Gene Page: SLC12A4

Summary ?
GeneID6560
SymbolSLC12A4
SynonymsCTC-479C5.17|KCC1|hKCC1
Descriptionsolute carrier family 12 member 4
ReferenceMIM:604119|HGNC:HGNC:10913|Ensembl:ENSG00000124067|HPRD:04987|Vega:OTTHUMG00000137535
Gene typeprotein-coding
Map location16q22.1
Pascal p-value1.564E-4
Sherlock p-value0.492
Fetal beta-0.798
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg236563861668003240SLC12A44.219E-40.3030.045DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs824004chr9113972608SLC12A465600.12trans
rs7306102chr1224607037SLC12A465600.01trans

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
LMNB10.960.88
NUP2050.950.87
IGF2BP30.950.78
ARID20.950.92
CDK5RAP20.940.93
SMC1A0.940.94
MSH60.940.90
NUP1600.940.91
VEZF10.940.92
NONO0.940.85
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.66-0.75
TNFSF12-0.64-0.68
PTH1R-0.64-0.72
FBXO2-0.63-0.66
SLC16A11-0.63-0.66
HLA-F-0.63-0.69
AIFM3-0.63-0.71
TMEM54-0.62-0.66
CA4-0.62-0.76
ALDOC-0.62-0.67

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413270All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT 241157All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 9465All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN 242165All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN 281186All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP 501327All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP 239157All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142669All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM2 153102All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
PENG GLUCOSE DEPRIVATION DN 169112All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS DN 8667All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS LATE PROGENITOR 544307All SZGR 2.0 genes in this pathway
VISALA RESPONSE TO HEAT SHOCK AND AGING UP 1510All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN 228146All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409268All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN 270181All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP 374247All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN 366257All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN PLASMA CELL VS MATURE B LYMPHOCYTE 6751All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN 668419All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA CLASSICAL 162122All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242146All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549316All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway