|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PHF20 |
Gene summary for PHF20 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PHF20 | Gene ID | 51230 |
| Gene name | PHD finger protein 20 | |
| Gene Alias | C20orf104 | |
| Cytomap | 20q11.22-q11.23 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9BVI0 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 51230 | PHF20 | AEH-subject2 | Human | Endometrium | AEH | 3.91e-05 | 3.04e-03 | -0.2525 |
| 51230 | PHF20 | EEC-subject1 | Human | Endometrium | EEC | 6.03e-04 | 1.04e-01 | -0.2682 |
| 51230 | PHF20 | EEC-subject3 | Human | Endometrium | EEC | 5.94e-08 | 2.21e-02 | -0.2525 |
| 51230 | PHF20 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.37e-15 | -8.38e-02 | -0.1869 |
| 51230 | PHF20 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.34e-17 | -1.71e-01 | -0.1875 |
| 51230 | PHF20 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.83e-18 | -1.37e-01 | -0.1883 |
| 51230 | PHF20 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.03e-14 | -1.01e-01 | -0.1934 |
| 51230 | PHF20 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 9.25e-24 | -8.07e-02 | -0.1917 |
| 51230 | PHF20 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 2.09e-21 | -1.40e-01 | -0.1916 |
| 51230 | PHF20 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 4.76e-04 | -1.04e-01 | -0.1269 |
| 51230 | PHF20 | LZE2T | Human | Esophagus | ESCC | 4.64e-02 | 1.70e-01 | 0.082 |
| 51230 | PHF20 | LZE4T | Human | Esophagus | ESCC | 1.19e-26 | 5.85e-01 | 0.0811 |
| 51230 | PHF20 | LZE5T | Human | Esophagus | ESCC | 1.67e-02 | 5.99e-01 | 0.0514 |
| 51230 | PHF20 | LZE7T | Human | Esophagus | ESCC | 6.81e-14 | 6.96e-01 | 0.0667 |
| 51230 | PHF20 | LZE8T | Human | Esophagus | ESCC | 7.21e-08 | 2.09e-01 | 0.067 |
| 51230 | PHF20 | LZE20T | Human | Esophagus | ESCC | 1.16e-10 | 2.71e-01 | 0.0662 |
| 51230 | PHF20 | LZE22D1 | Human | Esophagus | HGIN | 6.53e-03 | 1.54e-01 | 0.0595 |
| 51230 | PHF20 | LZE22T | Human | Esophagus | ESCC | 4.25e-11 | 4.70e-01 | 0.068 |
| 51230 | PHF20 | LZE24T | Human | Esophagus | ESCC | 3.02e-26 | 8.74e-01 | 0.0596 |
| 51230 | PHF20 | LZE21T | Human | Esophagus | ESCC | 1.09e-05 | 1.16e-01 | 0.0655 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0016570 | Colorectum | MSS | histone modification | 113/3467 | 463/18723 | 8.37e-04 | 8.68e-03 | 113 |
| GO:00165701 | Colorectum | FAP | histone modification | 94/2622 | 463/18723 | 1.06e-04 | 1.76e-03 | 94 |
| GO:00165702 | Colorectum | CRC | histone modification | 75/2078 | 463/18723 | 4.95e-04 | 7.06e-03 | 75 |
| GO:00182057 | Esophagus | HGIN | peptidyl-lysine modification | 88/2587 | 376/18723 | 2.99e-07 | 1.39e-05 | 88 |
| GO:00165708 | Esophagus | HGIN | histone modification | 92/2587 | 463/18723 | 1.70e-04 | 3.30e-03 | 92 |
| GO:00064735 | Esophagus | HGIN | protein acetylation | 45/2587 | 201/18723 | 6.17e-04 | 8.58e-03 | 45 |
| GO:00439844 | Esophagus | HGIN | histone H4-K16 acetylation | 9/2587 | 20/18723 | 7.18e-04 | 9.60e-03 | 9 |
| GO:00183945 | Esophagus | HGIN | peptidyl-lysine acetylation | 39/2587 | 169/18723 | 7.46e-04 | 9.90e-03 | 39 |
| GO:00435435 | Esophagus | HGIN | protein acylation | 51/2587 | 243/18723 | 1.33e-03 | 1.57e-02 | 51 |
