Gene Page:ABCA3
Summary?
| GeneID | 21 |
| Symbol | ABCA3 |
| Synonyms | ABC-C|ABC3|EST111653|LBM180|SMDP3 |
| Description | ATP binding cassette subfamily A member 3 |
| Reference | MIM:601615|HGNC:HGNC:33|Ensembl:ENSG00000167972|HPRD:03369|Vega:OTTHUMG00000128845 |
| Gene type | protein-coding |
| Map location | 16p13.3 |
| Pascal p-value | 0.128 |
| Sherlock p-value | 0.986 |
| Fetal beta | -0.789 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
| Support | CompositeSet Darnell FMRP targets |
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
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg09632163 | 16 | 2339292 | ABCA3 | 2.035E-4 | 0.23 | 0.035 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs16836102 | chr4 | 4716366 | ABCA3 | 21 | 0.08 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| SLC5A5 | 0.92 | 0.55 |
| SLC13A4 | 0.91 | 0.46 |
| KCNJ13 | 0.90 | 0.29 |
| CLIC6 | 0.90 | 0.46 |
| F5 | 0.90 | 0.40 |
| TRPV4 | 0.88 | 0.41 |
| CP | 0.88 | 0.33 |
| PRLR | 0.87 | 0.20 |
| RBM47 | 0.86 | 0.38 |
| FOLR1 | 0.84 | 0.30 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| ZNF32 | -0.21 | -0.41 |
| SNHG12 | -0.20 | -0.39 |
| RPL31 | -0.20 | -0.45 |
| COMMD3 | -0.20 | -0.40 |
| TCTEX1D2 | -0.19 | -0.37 |
| CYP2R1 | -0.19 | -0.34 |
| STRA13 | -0.19 | -0.37 |
| RPS21 | -0.19 | -0.43 |
| RPP21 | -0.19 | -0.33 |
| NDUFAF2 | -0.19 | -0.42 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG ABC TRANSPORTERS | 44 | 29 | All SZGR 2.0 genes in this pathway |
| PID ERA GENOMIC PATHWAY | 65 | 37 | All SZGR 2.0 genes in this pathway |
| REACTOME ABCA TRANSPORTERS IN LIPID HOMEOSTASIS | 18 | 11 | All SZGR 2.0 genes in this pathway |
| REACTOME ABC FAMILY PROTEINS MEDIATED TRANSPORT | 34 | 21 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES | 413 | 270 | All SZGR 2.0 genes in this pathway |
| BERTUCCI MEDULLARY VS DUCTAL BREAST CANCER UP | 206 | 111 | All SZGR 2.0 genes in this pathway |
| CHARAFE BREAST CANCER LUMINAL VS BASAL UP | 380 | 215 | All SZGR 2.0 genes in this pathway |
| SENESE HDAC3 TARGETS UP | 501 | 327 | All SZGR 2.0 genes in this pathway |
| GRUETZMANN PANCREATIC CANCER DN | 203 | 134 | All SZGR 2.0 genes in this pathway |
| INGRAM SHH TARGETS UP | 127 | 79 | All SZGR 2.0 genes in this pathway |
| KANNAN TP53 TARGETS UP | 58 | 40 | All SZGR 2.0 genes in this pathway |
| AFFAR YY1 TARGETS UP | 214 | 133 | All SZGR 2.0 genes in this pathway |
| ZHANG RESPONSE TO CANTHARIDIN DN | 69 | 46 | All SZGR 2.0 genes in this pathway |
| ZHANG GATA6 TARGETS DN | 64 | 46 | All SZGR 2.0 genes in this pathway |
| DAIRKEE CANCER PRONE RESPONSE BPA E2 | 118 | 65 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER LUMINAL B UP | 172 | 109 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER BASAL DN | 701 | 446 | All SZGR 2.0 genes in this pathway |
| RAY TUMORIGENESIS BY ERBB2 CDC25A UP | 104 | 57 | All SZGR 2.0 genes in this pathway |
| HUANG DASATINIB RESISTANCE DN | 69 | 44 | All SZGR 2.0 genes in this pathway |
| VANTVEER BREAST CANCER ESR1 UP | 167 | 99 | 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 |
| ZHANG TLX TARGETS 60HR UP | 293 | 203 | All SZGR 2.0 genes in this pathway |
| MILI PSEUDOPODIA CHEMOTAXIS DN | 457 | 302 | All SZGR 2.0 genes in this pathway |
| KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP | 756 | 494 | All SZGR 2.0 genes in this pathway |
| CHYLA CBFA2T3 TARGETS DN | 242 | 146 | All SZGR 2.0 genes in this pathway |
| FEVR CTNNB1 TARGETS UP | 682 | 433 | All SZGR 2.0 genes in this pathway |
| ALFANO MYC TARGETS | 239 | 156 | All SZGR 2.0 genes in this pathway |
| LIM MAMMARY STEM CELL DN | 428 | 246 | 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 |