Summary ?
GeneID23168
SymbolRTF1
SynonymsGTL7|KIAA0252
DescriptionRTF1 homolog, Paf1/RNA polymerase II complex component
ReferenceMIM:611633|HGNC:HGNC:28996|Ensembl:ENSG00000137815|HPRD:11071|Vega:OTTHUMG00000133744
Gene typeprotein-coding
Map location15q15.1
Pascal p-value0.785
Sherlock p-value0.185
Fetal beta0.643
DMG1 (# studies)
eGeneMyers' cis & trans

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. 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg167796261541709933RTF13.85E-9-0.0252.42E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10994209chr1061877705RTF1231680.05trans

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
MAPRE30.870.85
YWHAH0.840.86
PANK20.840.83
RNF1570.840.87
AP2M10.840.82
ATXN7L30.830.82
PNMA20.830.86
RAB6B0.830.91
PLEKHB20.830.84
OTUD50.830.79
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.59-0.34
AF347015.18-0.55-0.30
CLEC3B-0.51-0.50
IL32-0.51-0.35
MT-CO2-0.51-0.32
AF347015.2-0.51-0.26
AF347015.8-0.50-0.30
AP002478.3-0.50-0.42
NOSTRIN-0.50-0.31
GNG11-0.50-0.35

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
WANG CLIM2 TARGETS UP 269146All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN 514319All SZGR 2.0 genes in this pathway
ZHAN V2 LATE DIFFERENTIATION GENES 4534All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN 12376All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566371All SZGR 2.0 genes in this pathway
NICK RESPONSE TO PROC TREATMENT DN 2718All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS 289187All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway