Gene Page:ATP2B4

Summary?
GeneID 493
Symbol ATP2B4
Synonyms ATP2B2|MXRA1|PMCA4|PMCA4b|PMCA4x
Description ATPase plasma membrane Ca2+ transporting 4
Reference MIM:108732|HGNC:HGNC:817|Ensembl:ENSG00000058668|HPRD:00159|Vega:OTTHUMG00000035906
Gene type protein-coding
Map location 1q32.1
Fetal beta -1.682
DMG 2 (# studies)
Support ION BALANCE
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.human_clathrin
G2Cdb.human_PocklingtonH1
G2Cdb.human_Synaptosome
G2Cdb.humanNRC
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Darnell FMRP targets
Potential synaptic genes

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. 2
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). 2
DNM:Awadalla_2010 全外显子组测序分析 A survey of ~430 Mb of DNA from 401 synapse-expressed genes across all cases and 25 Mb of DNA in controls found 28 candidate DNMs.
Network Shortest path distance of core genes in the Human protein-protein interaction network Contribution to shortest path in PPI network: 0.1631

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
ATP2B4 chr1 203668781 C T ATP2B4:NM_001001396:exon4:c.C585T:p.N195N
ATP2B4:NM_001684:exon4:c.C585T:p.N195N		 N195N synonymous SNV Disorganized Schizophrenia DNM:Awadalla_2010

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg19087104 1 203643746 ATP2B4 1.93E-5 0.28 0.016 DMG:Wockner_2014
cg19791253 1 203595809 ATP2B4 -0.023 0.26 DMG:Nishioka_2013


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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0000166 nucleotide binding IEA -
GO:0000287 magnesium ion binding IEA -
GO:0005509 calcium ion binding IEA -
GO:0005516 calmodulin binding IEA -
GO:0005524 ATP binding IEA -
GO:0005388 calcium-transporting ATPase activity TAS 2137451
GO:0016787 水解酶作用ivity IEA -
GO:0016820 水解酶作用ivity, acting on acid anhydrides, catalyzing transmembrane movement of substances IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0008152 metabolic process IEA -
GO:0006816 calcium ion transport IEA -
GO:0006812 cation transport IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005886 plasma membrane TAS 2137451|10748016
GO:0005887 integral to plasma membrane TAS 2137451

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG CALCIUM SIGNALING PATHWAY 178 134 All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN 481 290 All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS UP 137 94 All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS DN 68 49 All SZGR 2.0 genes in this pathway
DAVICIONI RHABDOMYOSARCOMA PAX FOXO1 FUSION DN 15 11 All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE DN 66 44 All SZGR 2.0 genes in this pathway
PUIFFE INVASION INHIBITED BY ASCITES UP 82 51 All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP 177 110 All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION UP 119 66 All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP 162 116 All SZGR 2.0 genes in this pathway
WAMUNYOKOLI OVARIAN CANCER GRADES 1 2 DN 67 43 All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP 239 157 All SZGR 2.0 genes in this pathway
DUNNE TARGETS OF AML1 MTG8 FUSION UP 52 32 All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855 609 All SZGR 2.0 genes in this pathway
KIM MYC AMPLIFICATION TARGETS DN 97 51 All SZGR 2.0 genes in this pathway
TOMLINS PROSTATE CANCER DN 40 33 All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP 811 508 All SZGR 2.0 genes in this pathway
SCIAN INVERSED TARGETS OF TP53 AND TP73 DN 31 23 All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS DN 261 155 All SZGR 2.0 genes in this pathway
BALDWIN PRKCI TARGETS UP 35 26 All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP 283 177 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464 276 All SZGR 2.0 genes in this pathway
罗斯急性MYELOID LEUKEMIA CBF 82 57 All SZGR 2.0 genes in this pathway
BROCKE APOPTOSIS REVERSED BY IL6 144 98 All SZGR 2.0 genes in this pathway
SWEET KRAS TARGETS UP 84 51 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR DN 86 62 All SZGR 2.0 genes in this pathway
HENDRICKS SMARCA4 TARGETS UP 56 35 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR DN 148 102 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR DN 178 121 All SZGR 2.0 genes in this pathway
KUNINGER IGF1 VS PDGFB TARGETS UP 82 51 All SZGR 2.0 genes in this pathway
BILD MYC ONCOGENIC SIGNATURE 206 117 All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4 307 185 All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN 258 160 All SZGR 2.0 genes in this pathway
DAIRKEE CANCER PRONE RESPONSE E2 28 21 All SZGR 2.0 genes in this pathway
HUANG FOXA2 TARGETS DN 36 21 All SZGR 2.0 genes in this pathway
IZADPANAH STEM CELL ADIPOSE VS BONE DN 108 68 All SZGR 2.0 genes in this pathway
MATZUK SPERMATOZOA 114 77 All SZGR 2.0 genes in this pathway
RUIZ TNC TARGETS UP 153 107 All SZGR 2.0 genes in this pathway
SHEDDEN肺癌好生存A4 196 124 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 61 44 All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456 287 All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567 365 All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN 414 237 All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS 289 187 All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430 288 All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS UP 221 120 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
let-7/98 3308 3314 1A hsa-let-7abrain UGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrain UGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrain UGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrain AGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrain UGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrain UGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brain UGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZ UGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrain UGAGGUAGUAGUUUGUGCUGU
hsa-let-7abrain UGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrain UGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrain UGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrain AGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrain UGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrain UGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brain UGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZ UGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrain UGAGGUAGUAGUUUGUGCUGU
miR-124/506 1458 1464 m8 hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-129-5p 2241 2247 m8 hsa-miR-129brain CUUUUUGCGGUCUGGGCUUGC
hsa-miR-129-5p CUUUUUGCGGUCUGGGCUUGCU
miR-135 3524 3530 m8 hsa-miR-135a UAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135b UAUGGCUUUUCAUUCCUAUGUG
hsa-miR-135a UAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135b UAUGGCUUUUCAUUCCUAUGUG
miR-142-5p 2447 2453 1A hsa-miR-142-5p CAUAAAGUAGAAAGCACUAC
miR-148/152 4195 4202 1A,m8 hsa-miR-148a UCAGUGCACUACAGAACUUUGU
hsa-miR-152brain UCAGUGCAUGACAGAACUUGGG
hsa-miR-148b UCAGUGCAUCACAGAACUUUGU
miR-153 2238 2244 1A hsa-miR-153 UUGCAUAGUCACAAAAGUGA
miR-183 3714 3720 1A hsa-miR-183 UAUGGCACUGGUAGAAUUCACUG
miR-186 2256 2262 1A hsa-miR-186 CAAAGAAUUCUCCUUUUGGGCUU
miR-214 3615 3621 m8 hsa-miR-214brain ACAGCAGGCACAGACAGGCAG
miR-29 2635 2641 m8 hsa-miR-29aSZ UAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZ UAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZ UAGCACCAUUUGAAAUCGGU
miR-324-3p 2589 2595 m8 hsa-miR-324-3p CCACUGCCCCAGGUGCUGCUGG
miR-448 2237 2244 1A,m8 hsa-miR-448 UUGCAUAUGUAGGAUGUCCCAU
miR-450 2241 2247 1A hsa-miR-450 UUUUUGCGAUGUGUUCCUAAUA