| GO:00439675 | Esophagus | HGIN | histone H4 acetylation | 19/2587 | 67/18723 | 1.39e-03 | 1.63e-02 | 19 |
| GO:00064755 | Esophagus | HGIN | internal protein amino acid acetylation | 36/2587 | 160/18723 | 1.87e-03 | 2.01e-02 | 36 |
| GO:00183935 | Esophagus | HGIN | internal peptidyl-lysine acetylation | 35/2587 | 158/18723 | 2.82e-03 | 2.75e-02 | 35 |
| GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:001820514 | Esophagus | ESCC | peptidyl-lysine modification | 259/8552 | 376/18723 | 3.90e-20 | 5.26e-18 | 259 |
| GO:001839413 | Esophagus | ESCC | peptidyl-lysine acetylation | 123/8552 | 169/18723 | 6.58e-13 | 2.94e-11 | 123 |
| GO:004354313 | Esophagus | ESCC | protein acylation | 165/8552 | 243/18723 | 1.69e-12 | 7.14e-11 | 165 |
| GO:000647313 | Esophagus | ESCC | protein acetylation | 140/8552 | 201/18723 | 4.37e-12 | 1.69e-10 | 140 |
| GO:001839313 | Esophagus | ESCC | internal peptidyl-lysine acetylation | 114/8552 | 158/18723 | 1.16e-11 | 4.24e-10 | 114 |
| GO:000647513 | Esophagus | ESCC | internal protein amino acid acetylation | 115/8552 | 160/18723 | 1.43e-11 | 5.08e-10 | 115 |
| GO:00165735 | Esophagus | ESCC | histone acetylation | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PHF20 | SNV | Missense_Mutation | rs780164709 | c.1271C>T | p.Ser424Leu | p.S424L | Q9BVI0 | protein_coding | deleterious(0.01) | benign(0.122) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PHF20 | SNV | Missense_Mutation | c.2249A>T | p.Gln750Leu | p.Q750L | Q9BVI0 | protein_coding | tolerated(0.1) | possibly_damaging(0.728) | TCGA-B6-A0X0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PHF20 | SNV | Missense_Mutation | c.1998G>T | p.Met666Ile | p.M666I | Q9BVI0 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-D8-A1XZ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen+anastrozolum | SD | |
| PHF20 | SNV | Missense_Mutation | c.368N>C | p.Gly123Ala | p.G123A | Q9BVI0 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHF20 | SNV | Missense_Mutation | novel | c.2945N>T | p.Pro982Leu | p.P982L | Q9BVI0 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-S3-AA17-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD |
| PHF20 | insertion | Frame_Shift_Ins | novel | c.319_320insTATCTATAATGGTCCTGCTGCTTTTGGATCTGAC | p.Thr108SerfsTer15 | p.T108Sfs*15 | Q9BVI0 | protein_coding | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PHF20 | insertion | In_Frame_Ins | novel | c.189_190insACTGGCCGGGCACAGTGGTTCACCCTTGTAATC | p.Pro63_Tyr64insThrGlyArgAlaGlnTrpPheThrLeuValIle | p.P63_Y64insTGRAQWFTLVI | Q9BVI0 | protein_coding | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| PHF20 | insertion | Frame_Shift_Ins | novel | c.2379_2380insGTGGTCTCCT | p.Asn794ValfsTer4 | p.N794Vfs*4 | Q9BVI0 | protein_coding | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD | ||
| PHF20 | SNV | Missense_Mutation | rs200315522 | c.2600N>T | p.Ala867Val | p.A867V | Q9BVI0 | protein_coding | deleterious(0.04) | benign(0.038) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PHF20 | SNV | Missense_Mutation | novel | c.2845N>T | p.Leu949Phe | p.L949F | Q9BVI0 | protein_coding | deleterious(0.01) | probably_damaging(0.975) | TCGA-C5-A8XJ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |