Summary ?
GeneID22862
SymbolFNDC3A
SynonymsFNDC3|HUGO|bA203I16.1|bA203I16.5
Descriptionfibronectin type III domain containing 3A
ReferenceMIM:615794|HGNC:HGNC:20296|Ensembl:ENSG00000102531|HPRD:13548|Vega:OTTHUMG00000016911
Gene typeprotein-coding
Map location13q14.2
Pascal p-value0.102
Sherlock p-value0.664
Fetal beta0.164
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg023218711350159138FNDC3A0.002-3.287DMG:vanEijk_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7629431chr3189336841FNDC3A228620.2trans
rs4491879chr3189373908FNDC3A228620.01trans
rs4505678chr3189374356FNDC3A228620.02trans

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
ATXN100.920.91
ARMC80.920.91
NPEPPS0.910.90
ASB80.910.91
ATF20.910.92
SAR1A0.910.91
AC087742.20.910.90
BNIP3L0.910.92
SMAD20.900.91
FAF10.900.92
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
MT-CO2-0.84-0.85
AF347015.8-0.83-0.85
AF347015.31-0.82-0.82
MT-CYB-0.82-0.83
AF347015.27-0.81-0.83
AF347015.21-0.80-0.82
AF347015.15-0.80-0.83
AF347015.33-0.80-0.81
AF347015.2-0.79-0.81
AF347015.26-0.78-0.82

Section III. Gene Ontology annotation

Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007286spermatid developmentIEA-
GO:0009566fertilizationIEA-
GO:0016337cell-cell adhesionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0001669acrosomeIEA-
GO:0012506vesicle membraneIEA-
GO:0005829cytosolIEA-
GO:0005783endoplasmic reticulumIDA18029348 
GO:0042598vesicular fractionIEA-
GO:0031410cytoplasmic vesicleIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634384All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391222All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP 579346All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN 214133All SZGR 2.0 genes in this pathway
CASTELLANO NRAS TARGETS UP 6841All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF UP 215137All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552347All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS C UP 170114All SZGR 2.0 genes in this pathway
TAKADA GASTRIC CANCER COPY NUMBER DN 2915All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
WOTTON RUNX TARGETS DN 2918All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP 283177All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP 195138All SZGR 2.0 genes in this pathway
TCGA GLIOBLASTOMA COPY NUMBER DN 3121All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP 555346All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS DN 8667All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS UP 175116All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN 318220All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G6 153112All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN 271175All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409268All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN 281179All SZGR 2.0 genes in this pathway
LIN MELANOMA COPY NUMBER DN 4134All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS DN 14593All SZGR 2.0 genes in this pathway
EHLERS ANEUPLOIDY UP 4129All SZGR 2.0 genes in this pathway
MATZUK SPERMATID DIFFERENTIATION 3726All SZGR 2.0 genes in this pathway
MATZUK SPERMATOZOA 11477All SZGR 2.0 genes in this pathway
PODAR RESPONSE TO ADAPHOSTIN UP 14798All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518299All SZGR 2.0 genes in this pathway
IKEDA MIR1 TARGETS UP 5339All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP 11687All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
TIAN BHLHA15 TARGETS 168All SZGR 2.0 genes in this pathway
ZWANG CLASS 3 TRANSIENTLY INDUCED BY EGF 222159All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
let-7/98465471m8hsa-let-7abrainUGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrainUGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrainUGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrainAGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrainUGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrainUGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brainUGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZUGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrainUGAGGUAGUAGUUUGUGCUGU
hsa-let-7abrainUGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrainUGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrainUGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrainAGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrainUGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrainUGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brainUGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZUGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrainUGAGGUAGUAGUUUGUGCUGU
miR-1/206201720241A,m8hsa-miR-1UGGAAUGUAAAGAAGUAUGUA
hsa-miR-206SZUGGAAUGUAAGGAAGUGUGUGG
hsa-miR-613AGGAAUGUUCCUUCUUUGCC
miR-101201120171Ahsa-miR-101UACAGUACUGUGAUAACUGAAG
miR-129-5p159416001Ahsa-miR-129brainCUUUUUGCGGUCUGGGCUUGC
hsa-miR-129-5pCUUUUUGCGGUCUGGGCUUGCU
miR-137444450m8hsa-miR-137UAUUGCUUAAGAAUACGCGUAG
miR-142-3p20552061m8hsa-miR-142-3pUGUAGUGUUUCCUACUUUAUGGA
miR-142-5p814m8hsa-miR-142-5pCAUAAAGUAGAAAGCACUAC
miR-144201020171A,m8hsa-miR-144UACAGUAUAGAUGAUGUACUAG
hsa-miR-144UACAGUAUAGAUGAUGUACUAG
miR-145514520m8hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
miR-17-5p/20/93.mr/106/519.d11671173m8hsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU
miR-18118201826m8hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-18621882194m8hsa-miR-186CAAAGAAUUCUCCUUUUGGGCUU
miR-1910511057m8hsa-miR-19aUGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19bUGUGCAAAUCCAUGCAAAACUGA
miR-2084794851Ahsa-miR-208AUAAGACGAGCAAAAAGCUUGU
miR-221/222214121481A,m8hsa-miR-221brainAGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brainAGCUACAUCUGGCUACUGGGUCUC
miR-274384441Ahsa-miR-27abrainUUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrainUUCACAGUGGCUAAGUUCUGC
miR-30-5p166216691A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-31193419401Ahsa-miR-31AGGCAAGAUGCUGGCAUAGCUG
miR-326180018071A,m8hsa-miR-326CCUCUGGGCCCUUCCUCCAG
miR-376c213921451Ahsa-miR-376cAACAUAGAGGAAAUUCCACG
miR-381208120871Ahsa-miR-381UAUACAAGGGCAAGCUCUCUGU
miR-4994794851Ahsa-miR-499UUAAGACUUGCAGUGAUGUUUAA
miR-542-3p16411647m8hsa-miR-542-3pUGUGACAGAUUGAUAACUGAAA
miR-93.hd/291-3p/294/295/302/372/373/52014501456m8hsa-miR-93brainAAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302aUAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302bUAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302cUAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302dUAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520eAAAGUGCUUCCUUUUUGAGGG
hsa-miR-520aAAAGUGCUUCCCUUUGGACUGU
hsa-miR-520bAAAGUGCUUCCUUUUAGAGGG
hsa-miR-520cAAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520dAAAGUGCUUCUCUUUGGUGGGUU
hsa-miR-93brainAAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302aUAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302bUAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302cUAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302dUAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520eAAAGUGCUUCCUUUUUGAGGG
hsa-miR-520aAAAGUGCUUCCCUUUGGACUGU
hsa-miR-520bAAAGUGCUUCCUUUUAGAGGG
hsa-miR-520cAAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520dAAAGUGCUUCUCUUUGGUGGGUU