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Gene: PHYKPL |
Gene summary for PHYKPL |
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Gene information | Species | Human | Gene symbol | PHYKPL | Gene ID | 85007 |
Gene name | 5-phosphohydroxy-L-lysine phospho-lyase | |
Gene Alias | AGXT2L2 | |
Cytomap | 5q35.3 | |
Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q8IUZ5 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
85007 | PHYKPL | P65T-E | Human | Esophagus | ESCC | 5.72e-18 | 2.93e-01 | 0.0978 |
85007 | PHYKPL | P74T-E | Human | Esophagus | ESCC | 2.28e-22 | 6.75e-01 | 0.1479 |
85007 | PHYKPL | P75T-E | Human | Esophagus | ESCC | 2.43e-34 | 5.05e-01 | 0.1125 |
85007 | PHYKPL | P76T-E | Human | Esophagus | ESCC | 6.70e-14 | 1.90e-01 | 0.1207 |
85007 | PHYKPL | P79T-E | Human | Esophagus | ESCC | 8.36e-14 | 1.93e-01 | 0.1154 |
85007 | PHYKPL | P80T-E | Human | Esophagus | ESCC | 7.19e-31 | 8.17e-01 | 0.155 |
85007 | PHYKPL | P82T-E | Human | Esophagus | ESCC | 4.28e-11 | 5.71e-01 | 0.1072 |
85007 | PHYKPL | P83T-E | Human | Esophagus | ESCC | 2.10e-08 | 3.33e-01 | 0.1738 |
85007 | PHYKPL | P84T-E | Human | Esophagus | ESCC | 2.14e-02 | 1.52e-01 | 0.0933 |
85007 | PHYKPL | P89T-E | Human | Esophagus | ESCC | 8.10e-13 | 7.98e-01 | 0.1752 |
85007 | PHYKPL | P91T-E | Human | Esophagus | ESCC | 7.32e-08 | 4.92e-01 | 0.1828 |
85007 | PHYKPL | P94T-E | Human | Esophagus | ESCC | 2.05e-04 | 4.01e-01 | 0.0879 |
85007 | PHYKPL | P107T-E | Human | Esophagus | ESCC | 2.81e-22 | 6.19e-01 | 0.171 |
85007 | PHYKPL | P127T-E | Human | Esophagus | ESCC | 7.51e-06 | 5.83e-02 | 0.0826 |
85007 | PHYKPL | P128T-E | Human | Esophagus | ESCC | 3.32e-11 | 2.59e-01 | 0.1241 |
85007 | PHYKPL | P130T-E | Human | Esophagus | ESCC | 1.84e-43 | 6.89e-01 | 0.1676 |
85007 | PHYKPL | NAFLD1 | Human | Liver | NAFLD | 1.76e-06 | 7.61e-01 | -0.04 |
85007 | PHYKPL | S43 | Human | Liver | Cirrhotic | 1.19e-04 | -2.12e-01 | -0.0187 |
85007 | PHYKPL | HCC1_Meng | Human | Liver | HCC | 1.10e-64 | 4.31e-03 | 0.0246 |
85007 | PHYKPL | HCC2_Meng | Human | Liver | HCC | 2.75e-21 | 1.75e-02 | 0.0107 |
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∗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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00310 | Colorectum | AD | Lysine degradation | 27/2092 | 63/8465 | 1.17e-03 | 7.75e-03 | 4.94e-03 | 27 |
hsa003101 | Colorectum | AD | Lysine degradation | 27/2092 | 63/8465 | 1.17e-03 | 7.75e-03 | 4.94e-03 | 27 |
hsa003104 | Colorectum | FAP | Lysine degradation | 23/1404 | 63/8465 | 1.04e-04 | 9.46e-04 | 5.76e-04 | 23 |
hsa003105 | Colorectum | FAP | Lysine degradation | 23/1404 | 63/8465 | 1.04e-04 | 9.46e-04 | 5.76e-04 | 23 |
hsa003106 | Colorectum | CRC | Lysine degradation | 18/1091 | 63/8465 | 7.21e-04 | 6.34e-03 | 4.30e-03 | 18 |
hsa003107 | Colorectum | CRC | Lysine degradation | 18/1091 | 63/8465 | 7.21e-04 | 6.34e-03 | 4.30e-03 | 18 |
hsa0031010 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
hsa0031013 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
hsa003108 | Liver | NAFLD | Lysine degradation | 21/1043 | 63/8465 | 1.09e-05 | 3.58e-04 | 2.89e-04 | 21 |
hsa0031011 | Liver | NAFLD | Lysine degradation | 21/1043 | 63/8465 | 1.09e-05 | 3.58e-04 | 2.89e-04 | 21 |
hsa0031021 | Liver | Cirrhotic | Lysine degradation | 29/2530 | 63/8465 | 4.81e-03 | 1.74e-02 | 1.07e-02 | 29 |
hsa0031031 | Liver | Cirrhotic | Lysine degradation | 29/2530 | 63/8465 | 4.81e-03 | 1.74e-02 | 1.07e-02 | 29 |
hsa0031041 | Liver | HCC | Lysine degradation | 47/4020 | 63/8465 | 1.02e-05 | 7.58e-05 | 4.22e-05 | 47 |
hsa0031051 | Liver | HCC | Lysine degradation | 47/4020 | 63/8465 | 1.02e-05 | 7.58e-05 | 4.22e-05 | 47 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
PHYKPL | SNV | Missense_Mutation | novel | c.308A>C | p.Gln103Pro | p.Q103P | Q8IUZ5 | protein_coding | tolerated(0.48) | benign(0) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PHYKPL | SNV | Missense_Mutation | c.1043G>T | p.Gly348Val | p.G348V | Q8IUZ5 | protein_coding | tolerated(0.09) | benign(0.009) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PHYKPL | SNV | Missense_Mutation | novel | c.287N>A | p.Leu96Gln | p.L96Q | Q8IUZ5 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-EW-A3U0-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
PHYKPL | SNV | Missense_Mutation | novel | c.1147G>A | p.Glu383Lys | p.E383K | Q8IUZ5 | protein_coding | tolerated(0.38) | benign(0.005) | TCGA-OL-A5DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PHYKPL | SNV | Missense_Mutation | novel | c.739N>A | p.Glu247Lys | p.E247K | Q8IUZ5 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
PHYKPL | SNV | Missense_Mutation | c.1120N>C | p.Asp374His | p.D374H | Q8IUZ5 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-C5-A1BJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
PHYKPL | SNV | Missense_Mutation | novel | c.164N>A | p.Ser55Asn | p.S55N | Q8IUZ5 | protein_coding | tolerated(1) | benign(0) | TCGA-MA-AA3W-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PHYKPL | SNV | Missense_Mutation | rs757976712 | c.466N>T | p.Arg156Cys | p.R156C | Q8IUZ5 | protein_coding | deleterious(0.01) | possibly_damaging(0.846) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PHYKPL | SNV | Missense_Mutation | rs781248682 | c.536N>A | p.Arg179Gln | p.R179Q | Q8IUZ5 | protein_coding | deleterious(0.03) | benign(0.273) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PHYKPL | SNV | Missense_Mutation | rs756247782 | c.268N>A | p.Val90Met | p.V90M | Q8IUZ5 | protein_coding | deleterious(0.01) | probably_damaging(0.963) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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