Gene Page: TTC39A

Summary ?
GeneID22996
SymbolTTC39A
SynonymsC1orf34|DEME-6
Descriptiontetratricopeptide repeat domain 39A
ReferenceHGNC:HGNC:18657|Ensembl:ENSG00000085831|Vega:OTTHUMG00000008193
Gene typeprotein-coding
Map location1p32.3
Pascal p-value0.223
Fetal beta-1.853
DMG2 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg03397750151810503TTC39A3.163E-4-0.250.04DMG:Wockner_2014
cg13500576151796588TTC39A3.44E-8-0.0131.02E-5DMG:Jaffe_2016


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
MLLT10.890.88
TRABD0.890.91
ZNF5170.880.89
ZNF512B0.880.87
FZR10.880.86
CAPN100.880.86
RALGDS0.880.92
FBXL190.880.87
PPAN-P2RY110.880.89
SYMPK0.870.89
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.69-0.75
AF347015.27-0.65-0.72
AF347015.21-0.65-0.79
MT-CO2-0.64-0.71
C5orf53-0.63-0.63
MT-CYB-0.62-0.68
COPZ2-0.61-0.66
B2M-0.61-0.63
AF347015.8-0.61-0.70
AF347015.33-0.60-0.66

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
SCHUETZ BREAST CANCER DUCTAL INVASIVE DN 8453All SZGR 2.0 genes in this pathway
KIM RESPONSE TO TSA AND DECITABINE UP 12973All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL UP 380215All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP 450256All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP 11272All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP 456228All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN 781465All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN 378231All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP 329196All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP 239157All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL 330215All SZGR 2.0 genes in this pathway
LIEN BREAST CARCINOMA METAPLASTIC VS DUCTAL DN 11458All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4 307185All SZGR 2.0 genes in this pathway
LEIN MIDBRAIN MARKERS 8255All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS DN 292189All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN 258160All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
BHATI G2M ARREST BY 2METHOXYESTRADIOL UP 12568All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
PANGAS TUMOR SUPPRESSION BY SMAD1 AND SMAD5 UP 13485All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242146All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504321All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP 682433All SZGR 2.0 genes in this pathway
KRIEG KDM3A TARGETS NOT HYPOXIA 208107All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER CLUSTER 6 1613All SZGR 2.0 genes in this pathway