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Gene: PHF23 |
Gene summary for PHF23 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PHF23 | Gene ID | 79142 |
| Gene name | PHD finger protein 23 | |
| Gene Alias | hJUNE-1b | |
| Cytomap | 17p13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9BUL5 |
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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 |
| 79142 | PHF23 | LZE4T | Human | Esophagus | ESCC | 9.87e-07 | 9.05e-02 | 0.0811 |
| 79142 | PHF23 | LZE7T | Human | Esophagus | ESCC | 2.42e-02 | 1.59e-01 | 0.0667 |
| 79142 | PHF23 | LZE20T | Human | Esophagus | ESCC | 1.35e-02 | 3.37e-02 | 0.0662 |
| 79142 | PHF23 | LZE24T | Human | Esophagus | ESCC | 6.57e-12 | 3.82e-01 | 0.0596 |
| 79142 | PHF23 | P1T-E | Human | Esophagus | ESCC | 3.59e-03 | 2.73e-01 | 0.0875 |
| 79142 | PHF23 | P2T-E | Human | Esophagus | ESCC | 1.38e-11 | 2.71e-01 | 0.1177 |
| 79142 | PHF23 | P4T-E | Human | Esophagus | ESCC | 5.98e-20 | 4.73e-01 | 0.1323 |
| 79142 | PHF23 | P5T-E | Human | Esophagus | ESCC | 2.18e-12 | 9.24e-02 | 0.1327 |
| 79142 | PHF23 | P8T-E | Human | Esophagus | ESCC | 4.69e-14 | 1.17e-01 | 0.0889 |
| 79142 | PHF23 | P9T-E | Human | Esophagus | ESCC | 1.13e-08 | 1.97e-01 | 0.1131 |
| 79142 | PHF23 | P10T-E | Human | Esophagus | ESCC | 7.63e-10 | 1.25e-01 | 0.116 |
| 79142 | PHF23 | P12T-E | Human | Esophagus | ESCC | 7.05e-16 | 3.83e-01 | 0.1122 |
| 79142 | PHF23 | P15T-E | Human | Esophagus | ESCC | 5.82e-08 | 1.05e-01 | 0.1149 |
| 79142 | PHF23 | P16T-E | Human | Esophagus | ESCC | 4.38e-10 | 2.58e-01 | 0.1153 |
| 79142 | PHF23 | P17T-E | Human | Esophagus | ESCC | 4.10e-08 | 2.45e-01 | 0.1278 |
| 79142 | PHF23 | P20T-E | Human | Esophagus | ESCC | 1.63e-08 | 9.66e-02 | 0.1124 |
| 79142 | PHF23 | P21T-E | Human | Esophagus | ESCC | 1.23e-12 | 1.82e-01 | 0.1617 |
| 79142 | PHF23 | P22T-E | Human | Esophagus | ESCC | 2.23e-11 | 1.90e-01 | 0.1236 |
| 79142 | PHF23 | P23T-E | Human | Esophagus | ESCC | 2.41e-14 | 3.67e-01 | 0.108 |
| 79142 | PHF23 | P24T-E | Human | Esophagus | ESCC | 1.47e-10 | 2.28e-01 | 0.1287 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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. |
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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:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:0022411111 | Esophagus | ESCC | cellular component disassembly | 305/8552 | 443/18723 | 1.94e-23 | 4.57e-21 | 305 |
| GO:1903320111 | Esophagus | ESCC | regulation of protein modification by small protein conjugation or removal | 181/8552 | 242/18723 | 1.80e-20 | 2.60e-18 | 181 |
| GO:001050617 | Esophagus | ESCC | regulation of autophagy | 220/8552 | 317/18723 | 6.72e-18 | 6.36e-16 | 220 |
| GO:0031396111 | Esophagus | ESCC | regulation of protein ubiquitination | 154/8552 | 210/18723 | 2.70e-16 | 2.04e-14 | 154 |
| GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:003298416 | Esophagus | ESCC | protein-containing complex disassembly | 151/8552 | 224/18723 | 3.45e-11 | 1.15e-09 | 151 |
| GO:001624114 | Esophagus | ESCC | regulation of macroautophagy | 102/8552 | 141/18723 | 1.09e-10 | 3.27e-09 | 102 |
| GO:0009895111 | Esophagus | ESCC | negative regulation of catabolic process | 201/8552 | 320/18723 | 3.88e-10 | 1.05e-08 | 201 |
| GO:190332216 | Esophagus | ESCC | positive regulation of protein modification by small protein conjugation or removal | 99/8552 | 138/18723 | 4.39e-10 | 1.16e-08 | 99 |
