Summary ?
GeneID8604
SymbolSLC25A12
SynonymsAGC1|ARALAR
Descriptionsolute carrier family 25 member 12
ReferenceMIM:603667|HGNC:HGNC:10982|Ensembl:ENSG00000115840|HPRD:04719|Vega:OTTHUMG00000134290
Gene typeprotein-coding
Map location2q24
Pascal p-value9.778E-5
Sherlock p-value0.251
Fetal beta-0.717
DMG1 (# studies)
eGeneCerebellar Hemisphere
Cerebellum
Frontal Cortex BA9
Meta
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.human_mitochondria
G2Cdb.humanNRC
CompositeSet
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 4 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
SLC25A12chr2172666145GANM_003705
NR_047549
p.426L>F
.
missense
npcRNA
SchizophreniaDNM:Fromer_2014

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg201045352172750996SLC25A121.07E-8-0.0094.57E-6DMG:Jaffe_2016


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
GenePearson's Correlation Spearman's Correlation
LST10.790.79
GMFG0.780.78
PYCARD0.730.68
IFI27L20.720.63
TREM20.720.65
VAMP50.710.72
CD630.710.69
TYROBP0.690.69
MGST20.690.71
LY960.690.73
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
SPTAN1-0.51-0.62
MYO18A-0.51-0.56
SUPT6H-0.51-0.56
PTPN23-0.51-0.60
HNRNPUL2-0.50-0.51
TCOF1-0.50-0.60
TNKS1BP1-0.50-0.57
SMG6-0.50-0.57
USP20-0.50-0.57
KDM5C-0.50-0.61

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0015183L-aspartate transmembrane transporter activityIDAglutamate (GO term level: 9)11566871 
GO:0005313L-glutamate transmembrane transporter activityIDAglutamate (GO term level: 9)11566871 
GO:0005488bindingIEA-
GO:0005509calcium ion bindingIDA9722566 
GO:0005215transporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0015813L-glutamate transportIDAglutamate (GO term level: 9)11566871 
GO:0015810aspartate transportIDAglutamate (GO term level: 9)11566871 
GO:0006810transportIEA-
GO:0043490malate-aspartate shuttleIDA11566871 
GO:0051592response to calcium ionIDA11566871 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005739mitochondrionIDA9722566 |11566871 
GO:0005743mitochondrial inner membraneIEA-
GO:0016020membraneIEA-
GO:0016021integral to membraneNAS9722566 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME MITOCHONDRIAL PROTEIN IMPORT 5824All SZGR 2.0 genes in this pathway
REACTOME GLUCONEOGENESIS 3421All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS 518242All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF CARBOHYDRATES 247154All SZGR 2.0 genes in this pathway
REACTOME GLUCOSE METABOLISM 6942All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN 481290All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 XPCS DN 8871All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS UP 769437All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP 176115All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP 424268All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN 298200All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A DN 7657All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911527All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN 1011592All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022619All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS UP 388234All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 2G 17196All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K9ME3 DN 12071All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002 429260All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA 447277All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP 442263All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS 535325All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN 15099All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN 254158All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756494All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE MIDDLE 9856All SZGR 2.0 genes in this pathway
KRIEG KDM3A TARGETS NOT HYPOXIA 208107All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-3201942001Ahsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA