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Gene: PLOD2 |
Gene summary for PLOD2 |
 Gene summary. |
| 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 |
| 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 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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. |
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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:003629327 | Thyroid | HT | response to decreased oxygen levels | 46/1272 | 322/18723 | 1.34e-06 | 5.14e-05 | 46 |
| GO:000166627 | Thyroid | HT | response to hypoxia | 44/1272 | 307/18723 | 2.07e-06 | 7.53e-05 | 44 |
| GO:00065759 | Thyroid | HT | cellular modified amino acid metabolic process | 28/1272 | 188/18723 | 7.21e-05 | 1.31e-03 | 28 |
| GO:00423988 | Thyroid | HT | cellular modified amino acid biosynthetic process | 9/1272 | 46/18723 | 3.35e-03 | 2.60e-02 | 9 |
| GO:00182059 | Thyroid | PTC | peptidyl-lysine modification | 188/5968 | 376/18723 | 1.34e-13 | 7.09e-12 | 188 |
| GO:0070482113 | Thyroid | PTC | response to oxygen levels | 167/5968 | 347/18723 | 1.51e-10 | 5.03e-09 | 167 |
| GO:0036293113 | Thyroid | PTC | response to decreased oxygen levels | 153/5968 | 322/18723 | 2.71e-09 | 7.52e-08 | 153 |
| GO:0001666113 | Thyroid | PTC | response to hypoxia | 145/5968 | 307/18723 | 1.14e-08 | 2.74e-07 | 145 |
| GO:000657513 | Thyroid | PTC | cellular modified amino acid metabolic process | 85/5968 | 188/18723 | 8.29e-05 | 7.01e-04 | 85 |
| GO:00090676 | Thyroid | PTC | aspartate family amino acid biosynthetic process | 15/5968 | 21/18723 | 2.31e-04 | 1.67e-03 | 15 |
| GO:00181265 | Thyroid | PTC | protein hydroxylation | 17/5968 | 27/18723 | 8.67e-04 | 5.30e-03 | 17 |
| GO:004239813 | Thyroid | PTC | cellular modified amino acid biosynthetic process | 25/5968 | 46/18723 | 1.31e-03 | 7.43e-03 | 25 |
| GO:19016077 | Thyroid | PTC | alpha-amino acid biosynthetic process | 33/5968 | 68/18723 | 3.04e-03 | 1.50e-02 | 33 |
| GO:00086527 | Thyroid | PTC | cellular amino acid biosynthetic process | 35/5968 | 76/18723 | 6.68e-03 | 2.89e-02 | 35 |
| GO:007048228 | Thyroid | ATC | response to oxygen levels | 193/6293 | 347/18723 | 1.83e-17 | 1.93e-15 | 193 |
| GO:003629328 | Thyroid | ATC | response to decreased oxygen levels | 177/6293 | 322/18723 | 1.81e-15 | 1.32e-13 | 177 |
| GO:000166628 | Thyroid | ATC | response to hypoxia | 169/6293 | 307/18723 | 6.58e-15 | 4.12e-13 | 169 |
| GO:001820516 | Thyroid | ATC | peptidyl-lysine modification | 193/6293 | 376/18723 | 6.92e-13 | 3.06e-11 | 193 |
| GO:000906711 | Thyroid | ATC | aspartate family amino acid biosynthetic process | 15/6293 | 21/18723 | 4.45e-04 | 2.64e-03 | 15 |
| GO:000865212 | Thyroid | ATC | cellular amino acid biosynthetic process | 39/6293 | 76/18723 | 1.07e-03 | 5.63e-03 | 39 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched KEGG pathways. |
| 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 |
| 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 |
| 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 |
| 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 |
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