Gene Page: TCOF1

Summary ?
GeneID6949
SymbolTCOF1
SynonymsMFD1|TCS|TCS1|treacle
Descriptiontreacle ribosome biogenesis factor 1
ReferenceMIM:606847|HGNC:HGNC:11654|Ensembl:ENSG00000070814|HPRD:06026|Vega:OTTHUMG00000130081
Gene typeprotein-coding
Map location5q32
Pascal p-value0.993
Sherlock p-value0.439
Fetal beta-0.372
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:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 2
GSMA_IGenome scan meta-analysisPsr: 0.0032 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01718 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00459 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg089839755149737654TCOF1-0.0180.75DMG:Nishioka_2013
cg089839755149737654TCOF11.05E-8-0.0084.5E-6DMG: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
CREBZF0.660.63
ZNF2110.650.65
KIAA09070.640.65
ZNF6710.640.64
TIA10.640.63
MTERFD20.640.65
TRA2A0.640.63
LAS1L0.640.61
ZNF5480.640.62
PRPF30.630.63
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
PTH1R-0.49-0.54
IFI27-0.48-0.59
AF347015.31-0.48-0.57
FXYD1-0.48-0.59
MT-CO2-0.48-0.56
AF347015.27-0.48-0.57
TSC22D4-0.47-0.54
AF347015.33-0.47-0.56
HIGD1B-0.47-0.59
HLA-F-0.47-0.50

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI17353931 
GO:0005215transporter activityTAS9096354 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001501skeletal system developmentTAS9096354 
GO:0006810transportIEA-
GO:0042790transcription of nuclear rRNA large RNA polymerase I transcriptIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005730nucleolusIDA15249688 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BERTUCCI MEDULLARY VS DUCTAL BREAST CANCER UP 206111All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN 180101All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN 770415All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP 380213All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479299All 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
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
MANTOVANI VIRAL GPCR SIGNALING DN 4937All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE UP 16792All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS UP 12684All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN 228146All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS DN 14192All SZGR 2.0 genes in this pathway
BILD MYC ONCOGENIC SIGNATURE 206117All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911527All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN 1011592All SZGR 2.0 genes in this pathway
ALONSO METASTASIS DN 2617All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299189All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
KOBAYASHI EGFR SIGNALING 24HR DN 251151All SZGR 2.0 genes in this pathway
WINNEPENNINCKX MELANOMA METASTASIS UP 16286All SZGR 2.0 genes in this pathway
WONG EMBRYONIC STEM CELL CORE 335193All SZGR 2.0 genes in this pathway
BAE BRCA1 TARGETS DN 3227All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN 254158All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570339All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 14888All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS DN 7252All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS 239156All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway