Gene Page: AFF2
Summary ?
| GeneID | 2334 |
| Symbol | AFF2 |
| Synonyms | FMR2|FMR2P|FRAXE|MRX2|OX19 |
| Description | AF4/FMR2 family member 2 |
| Reference | MIM:300806|HGNC:HGNC:3776|Ensembl:ENSG00000155966|HPRD:02397|Vega:OTTHUMG00000022613 |
| Gene type | protein-coding |
| Map location | Xq28 |
| Sherlock p-value | 0.137 |
| Fetal beta | 2.166 |
| eGene | Myers' cis & trans |
| Support | Potential synaptic genes |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 1 |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs7584986 | chr2 | 184111432 | AFF2 | 2334 | 0.05 | trans | ||
| rs16955618 | chr15 | 29937543 | AFF2 | 2334 | 1.195E-4 | trans | ||
| rs1041786 | chr21 | 22617710 | AFF2 | 2334 | 0.01 | 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 |
| HCK | 0.83 | 0.71 |
| CD68 | 0.81 | 0.72 |
| CD14 | 0.81 | 0.75 |
| ITGB2 | 0.80 | 0.74 |
| TREM2 | 0.79 | 0.75 |
| FCGR1A | 0.76 | 0.64 |
| VSIG4 | 0.76 | 0.68 |
| NCKAP1L | 0.76 | 0.67 |
| LAPTM5 | 0.75 | 0.76 |
| PGDS | 0.74 | 0.74 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AC010300.1 | -0.30 | -0.41 |
| AC005921.3 | -0.26 | -0.39 |
| AF347015.18 | -0.26 | -0.21 |
| AP000769.2 | -0.26 | -0.35 |
| AF347015.26 | -0.26 | -0.21 |
| MALAT1 | -0.26 | -0.33 |
| AC016705.1 | -0.26 | -0.31 |
| C10orf108 | -0.25 | -0.30 |
| ERVWE1 | -0.25 | -0.31 |
| MICALL2 | -0.24 | -0.23 |
Section III. Gene Ontology annotation
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0007420 | brain development | TAS | Brain (GO term level: 7) | 8673086 |
| GO:0007611 | learning or memory | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005634 | nucleus | IDA | 18029348 | |
| GO:0005737 | cytoplasm | IDA | 18029348 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP | 177 | 110 | All SZGR 2.0 genes in this pathway |
| PUJANA BRCA1 PCC NETWORK | 1652 | 1023 | All SZGR 2.0 genes in this pathway |
| PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
| PUJANA CHEK2 PCC NETWORK | 779 | 480 | All SZGR 2.0 genes in this pathway |
| BENPORATH SUZ12 TARGETS | 1038 | 678 | All SZGR 2.0 genes in this pathway |
| BENPORATH EED TARGETS | 1062 | 725 | All SZGR 2.0 genes in this pathway |
| ROSS AML WITH PML RARA FUSION | 77 | 62 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 6HR UP | 71 | 48 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 TARGETS DN | 543 | 317 | All SZGR 2.0 genes in this pathway |
| MARTINEZ TP53 TARGETS DN | 593 | 372 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 AND TP53 TARGETS DN | 591 | 366 | All SZGR 2.0 genes in this pathway |
| VALK AML CLUSTER 12 | 30 | 20 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 1HR UP | 61 | 44 | All SZGR 2.0 genes in this pathway |
| LEE BMP2 TARGETS UP | 745 | 475 | All SZGR 2.0 genes in this pathway |
| RATTENBACHER BOUND BY CELF1 | 467 | 251 | 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 | |||
| miR-103/107 | 4499 | 4506 | 1A,m8 | hsa-miR-103brain | AGCAGCAUUGUACAGGGCUAUGA |
| hsa-miR-107brain | AGCAGCAUUGUACAGGGCUAUCA | ||||
| miR-140 | 2907 | 2913 | 1A | hsa-miR-140brain | AGUGGUUUUACCCUAUGGUAG |
| miR-142-3p | 163 | 170 | 1A,m8 | hsa-miR-142-3p | UGUAGUGUUUCCUACUUUAUGGA |
| miR-145 | 3586 | 3592 | m8 | hsa-miR-145 | GUCCAGUUUUCCCAGGAAUCCCUU |
| miR-149 | 1740 | 1746 | 1A | hsa-miR-149brain | UCUGGCUCCGUGUCUUCACUCC |
| hsa-miR-149brain | UCUGGCUCCGUGUCUUCACUCC | ||||
| miR-150 | 3575 | 3581 | 1A | hsa-miR-150 | UCUCCCAACCCUUGUACCAGUG |
| miR-188 | 2696 | 2702 | 1A | hsa-miR-188 | CAUCCCUUGCAUGGUGGAGGGU |
| miR-214 | 1530 | 1536 | m8 | hsa-miR-214brain | ACAGCAGGCACAGACAGGCAG |
| miR-218 | 5631 | 5637 | 1A | hsa-miR-218brain | UUGUGCUUGAUCUAACCAUGU |
| miR-24 | 3753 | 3759 | 1A | hsa-miR-24SZ | UGGCUCAGUUCAGCAGGAACAG |
| miR-320 | 1902 | 1908 | 1A | hsa-miR-320 | AAAAGCUGGGUUGAGAGGGCGAA |
| miR-328 | 2869 | 2875 | m8 | hsa-miR-328brain | CUGGCCCUCUCUGCCCUUCCGU |
| miR-33 | 9301 | 9307 | 1A | hsa-miR-33 | GUGCAUUGUAGUUGCAUUG |
| hsa-miR-33b | GUGCAUUGCUGUUGCAUUGCA | ||||
| miR-346 | 3785 | 3791 | m8 | hsa-miR-346brain | UGUCUGCCCGCAUGCCUGCCUCU |
| miR-361 | 3996 | 4002 | m8 | hsa-miR-361brain | UUAUCAGAAUCUCCAGGGGUAC |
| miR-369-3p | 7116 | 7122 | m8 | hsa-miR-369-3p | AAUAAUACAUGGUUGAUCUUU |
| miR-409-3p | 1413 | 1419 | 1A | hsa-miR-409-3p | CGAAUGUUGCUCGGUGAACCCCU |
| miR-448 | 226 | 232 | m8 | hsa-miR-448 | UUGCAUAUGUAGGAUGUCCCAU |
| miR-452 | 1630 | 1636 | m8 | hsa-miR-452 | UGUUUGCAGAGGAAACUGAGAC |
| miR-494 | 4334 | 4340 | 1A | hsa-miR-494brain | UGAAACAUACACGGGAAACCUCUU |
| miR-495 | 108 | 114 | m8 | hsa-miR-495brain | AAACAAACAUGGUGCACUUCUUU |
| miR-539 | 232 | 239 | 1A,m8 | hsa-miR-539 | GGAGAAAUUAUCCUUGGUGUGU |
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.