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Gene: PLOD2 |
Gene summary for PLOD2 |
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Gene information | Species | Human | Gene symbol | PLOD2 | Gene ID | 5352 |
Gene name | procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 | |
Gene Alias | BRKS2 | |
Cytomap | 3q24 | |
Gene Type | protein-coding | GO ID | GO:0001666 | UniProtAcc | O00469 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
5352 | PLOD2 | GSM4909291 | Human | Breast | IDC | 1.50e-02 | -2.21e-01 | 0.1753 |
5352 | PLOD2 | GSM4909294 | Human | Breast | IDC | 2.59e-07 | -2.73e-01 | 0.2022 |
5352 | PLOD2 | GSM4909296 | Human | Breast | IDC | 3.34e-07 | -2.58e-01 | 0.1524 |
5352 | PLOD2 | GSM4909297 | Human | Breast | IDC | 2.01e-07 | -2.43e-01 | 0.1517 |
5352 | PLOD2 | GSM4909302 | Human | Breast | IDC | 1.15e-03 | -1.74e-01 | 0.1545 |
5352 | PLOD2 | GSM4909304 | Human | Breast | IDC | 1.81e-05 | 3.08e-01 | 0.1636 |
5352 | PLOD2 | GSM4909306 | Human | Breast | IDC | 4.06e-03 | -2.56e-01 | 0.1564 |
5352 | PLOD2 | GSM4909307 | Human | Breast | IDC | 1.08e-06 | -2.62e-01 | 0.1569 |
5352 | PLOD2 | GSM4909308 | Human | Breast | IDC | 2.67e-14 | -2.78e-01 | 0.158 |
5352 | PLOD2 | GSM4909309 | Human | Breast | IDC | 1.66e-02 | -1.78e-01 | 0.0483 |
5352 | PLOD2 | GSM4909311 | Human | Breast | IDC | 3.69e-10 | -2.78e-01 | 0.1534 |
5352 | PLOD2 | GSM4909312 | Human | Breast | IDC | 1.69e-10 | -2.78e-01 | 0.1552 |
5352 | PLOD2 | GSM4909313 | Human | Breast | IDC | 2.49e-03 | -1.86e-01 | 0.0391 |
5352 | PLOD2 | GSM4909315 | Human | Breast | IDC | 1.21e-02 | -2.45e-01 | 0.21 |
5352 | PLOD2 | GSM4909316 | Human | Breast | IDC | 6.13e-04 | -2.78e-01 | 0.21 |
5352 | PLOD2 | GSM4909317 | Human | Breast | IDC | 2.07e-04 | -2.16e-01 | 0.1355 |
5352 | PLOD2 | GSM4909319 | Human | Breast | IDC | 3.07e-08 | -2.60e-01 | 0.1563 |
5352 | PLOD2 | GSM4909321 | Human | Breast | IDC | 2.30e-02 | -1.72e-01 | 0.1559 |
5352 | PLOD2 | ctrl6 | Human | Breast | Precancer | 2.57e-14 | 8.20e-01 | -0.0061 |
5352 | PLOD2 | brca3 | Human | Breast | Precancer | 1.09e-09 | 3.08e-01 | -0.0263 |
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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 |
GO:0070482110 | Oral cavity | LP | response to oxygen levels | 122/4623 | 347/18723 | 7.10e-06 | 1.37e-04 | 122 |
GO:0001666110 | Oral cavity | LP | response to hypoxia | 106/4623 | 307/18723 | 6.38e-05 | 8.61e-04 | 106 |
GO:0036293110 | Oral cavity | LP | response to decreased oxygen levels | 109/4623 | 322/18723 | 1.25e-04 | 1.46e-03 | 109 |
GO:004239812 | Oral cavity | LP | cellular modified amino acid biosynthetic process | 21/4623 | 46/18723 | 1.56e-03 | 1.20e-02 | 21 |
GO:190160711 | Oral cavity | LP | alpha-amino acid biosynthetic process | 28/4623 | 68/18723 | 2.01e-03 | 1.49e-02 | 28 |
GO:001812611 | Oral cavity | LP | protein hydroxylation | 14/4623 | 27/18723 | 2.14e-03 | 1.57e-02 | 14 |
GO:000657512 | Oral cavity | LP | cellular modified amino acid metabolic process | 64/4623 | 188/18723 | 2.43e-03 | 1.73e-02 | 64 |
GO:000865211 | Oral cavity | LP | cellular amino acid biosynthetic process | 30/4623 | 76/18723 | 3.07e-03 | 2.09e-02 | 30 |
GO:00090673 | Oral cavity | LP | aspartate family amino acid biosynthetic process | 11/4623 | 21/18723 | 5.78e-03 | 3.44e-02 | 11 |
GO:007048226 | Skin | cSCC | response to oxygen levels | 133/4864 | 347/18723 | 2.39e-07 | 5.07e-06 | 133 |
GO:000166626 | Skin | cSCC | response to hypoxia | 116/4864 | 307/18723 | 3.09e-06 | 4.81e-05 | 116 |
