG00000196655.5 | 1.437E-8 | 0 | -721 | gtex_brain_putamen_basal |
| rs11217125 | 11 | 118889185 | TRAPPC4 | ENSG00000196655.5 | 1.767E-8 | 0 | -668 | gtex_brain_putamen_basal |
| rs7113753 | 11 | 118889378 | TRAPPC4 | ENSG00000196655.5 | 6.261E-7 | 0 | -475 | gtex_brain_putamen_basal |
| rs3802884 | 11 | 118889810 | TRAPPC4 | ENSG00000196655.5 | 1.175E-6 | 0 | -43 | gtex_brain_putamen_basal |
| rs3802883 | 11 | 118889813 | TRAPPC4 | ENSG00000196655.5 | 1.175E-6 | 0 | -40 | gtex_brain_putamen_basal |
| rs3802882 | 11 | 118889822 | TRAPPC4 | ENSG00000196655.5 | 1.175E-6 | 0 | -31 | gtex_brain_putamen_basal |
| rs3802881 | 11 | 118890022 | TRAPPC4 | ENSG00000196655.5 | 1.171E-6 | 0 | 169 | gtex_brain_putamen_basal |
| rs201538807 | 11 | 118890539 | TRAPPC4 | ENSG00000196655.5 | 6.663E-7 | 0 | 686 | gtex_brain_putamen_basal |
| rs4938621 | 11 | 118892277 | TRAPPC4 | ENSG00000196655.5 | 5.278E-11 | 0 | 2424 | gtex_brain_putamen_basal |
| rs117289748 | 11 | 118892757 | TRAPPC4 | ENSG00000196655.5 | 1.262E-10 | 0 | 2904 | gtex_brain_putamen_basal |
| rs143660533 | 11 | 118892759 | TRAPPC4 | ENSG00000196655.5 | 1.259E-10 | 0 | 2906 | gtex_brain_putamen_basal |
| rs61179449 | 11 | 118892835 | TRAPPC4 | ENSG00000196655.5 | 4.956E-11 | 0 | 2982 | gtex_brain_putamen_basal |
| rs58955701 | 11 | 118892872 | TRAPPC4 | ENSG00000196655.5 | 4.935E-11 | 0 | 3019 | gtex_brain_putamen_basal |
| rs12280288 | 11 | 118892940 | TRAPPC4 | ENSG00000196655.5 | 1.593E-9 | 0 | 3087 | gtex_brain_putamen_basal |
| rs7127188 | 11 | 118893023 | TRAPPC4 | ENSG00000196655.5 | 4.848E-11 | 0 | 3170 | gtex_brain_putamen_basal |
| rs111230411 | 11 | 118893134 | TRAPPC4 | ENSG00000196655.5 | 8.216E-10 | 0 | 3281 | gtex_brain_putamen_basal |
| rs199590107 | 11 | 118893671 | TRAPPC4 | ENSG00000196655.5 | 1.29E-9 | 0 | 3818 | gtex_brain_putamen_basal |
| rs111322300 | 11 | 118893878 | TRAPPC4 | ENSG00000196655.5 | 1.068E-10 | 0 | 4025 | gtex_brain_putamen_basal |
| rs569 | 11 | 118894287 | TRAPPC4 | ENSG00000196655.5 | 4.896E-11 | 0 | 4434 | gtex_brain_putamen_basal |
| rs11006 | 11 | 118895202 | TRAPPC4 | ENSG00000196655.5 | 4.896E-11 | 0 | 5349 | gtex_brain_putamen_basal |
| rs8192696 | 11 | 118895686 | TRAPPC4 | ENSG00000196655.5 | 4.323E-11 | 0 | 5833 | gtex_brain_putamen_basal |
| rs2276072 | 11 | 118896115 | TRAPPC4 | ENSG00000196655.5 | 1.904E-8 | 0 | 6262 | gtex_brain_putamen_basal |
| rs2276071 | 11 | 118896116 | TRAPPC4 | ENSG00000196655.5 | 1.9E-8 | 0 | 6263 | gtex_brain_putamen_basal |
| rs57156480 | 11 | 118896959 | TRAPPC4 | ENSG00000196655.5 | 3.587E-8 | 0 | 7106 | gtex_brain_putamen_basal |
Section II. Transcriptome annotation
General gene expression (GTEx)
Gene expression during devlopment (BrainCloud)
Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.
Gene expression of temporal and spatial changes (BrainSpan)
Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.
No co-expressed genes in brain regions
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005515 | protein binding | ISS | 11018053 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0016358 | dendrite development | ISS | neurite, dendrite (GO term level: 11) | 11018053 |
| GO:0006888 | ER to Golgi vesicle-mediated transport | IEA | - | |
| GO:0016192 | vesicle-mediated transport | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0008021 | synaptic vesicle | ISS | Synap, Neurotransmitter (GO term level: 12) | 11018053 |
| GO:0030425 | dendrite | ISS | neuron, axon, dendrite (GO term level: 6) | 11018053 |
| GO:0045202 | synapse | ISS | neuron, Synap, Neurotransmitter, Glial (GO term level: 2) | 11018053 |
| GO:0005794 | Golgi apparatus | IEA | - | |
| GO:0005795 | Golgi stack | ISS | 11018053 | |
| GO:0005801 | cis-Golgi network | IEA | - | |
| GO:0005783 | endoplasmic reticulum | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PID SYNDECAN 2 PATHWAY | 33 | 27 | All SZGR 2.0 genes in this pathway |
| NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP | 285 | 181 | All SZGR 2.0 genes in this pathway |
| GARY CD5 TARGETS DN | 431 | 263 | All SZGR 2.0 genes in this pathway |
| TIEN INTESTINE PROBIOTICS 24HR UP | 557 | 331 | All SZGR 2.0 genes in this pathway |
| LIAO METASTASIS | 539 | 324 | All SZGR 2.0 genes in this pathway |
| SHEN SMARCA2 TARGETS UP | 424 | 268 | All SZGR 2.0 genes in this pathway |
| ZUCCHI METASTASIS DN | 44 | 29 | All SZGR 2.0 genes in this pathway |
| PELLICCIOTTA HDAC IN ANTIGEN PRESENTATION UP | 64 | 40 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER CANCER UP | 973 | 570 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP | 863 | 514 | All SZGR 2.0 genes in this pathway |
| YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 17 | 181 | 101 | All SZGR 2.0 genes in this pathway |
| MARTENS TRETINOIN RESPONSE DN | 841 | 431 | All SZGR 2.0 genes in this pathway |
| LEE BMP2 TARGETS DN | 882 | 538 | All SZGR 2.0 genes in this pathway |
| PHONG TNF RESPONSE VIA P38 PARTIAL | 160 | 106 | All SZGR 2.0 genes in this pathway |
| PHONG TNF RESPONSE NOT VIA P38 | 337 | 236 | All SZGR 2.0 genes in this pathway |