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Gene: PLOD3 |
Gene summary for PLOD3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLOD3 | Gene ID | 8985 |
| Gene name | procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | |
| Gene Alias | LH3 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O60568 |
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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 |
| 8985 | PLOD3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.56e-06 | 4.94e-01 | -0.0811 |
| 8985 | PLOD3 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.15e-03 | 3.68e-01 | -0.1088 |
| 8985 | PLOD3 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.75e-04 | 2.62e-01 | -0.1954 |
| 8985 | PLOD3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.36e-04 | 4.25e-01 | -0.1207 |
| 8985 | PLOD3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.79e-10 | 3.62e-01 | -0.1464 |
| 8985 | PLOD3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.69e-08 | 5.23e-01 | -0.059 |
| 8985 | PLOD3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.09e-02 | 2.69e-01 | 0.0674 |
| 8985 | PLOD3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.45e-03 | 2.10e-01 | 0.294 |
| 8985 | PLOD3 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.27e-04 | 9.74e-01 | 0.3487 |
| 8985 | PLOD3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 9.58e-09 | 6.04e-01 | 0.281 |
| 8985 | PLOD3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.53e-26 | 7.83e-01 | 0.3859 |
| 8985 | PLOD3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.41e-03 | 4.98e-01 | 0.2585 |
| 8985 | PLOD3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.66e-15 | 4.79e-01 | 0.3005 |
| 8985 | PLOD3 | LZE4T | Human | Esophagus | ESCC | 3.50e-11 | 1.70e-01 | 0.0811 |
| 8985 | PLOD3 | LZE7T | Human | Esophagus | ESCC | 1.71e-12 | 5.40e-01 | 0.0667 |
| 8985 | PLOD3 | LZE8T | Human | Esophagus | ESCC | 6.34e-08 | 2.03e-01 | 0.067 |
| 8985 | PLOD3 | LZE22T | Human | Esophagus | ESCC | 1.81e-06 | 4.38e-01 | 0.068 |
| 8985 | PLOD3 | LZE24T | Human | Esophagus | ESCC | 7.77e-14 | 2.14e-01 | 0.0596 |
| 8985 | PLOD3 | LZE6T | Human | Esophagus | ESCC | 2.23e-07 | 4.39e-01 | 0.0845 |
| 8985 | PLOD3 | P1T-E | Human | Esophagus | ESCC | 4.75e-09 | 3.79e-01 | 0.0875 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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:0002064 | Colorectum | AD | epithelial cell development | 89/3918 | 220/18723 | 2.98e-11 | 3.52e-09 | 89 |
| GO:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
| GO:0001885 | Colorectum | AD | endothelial cell development | 26/3918 | 64/18723 | 2.67e-04 | 3.29e-03 | 26 |
| GO:0006575 | Colorectum | AD | cellular modified amino acid metabolic process | 59/3918 | 188/18723 | 4.80e-04 | 5.27e-03 | 59 |
| GO:0003158 | Colorectum | AD | endothelium development | 44/3918 | 136/18723 | 1.20e-03 | 1.07e-02 | 44 |
| GO:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
| GO:0045446 | Colorectum | AD | endothelial cell differentiation | 39/3918 | 118/18723 | 1.42e-03 | 1.22e-02 | 39 |
| GO:0060425 | Colorectum | AD | lung morphogenesis | 20/3918 | 50/18723 | 1.65e-03 | 1.38e-02 | 20 |
| GO:0042398 | Colorectum | AD | cellular modified amino acid biosynthetic process | 18/3918 | 46/18723 | 3.67e-03 | 2.60e-02 | 18 |
| GO:0006486 | Colorectum | AD | protein glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
| GO:0043413 | Colorectum | AD | macromolecule glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
| GO:0070085 | Colorectum | AD | glycosylation | 67/3918 | 240/18723 | 5.78e-03 | 3.67e-02 | 67 |
| GO:0008544 | Colorectum | AD | epidermis development | 87/3918 | 324/18723 | 5.99e-03 | 3.76e-02 | 87 |
| GO:0021915 | Colorectum | AD | neural tube development | 45/3918 | 152/18723 | 7.05e-03 | 4.31e-02 | 45 |
| GO:00020642 | Colorectum | MSS | epithelial cell development | 81/3467 | 220/18723 | 1.02e-10 | 1.06e-08 | 81 |
| GO:00017012 | Colorectum | MSS | in utero embryonic development | 99/3467 | 367/18723 | 3.71e-05 | 7.10e-04 | 99 |
| GO:00423981 | Colorectum | MSS | cellular modified amino acid biosynthetic process | 20/3467 | 46/18723 | 8.26e-05 | 1.35e-03 | 20 |
| GO:00065751 | Colorectum | MSS | cellular modified amino acid metabolic process | 55/3467 | 188/18723 | 2.16e-04 | 3.01e-03 | 55 |
| GO:00604251 | Colorectum | MSS | lung morphogenesis | 20/3467 | 50/18723 | 3.25e-04 | 4.21e-03 | 20 |
| GO:00018851 | Colorectum | MSS | endothelial cell development | 22/3467 | 64/18723 | 1.86e-03 | 1.64e-02 | 22 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 |
| 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 |
| 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 |
| 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 |
| PLOD3 | SNV | Missense_Mutation | novel | c.1082N>T | p.Gly361Val | p.G361V | O60568 | protein_coding | deleterious(0.04) | probably_damaging(0.998) | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| PLOD3 | SNV | Missense_Mutation | rs776439156 | c.889N>T | p.Arg297Trp | p.R297W | O60568 | protein_coding | deleterious(0.03) | possibly_damaging(0.586) | TCGA-AN-A0AM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PLOD3 | SNV | Missense_Mutation | c.275G>T | p.Trp92Leu | p.W92L | O60568 | protein_coding | tolerated(1) | benign(0.006) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| PLOD3 | SNV | Missense_Mutation | c.839N>C | p.Gly280Ala | p.G280A | O60568 | protein_coding | tolerated(0.77) | benign(0.013) | TCGA-E9-A248-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| PLOD3 | insertion | Nonsense_Mutation | novel | c.440_441insCAAAAATTAGCCAGGC | p.Glu147AspfsTer4 | p.E147Dfs*4 | O60568 | protein_coding | TCGA-A8-A09E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | ||
| PLOD3 | SNV | Missense_Mutation | rs146795873 | c.982G>C | p.Val328Leu | p.V328L | O60568 | protein_coding | tolerated(1) | benign(0) | TCGA-C5-A3HL-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| PLOD3 | SNV | Missense_Mutation | rs777238858 | c.1493N>A | p.Arg498Gln | p.R498Q | O60568 | protein_coding | deleterious(0) | possibly_damaging(0.82) | TCGA-DG-A2KM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PLOD3 | SNV | Missense_Mutation | rs376302927 | c.1940N>A | p.Arg647Gln | p.R647Q | O60568 | protein_coding | tolerated(0.53) | benign(0.041) | TCGA-HM-A6W2-06 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PLOD3 | insertion | Frame_Shift_Ins | rs746342377 | c.876dupG | p.Gln293AlafsTer48 | p.Q293Afs*48 | O60568 | protein_coding | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| PLOD3 | SNV | Missense_Mutation | c.379N>C | p.Lys127Gln | p.K127Q | O60568 | protein_coding | tolerated(0.06) | benign(0.322) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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