| GO:0010639110 | Esophagus | ESCC | negative regulation of organelle organization | 215/8552 | 348/18723 | 8.20e-10 | 2.01e-08 | 215 |
| GO:0031330111 | Esophagus | ESCC | negative regulation of cellular catabolic process | 166/8552 | 262/18723 | 5.17e-09 | 1.08e-07 | 166 |
| GO:190503712 | Esophagus | ESCC | autophagosome organization | 73/8552 | 103/18723 | 1.88e-07 | 2.93e-06 | 73 |
| GO:003139816 | Esophagus | ESCC | positive regulation of protein ubiquitination | 82/8552 | 119/18723 | 2.41e-07 | 3.64e-06 | 82 |
| GO:000004513 | Esophagus | ESCC | autophagosome assembly | 69/8552 | 99/18723 | 1.10e-06 | 1.38e-05 | 69 |
| GO:190211514 | Esophagus | ESCC | regulation of organelle assembly | 116/8552 | 186/18723 | 3.15e-06 | 3.53e-05 | 116 |
| GO:00973523 | Esophagus | ESCC | autophagosome maturation | 31/8552 | 40/18723 | 4.04e-05 | 3.26e-04 | 31 |
| GO:001050712 | Esophagus | ESCC | negative regulation of autophagy | 56/8552 | 85/18723 | 1.34e-04 | 9.09e-04 | 56 |
| GO:00432446 | Esophagus | ESCC | regulation of protein-containing complex disassembly | 75/8552 | 121/18723 | 2.17e-04 | 1.36e-03 | 75 |
| GO:001624211 | Esophagus | ESCC | negative regulation of macroautophagy | 26/8552 | 34/18723 | 2.53e-04 | 1.55e-03 | 26 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
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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 |
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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 |
| PHF23 | SNV | Missense_Mutation | novel | c.536N>A | p.Arg179Gln | p.R179Q | Q9BUL5 | protein_coding | tolerated_low_confidence(0.17) | possibly_damaging(0.457) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PHF23 | SNV | Missense_Mutation | c.157N>C | p.Glu53Gln | p.E53Q | Q9BUL5 | protein_coding | tolerated(0.05) | benign(0.27) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| PHF23 | insertion | Frame_Shift_Ins | novel | c.1087_1088insCTTCCTGGGTATC | p.Ile363ThrfsTer11 | p.I363Tfs*11 | Q9BUL5 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| PHF23 | SNV | Missense_Mutation | rs201898433 | c.557N>A | p.Arg186Gln | p.R186Q | Q9BUL5 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.629) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PHF23 | SNV | Missense_Mutation | c.64N>A | p.Gln22Lys | p.Q22K | Q9BUL5 | protein_coding | tolerated(1) | benign(0.258) | TCGA-EK-A2PL-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PHF23 | SNV | Missense_Mutation | c.552N>T | p.Lys184Asn | p.K184N | Q9BUL5 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.991) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PHF23 | SNV | Missense_Mutation | novel | c.86N>T | p.Arg29Ile | p.R29I | Q9BUL5 | protein_coding | deleterious(0) | possibly_damaging(0.694) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PHF23 | SNV | Missense_Mutation | novel | c.815N>C | p.Val272Ala | p.V272A | Q9BUL5 | protein_coding | tolerated_low_confidence(0.89) | benign(0) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PHF23 | SNV | Missense_Mutation | c.1072N>A | p.Leu358Met | p.L358M | Q9BUL5 | protein_coding | tolerated(0.14) | possibly_damaging(0.652) | TCGA-G4-6586-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHF23 | SNV | Missense_Mutation | rs201898433 | c.557N>A | p.Arg186Gln | p.R186Q | Q9BUL5 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.629) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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 |
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