GO:001820515 | Skin | cSCC | peptidyl-lysine modification | 137/4864 | 376/18723 | 4.09e-06 | 6.09e-05 | 137 |
GO:003629326 | Skin | cSCC | response to decreased oxygen levels | 119/4864 | 322/18723 | 7.98e-06 | 1.09e-04 | 119 |
GO:00065758 | Skin | cSCC | cellular modified amino acid metabolic process | 73/4864 | 188/18723 | 7.11e-05 | 6.85e-04 | 73 |
GO:00423987 | Skin | cSCC | cellular modified amino acid biosynthetic process | 24/4864 | 46/18723 | 1.32e-04 | 1.19e-03 | 24 |
GO:19016076 | Skin | cSCC | alpha-amino acid biosynthetic process | 30/4864 | 68/18723 | 8.91e-04 | 6.10e-03 | 30 |
GO:00090675 | Skin | cSCC | aspartate family amino acid biosynthetic process | 12/4864 | 21/18723 | 2.40e-03 | 1.38e-02 | 12 |
GO:00181264 | Skin | cSCC | protein hydroxylation | 14/4864 | 27/18723 | 3.58e-03 | 1.93e-02 | 14 |
GO:00086526 | Skin | cSCC | cellular amino acid biosynthetic process | 30/4864 | 76/18723 | 6.79e-03 | 3.29e-02 | 30 |
GO:007048227 | Thyroid | HT | response to oxygen levels | 50/1272 | 347/18723 | 3.61e-07 | 1.65e-05 | 50 |
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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 |
hsa003102 | Colorectum | MSS | Lysine degradation | 24/1875 | 63/8465 | 2.94e-03 | 1.39e-02 | 8.50e-03 | 24 |
hsa003103 | Colorectum | MSS | Lysine degradation | 24/1875 | 63/8465 | 2.94e-03 | 1.39e-02 | 8.50e-03 | 24 |
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 |
hsa003109 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
hsa0031012 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
hsa0031022 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
hsa0031032 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
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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 |
PLOD2 | SNV | Missense_Mutation | novel | c.2140N>G | p.Leu714Val | p.L714V | O00469 | protein_coding | tolerated(0.07) | benign(0.349) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
PLOD2 | SNV | Missense_Mutation | rs376497013 | c.1703N>A | p.Arg568His | p.R568H | O00469 | protein_coding | deleterious(0.05) | benign(0.003) | TCGA-BH-A203-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PLOD2 | SNV | Missense_Mutation | rs774991815 | c.484C>T | p.Arg162Cys | p.R162C | O00469 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PLOD2 | SNV | Missense_Mutation | c.1340N>C | p.Ile447Thr | p.I447T | O00469 | protein_coding | deleterious(0.02) | possibly_damaging(0.517) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PLOD2 | SNV | Missense_Mutation | novel | c.119N>C | p.Leu40Ser | p.L40S | O00469 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PLOD2 | SNV | Missense_Mutation | c.862N>A | p.Asp288Asn | p.D288N | O00469 | protein_coding | tolerated(0.21) | benign(0.036) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PLOD2 | SNV | Missense_Mutation | rs758538664 | c.1484N>A | p.Arg495Gln | p.R495Q | O00469 | protein_coding | tolerated(0.34) | benign(0.392) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
PLOD2 | SNV | Missense_Mutation | rs141419117 | c.853N>A | p.Asp285Asn | p.D285N | O00469 | protein_coding | tolerated(0.32) | benign(0.03) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
PLOD2 | SNV | Missense_Mutation | novel | c.723N>T | p.Lys241Asn | p.K241N | O00469 | protein_coding | deleterious(0.01) | benign(0.253) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
PLOD2 | SNV | Missense_Mutation | c.2257G>A | p.Val753Met | p.V753M | O00469 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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