Gene Page:SLC12A4

Summary?
GeneID 6560
Symbol SLC12A4
Synonyms CTC-479C5.17|KCC1|hKCC1
Description solute carrier family 12 member 4
Reference MIM:604119|HGNC:HGNC:10913|Ensembl:ENSG00000124067|HPRD:04987|Vega:OTTHUMG00000137535
Gene type protein-coding
Map location 16q22.1
Pascal p-value 1.564E-4
Sherlock p-value 0.492
Fetal beta -0.798
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Wockner_2014 Genome-wide DNA methylation analysis This 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

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg23656386 16 68003240 SLC12A4 4.219E-4 0.303 0.045 DMG:Wockner_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs824004 chr9 113972608 SLC12A4 6560 0.12 trans
rs7306102 chr12 24607037 SLC12A4 6560 0.01 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
死神:胎儿(13 - 26 postconception周),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
LMNB1 0.96 0.88
NUP205 0.95 0.87
IGF2BP3 0.95 0.78
ARID2 0.95 0.92
CDK5RAP2 0.94 0.93
SMC1A 0.94 0.94
MSH6 0.94 0.90
NUP160 0.94 0.91
VEZF1 0.94 0.92
NONO 0.94 0.85
Top 10 negatively co-expressed genes
Gene Pearson'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 name Pathway size # SZGR 2.0 genes in pathway Info
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413 270 All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT 241 157 All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 94 65 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN 242 165 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN 281 186 All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP 501 327 All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530 342 All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP 239 157 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142 669 All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM2 153 102 All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442 892 All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957 597 All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882 572 All SZGR 2.0 genes in this pathway
PENG GLUCOSE DEPRIVATION DN 169 112 All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS DN 86 67 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS LATE PROGENITOR 544 307 All SZGR 2.0 genes in this pathway
VISALA RESPONSE TO HEAT SHOCK AND AGING UP 15 10 All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN 228 146 All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419 273 All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409 268 All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN 270 181 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476 285 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510 309 All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP 374 247 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN 366 257 All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN PLASMA CELL VS MATURE B LYMPHOCYTE 67 51 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069 729 All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457 302 All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN 668 419 All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA CLASSICAL 162 122 All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242 146 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549 316 All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784 464 All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489 314 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725 838 All SZGR 2.0 genes in this pathway