Gene Page:FREM2

Summary?
GeneID 341640
Symbol FREM2
Synonyms -
Description FRAS1 related extracellular matrix protein 2
Reference MIM:608945|HGNC:HGNC:25396|Ensembl:ENSG00000150893|HPRD:10602|Vega:OTTHUMG00000016759
Gene type protein-coding
Map location 13q13.3
Pascal p-value 0.35
Fetal beta -0.686
DMG 1 (# studies)
eGene Anterior cingulate cortex BA24
Caudate basal ganglia
Cortex
Frontal Cortex BA9
Putamen basal ganglia
Myers' cis & trans
Support Ascano FMRP targets

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
DNM:Ambalavanan_2016 Whole Exome Sequencing This dataset includes 20 de novo mutations detected in 17 COS probands.

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
FREM2 chr13 39450228 G A NM_207361 p.(Arg2784Lys) nonsynonymous SNV 0.941 Childhood-onset schizophrenia DNM:Ambalavanan_2016

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg26063106 13 39261796 FREM2 9.5E-11 -0.012 4.49E-7 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs16843589 chr4 2916930 FREM2 341640 0.18 trans
rs9548430 13 39277956 FREM2 ENSG00000150893.9 1.402E-6 0 16690 gtex_brain_ba24
rs9548438 13 39298288 FREM2 ENSG00000150893.9 2.54E-7 0 37022 gtex_brain_ba24
rs9532272 13 39306690 FREM2 ENSG00000150893.9 1.274E-8 0 45424 gtex_brain_ba24
rs9548446 13 39324093 FREM2 ENSG00000150893.9 1.213E-6 0 62827 gtex_brain_ba24
rs34692381 13 39331723 FREM2 ENSG00000150893.9 2.99E-8 0 70457 gtex_brain_ba24
rs9532275 13 39338062 FREM2 ENSG00000150893.9 1.812E-8 0 76796 gtex_brain_ba24
rs12020645 13 39341638 FREM2 ENSG00000150893.9 1.812E-8 0 80372 gtex_brain_ba24
rs9548450 13 39346192 FREM2 ENSG00000150893.9 1.811E-8 0 84926 gtex_brain_ba24
rs2496446 13 39301453 FREM2 ENSG00000150893.9 3.55E-7 0.01 40187 gtex_brain_putamen_basal
rs2197887 13 39304279 FREM2 ENSG00000150893.9 3.675E-7 0.01 43013 gtex_brain_putamen_basal
rs2442359 13 39304814 FREM2 ENSG00000150893.9 3.675E-7 0.01 43548 gtex_brain_putamen_basal
rs2496448 13 39305383 FREM2 ENSG00000150893.9 3.675E-7 0.01 44117 gtex_brain_putamen_basal
rs2496449 13 39305413 FREM2 ENSG00000150893.9 3.675E-7 0.01 44147 gtex_brain_putamen_basal
rs9532272 13 39306690 FREM2 ENSG00000150893.9 7.835E-7 0.01 45424 gtex_brain_putamen_basal
rs2496451 13 39307025 FREM2 ENSG00000150893.9 3.675E-7 0.01 45759 gtex_brain_putamen_basal
rs9548443 13 39307884 FREM2 ENSG00000150893.9 3.683E-7 0.01 46618 gtex_brain_putamen_basal
rs1037254 13 39320761 FREM2 ENSG00000150893.9 3.936E-6 0.01 59495 gtex_brain_putamen_basal
rs9548446 13 39324093 FREM2 ENSG00000150893.9 7.169E-7 0.01 62827 gtex_brain_putamen_basal
rs34692381 13 39331723 FREM2 ENSG00000150893.9 7.624E-8 0.01 70457 gtex_brain_putamen_basal
rs9532275 13 39338062 FREM2 ENSG00000150893.9 7.858E-8 0.01 76796 gtex_brain_putamen_basal
rs12020645 13 39341638 FREM2 ENSG00000150893.9 7.858E-8 0.01 80372 gtex_brain_putamen_basal
rs9548450 13 39346192 FREM2 ENSG00000150893.9 7.977E-8 0.01 84926 gtex_brain_putamen_basal

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 去的术语 Evidence Neuro keywords PubMed ID
GO:0005509 calcium ion binding IEA -
GO:0005515 protein binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0007154 cell communication IEA -
GO:0007155 cell adhesion IEA -
GO:0007156 homophilic cell adhesion IEA -
GO:0007275 multicellular organismal development IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0016021 integral to membrane IEA -
GO:0005886 plasma membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
WATANABE COLON CANCER MSI VS MSS DN 81 42 All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391 222 All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 DN 175 82 All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP 450 256 All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS UP 372 227 All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA UP 141 75 All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 528 324 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
IWANAGA CARCINOGENESIS BY KRAS PTEN UP 181 112 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
DUTERTRE雌二醇反应24小时 324 193 All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 4 110 66 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
NABA ECM附属 171 89 All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753 411 All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028 559 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-200bc/429 891 897 m8 hsa-miR-200b UAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200c UAAUACUGCCGGGUAAUGAUGG
hsa-miR-429 UAAUACUGUCUGGUAAAACCGU
miR-24 874 880 m8 hsa-miR-24SZ UGGCUCAGUUCAGCAGGAACAG
miR-299-5p 669 675 1A hsa-miR-299-5p UGGUUUACCGUCCCACAUACAU
miR-9 672 679 1A,m8 hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA