Gene Page:VAPB

Summary?
GeneID 9217
Symbol VAPB
Synonyms ALS8|VAMP-B|VAP-B
Description VAMP (vesicle-associated membrane protein)-associated protein B and C
Reference MIM:605704|HGNC:HGNC:12649|Ensembl:ENSG00000124164|HPRD:09300|Vega:OTTHUMG00000032840
Gene type protein-coding
Map location 20q13.33
Pascal p-value 0.362
Sherlock p-value 0.13
Fetal beta -0.843
DMG 1 (# studies)
eGene Hippocampus
Myers' cis & trans
元
Support G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
CompositeSet

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg07628558 20 56964831 VAPB 1.36E-9 -0.021 1.37E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs12790959 chr11 131620615 VAPB 9217 0.18 trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
COPS3 0.92 0.90
EIF3M 0.92 0.92
RBM34 0.92 0.90
RSL24D1 0.92 0.91
PSMD14 0.92 0.88
PSMA2 0.91 0.90
CCT4 0.91 0.91
MMADHC 0.91 0.91
BXDC2 0.91 0.89
PPA1 0.91 0.84
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.26 -0.68 -0.73
AF347015.2 -0.67 -0.72
AF347015.15 -0.66 -0.71
MT-CYB -0.66 -0.71
AF347015.33 -0.66 -0.71
AF347015.8 -0.65 -0.70
MT-CO2 -0.65 -0.67
FAM38A -0.64 -0.69
GPT -0.64 -0.68
SLC6A12 -0.63 -0.69

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0005198 structural molecule activity IEA -
GO:0042803 protein homodimerization activity IPI 9920726|16227268|17540579
GO:0019899 enzyme binding IPI 17540579
GO:0046982 protein heterodimerization activity IPI 9920726|16227268
GO:0048487 beta-tubulin binding IDA 17540579
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0019048 virus-host interaction IDA 16227268
GO:0030968 内质网unfolded protein response 小鬼 16891305
GO:0045070 positive regulation of viral genome replication 小鬼 16227268
GO:0044419 interspecies interaction between organisms IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0012505 endomembrane system IEA -
GO:0005794 Golgi apparatus IDA 16227268
GO:0005789 内质网membrane IDA 16227268
GO:0005624 membrane fraction IEA -
GO:0005783 内质网 IDA 15372378|16891305
GO:0016021 integral to membrane IEA -
GO:0005886 plasma membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS 31 18 All SZGR 2.0 genes in this pathway
REACTOME PHOSPHOLIPID METABOLISM 198 112 All SZGR 2.0 genes in this pathway
REACTOME SPHINGOLIPID METABOLISM 69 40 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478 302 All SZGR 2.0 genes in this pathway
WINTER HYPOXIA UP 92 57 All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567 375 All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391 222 All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485 293 All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN 805 505 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 5 6WK DN 137 97 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 6 7WK UP 197 135 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN 62 44 All SZGR 2.0 genes in this pathway
LUI THYROID CANCER CLUSTER 2 42 31 All SZGR 2.0 genes in this pathway
JAZAG TGFB1 SIGNALING VIA SMAD4 DN 66 38 All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988 594 All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 20Q12 Q13 AMPLICON 149 76 All SZGR 2.0 genes in this pathway
CHEOK RESPONSE TO MERCAPTOPURINE DN 22 15 All SZGR 2.0 genes in this pathway
KAAB FAILED HEART ATRIUM DN 141 99 All SZGR 2.0 genes in this pathway
RAMASWAMY METASTASIS DN 61 47 All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS 138 91 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504 323 All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL 311 205 All SZGR 2.0 genes in this pathway
JIANG HYPOXIA CANCER 83 52 All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE DN 373 196 All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS DN 543 317 All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS UP 602 364 All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS UP 601 369 All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D UP 210 124 All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS DN 202 132 All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP 442 263 All SZGR 2.0 genes in this pathway
YOSHIOKA LIVER CANCER EARLY RECURRENCE UP 40 23 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN 150 99 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR DN 222 147 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN 254 158 All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP 682 433 All SZGR 2.0 genes in this pathway
JUBAN TARGETS OF SPI1 AND FLI1 UP 115 73 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

microrna的家庭 Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-133 639 646 1A,m8 hsa-miR-133a UUGGUCCCCUUCAACCAGCUGU
hsa-miR-133b UUGGUCCCCUUCAACCAGCUA
miR-143 102 108 1A hsa-miR-143brain UGAGAUGAAGCACUGUAGCUCA
hsa-miR-143brain UGAGAUGAAGCACUGUAGCUCA
miR-183 1236 1242 1A hsa-miR-183 UAUGGCACUGGUAGAAUUCACUG
miR-221/222 1269 1276 1A,m8 hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
miR-31 113 119 m8 hsa-miR-31 AGGCAAGAUGCUGGCAUAGCUG
miR-376c 1267 1273 1A hsa-miR-376c AACAUAGAGGAAAUUCCACG
miR-485-3p 92 98 m8 hsa-miR-485-3p GUCAUACACGGCUCUCCUCUCU