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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:19050374 | Oral cavity | OSCC | autophagosome organization | 63/7305 | 103/18723 | 4.30e-06 | 4.98e-05 | 63 |
| GO:00000454 | Oral cavity | OSCC | autophagosome assembly | 60/7305 | 99/18723 | 1.09e-05 | 1.14e-04 | 60 |
| GO:00440883 | Oral cavity | OSCC | regulation of vacuole organization | 31/7305 | 45/18723 | 4.70e-05 | 3.95e-04 | 31 |
| GO:00973522 | Oral cavity | OSCC | autophagosome maturation | 28/7305 | 40/18723 | 7.00e-05 | 5.60e-04 | 28 |
| GO:00105075 | Oral cavity | OSCC | negative regulation of autophagy | 51/7305 | 85/18723 | 7.08e-05 | 5.62e-04 | 51 |
| GO:20007852 | Oral cavity | OSCC | regulation of autophagosome assembly | 26/7305 | 39/18723 | 4.33e-04 | 2.63e-03 | 26 |
| GO:00162421 | Oral cavity | OSCC | negative regulation of macroautophagy | 23/7305 | 34/18723 | 6.77e-04 | 3.78e-03 | 23 |
| GO:00432445 | Oral cavity | OSCC | regulation of protein-containing complex disassembly | 65/7305 | 121/18723 | 7.08e-04 | 3.90e-03 | 65 |
| GO:19021161 | Oral cavity | OSCC | negative regulation of organelle assembly | 26/7305 | 41/18723 | 1.34e-03 | 6.62e-03 | 26 |
| GO:1902902 | Oral cavity | OSCC | negative regulation of autophagosome assembly | 12/7305 | 15/18723 | 1.49e-03 | 7.13e-03 | 12 |
| GO:0022411112 | Skin | cSCC | cellular component disassembly | 201/4864 | 443/18723 | 4.09e-19 | 5.69e-17 | 201 |
| GO:190332029 | Skin | cSCC | regulation of protein modification by small protein conjugation or removal | 125/4864 | 242/18723 | 9.50e-18 | 1.05e-15 | 125 |
| GO:003139629 | Skin | cSCC | regulation of protein ubiquitination | 107/4864 | 210/18723 | 7.17e-15 | 5.35e-13 | 107 |
| GO:001623619 | Skin | cSCC | macroautophagy | 136/4864 | 291/18723 | 1.36e-14 | 9.78e-13 | 136 |
| GO:003133028 | Skin | cSCC | negative regulation of cellular catabolic process | 115/4864 | 262/18723 | 2.03e-10 | 8.72e-09 | 115 |
| GO:000989527 | Skin | cSCC | negative regulation of catabolic process | 133/4864 | 320/18723 | 6.99e-10 | 2.77e-08 | 133 |
| GO:0010639111 | Skin | cSCC | negative regulation of organelle organization | 140/4864 | 348/18723 | 3.35e-09 | 1.15e-07 | 140 |
| GO:003298418 | Skin | cSCC | protein-containing complex disassembly | 98/4864 | 224/18723 | 5.31e-09 | 1.77e-07 | 98 |
| GO:001050619 | Skin | cSCC | regulation of autophagy | 127/4864 | 317/18723 | 2.36e-08 | 6.71e-07 | 127 |
| GO:190332217 | Skin | cSCC | positive regulation of protein modification by small protein conjugation or removal | 64/4864 | 138/18723 | 1.79e-07 | 3.94e-06 | 64 |
| 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 |
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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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