Gene Page: PHTF1
Summary ?
| GeneID | 10745 |
| Symbol | PHTF1 |
| Synonyms | PHTF |
| Description | putative homeodomain transcription factor 1 |
| Reference | MIM:604950|HGNC:HGNC:8939|Ensembl:ENSG00000116793|HPRD:09227|Vega:OTTHUMG00000011800 |
| Gene type | protein-coding |
| Map location | 1p13 |
| Pascal p-value | 0.415 |
| Sherlock p-value | 0.467 |
| Fetal beta | 0.452 |
| DMG | 1 (# studies) |
| eGene | Cerebellum Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). | 1 |
| GSMA_I | Genome scan meta-analysis | Psr: 0.0235 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg01580044 | 1 | 114300656 | PHTF1 | 3.184E-4 | 0.544 | 0.04 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs17745470 | chr4 | 57080197 | PHTF1 | 10745 | 0.14 | trans | ||
| rs16955618 | chr15 | 29937543 | PHTF1 | 10745 | 0.15 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| C20orf175 | 0.75 | 0.63 |
| C7orf63 | 0.71 | 0.53 |
| AC023055.4 | 0.71 | 0.62 |
| AC015724.2 | 0.70 | 0.55 |
| GDPD2 | 0.70 | 0.56 |
| DNAH11 | 0.70 | 0.31 |
| STK33 | 0.70 | 0.64 |
| SULT1C4 | 0.70 | 0.62 |
| WDR52 | 0.69 | 0.52 |
| GLB1L | 0.69 | 0.62 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| GPR22 | -0.31 | -0.28 |
| MEF2C | -0.29 | -0.26 |
| KLHL1 | -0.29 | -0.17 |
| IER5L | -0.28 | -0.24 |
| MPPED1 | -0.26 | -0.22 |
| NEUROD6 | -0.26 | -0.23 |
| SATB2 | -0.26 | -0.24 |
| NDRG1 | -0.25 | -0.18 |
| DPP4 | -0.25 | -0.24 |
| LMO7 | -0.25 | -0.16 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003677 | DNA binding | IEA | - | |
| GO:0003700 | transcription factor activity | TAS | 10729229 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
| GO:0006350 | transcription | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005634 | nucleus | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP | 633 | 376 | All SZGR 2.0 genes in this pathway |
| CONCANNON APOPTOSIS BY EPOXOMICIN UP | 239 | 157 | All SZGR 2.0 genes in this pathway |
| MOHANKUMAR TLX1 TARGETS UP | 414 | 287 | All SZGR 2.0 genes in this pathway |
| KIM MYCL1 AMPLIFICATION TARGETS DN | 20 | 12 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS DN | 848 | 527 | All SZGR 2.0 genes in this pathway |
| NUYTTEN EZH2 TARGETS UP | 1037 | 673 | All SZGR 2.0 genes in this pathway |
| BUYTAERT PHOTODYNAMIC THERAPY STRESS DN | 637 | 377 | All SZGR 2.0 genes in this pathway |
| AMIT EGF RESPONSE 20 MCF10A | 14 | 9 | All SZGR 2.0 genes in this pathway |
| GEORGES TARGETS OF MIR192 AND MIR215 | 893 | 528 | All SZGR 2.0 genes in this pathway |
| ZHAN MULTIPLE MYELOMA CD1 AND CD2 UP | 89 | 51 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE DN | 1237 | 837 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 2 | 473 | 224 | All SZGR 2.0 genes in this pathway |
| PALOMERO GSI SENSITIVITY UP | 7 | 6 | All SZGR 2.0 genes in this pathway |
| HAN SATB1 TARGETS DN | 442 | 275 | All SZGR 2.0 genes in this pathway |
| WHITFIELD CELL CYCLE S | 162 | 86 | All SZGR 2.0 genes in this pathway |
| BRUINS UVC RESPONSE VIA TP53 GROUP B | 549 | 316 | All SZGR 2.0 genes in this pathway |
| JUBAN TARGETS OF SPI1 AND FLI1 UP | 115 | 73 | All SZGR 2.0 genes in this pathway |
| FORTSCHEGGER PHF8 TARGETS DN | 784 | 464 | All SZGR 2.0 genes in this pathway |