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Gene: LOX |
Gene summary for LOX |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LOX | Gene ID | 4015 |
| Gene name | lysyl oxidase | |
| Gene Alias | AAT10 | |
| Cytomap | 5q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | B7ZAJ4 |
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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 |
| 4015 | LOX | P4T-E | Human | Esophagus | ESCC | 3.52e-03 | 3.03e-01 | 0.1323 |
| 4015 | LOX | P8T-E | Human | Esophagus | ESCC | 7.98e-04 | 2.02e-01 | 0.0889 |
| 4015 | LOX | P16T-E | Human | Esophagus | ESCC | 2.51e-10 | 3.41e-01 | 0.1153 |
| 4015 | LOX | P17T-E | Human | Esophagus | ESCC | 1.22e-04 | 5.42e-01 | 0.1278 |
| 4015 | LOX | P23T-E | Human | Esophagus | ESCC | 8.95e-05 | 2.66e-01 | 0.108 |
| 4015 | LOX | P32T-E | Human | Esophagus | ESCC | 7.80e-22 | 9.89e-01 | 0.1666 |
| 4015 | LOX | P37T-E | Human | Esophagus | ESCC | 9.32e-18 | 6.36e-01 | 0.1371 |
| 4015 | LOX | P42T-E | Human | Esophagus | ESCC | 9.84e-07 | 3.99e-01 | 0.1175 |
| 4015 | LOX | P44T-E | Human | Esophagus | ESCC | 2.72e-04 | 6.69e-01 | 0.1096 |
| 4015 | LOX | P52T-E | Human | Esophagus | ESCC | 1.68e-10 | 5.54e-01 | 0.1555 |
| 4015 | LOX | P61T-E | Human | Esophagus | ESCC | 3.95e-07 | 2.81e-01 | 0.099 |
| 4015 | LOX | P62T-E | Human | Esophagus | ESCC | 1.12e-04 | 2.69e-01 | 0.1302 |
| 4015 | LOX | P74T-E | Human | Esophagus | ESCC | 1.39e-02 | 1.59e-01 | 0.1479 |
| 4015 | LOX | P76T-E | Human | Esophagus | ESCC | 1.70e-17 | 7.18e-01 | 0.1207 |
| 4015 | LOX | P89T-E | Human | Esophagus | ESCC | 1.46e-19 | 1.93e+00 | 0.1752 |
| 4015 | LOX | P91T-E | Human | Esophagus | ESCC | 1.63e-05 | 1.14e+00 | 0.1828 |
| 4015 | LOX | P130T-E | Human | Esophagus | ESCC | 2.01e-15 | 5.56e-01 | 0.1676 |
| 4015 | LOX | C21 | Human | Oral cavity | OSCC | 1.02e-16 | 8.01e-01 | 0.2678 |
| 4015 | LOX | C30 | Human | Oral cavity | OSCC | 8.45e-06 | 6.01e-01 | 0.3055 |
| 4015 | LOX | C43 | Human | Oral cavity | OSCC | 1.19e-30 | 5.57e-01 | 0.1704 |
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| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00224099 | Cervix | CC | positive regulation of cell-cell adhesion | 61/2311 | 284/18723 | 9.30e-06 | 2.11e-04 | 61 |
| GO:00313494 | Cervix | CC | positive regulation of defense response | 60/2311 | 278/18723 | 9.38e-06 | 2.11e-04 | 60 |
| GO:19030397 | Cervix | CC | positive regulation of leukocyte cell-cell adhesion | 53/2311 | 239/18723 | 1.37e-05 | 2.74e-04 | 53 |
| GO:00610418 | Cervix | CC | regulation of wound healing | 34/2311 | 134/18723 | 2.70e-05 | 4.52e-04 | 34 |
| GO:00507273 | Cervix | CC | regulation of inflammatory response | 75/2311 | 386/18723 | 3.95e-05 | 6.18e-04 | 75 |
| GO:19907489 | Cervix | CC | cellular detoxification | 30/2311 | 116/18723 | 5.34e-05 | 7.94e-04 | 30 |
| GO:00972379 | Cervix | CC | cellular response to toxic substance | 31/2311 | 124/18723 | 8.09e-05 | 1.10e-03 | 31 |
| GO:00507294 | Cervix | CC | positive regulation of inflammatory response | 34/2311 | 142/18723 | 9.51e-05 | 1.25e-03 | 34 |
| GO:00096369 | Cervix | CC | response to toxic substance | 52/2311 | 262/18723 | 3.34e-04 | 3.52e-03 | 52 |
| GO:00321022 | Cervix | CC | negative regulation of response to external stimulus | 75/2311 | 420/18723 | 5.96e-04 | 5.61e-03 | 75 |
| GO:0045598 | Cervix | CC | regulation of fat cell differentiation | 31/2311 | 139/18723 | 7.06e-04 | 6.41e-03 | 31 |
| GO:00425939 | Cervix | CC | glucose homeostasis | 50/2311 | 258/18723 | 7.57e-04 | 6.76e-03 | 50 |
| GO:00725939 | Cervix | CC | reactive oxygen species metabolic process | 47/2311 | 239/18723 | 7.74e-04 | 6.87e-03 | 47 |
| GO:00987549 | Cervix | CC | detoxification | 33/2311 | 152/18723 | 7.97e-04 | 7.00e-03 | 33 |
| GO:00335009 | Cervix | CC | carbohydrate homeostasis | 50/2311 | 259/18723 | 8.28e-04 | 7.22e-03 | 50 |
| GO:00716745 | Cervix | CC | mononuclear cell migration | 40/2311 | 196/18723 | 8.79e-04 | 7.62e-03 | 40 |
| GO:001003810 | Cervix | CC | response to metal ion | 67/2311 | 373/18723 | 9.67e-04 | 8.10e-03 | 67 |
| GO:00015037 | Cervix | CC | ossification | 71/2311 | 408/18723 | 1.67e-03 | 1.28e-02 | 71 |
| GO:0031348 | Cervix | CC | negative regulation of defense response | 48/2311 | 258/18723 | 2.30e-03 | 1.65e-02 | 48 |
| GO:00515926 | Cervix | CC | response to calcium ion | 31/2311 | 149/18723 | 2.31e-03 | 1.65e-02 | 31 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 |
| 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 |
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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. |
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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 |
| LOX | insertion | In_Frame_Ins | novel | c.899_900insAAGATATCTCTGTTTTTTCACCTGTGAAACCATTCCTTCCTTCTGTTT | p.Glu300_Phe301insArgTyrLeuCysPhePheThrCysGluThrIleProSerPheCysLeu | p.E300_F301insRYLCFFTCETIPSFCL | P28300 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| LOX | SNV | Missense_Mutation | novel | c.1202G>A | p.Arg401His | p.R401H | P28300 | protein_coding | tolerated(0.66) | benign(0.07) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LOX | SNV | Missense_Mutation | c.1010N>A | p.Arg337Gln | p.R337Q | P28300 | protein_coding | deleterious(0.02) | probably_damaging(0.98) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| LOX | SNV | Missense_Mutation | c.49G>A | p.Ala17Thr | p.A17T | P28300 | protein_coding | tolerated(0.37) | benign(0) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |
| LOX | SNV | Missense_Mutation | novel | c.761N>C | p.Val254Ala | p.V254A | P28300 | protein_coding | tolerated(0.52) | benign(0.048) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| LOX | SNV | Missense_Mutation | c.19G>A | p.Val7Met | p.V7M | P28300 | protein_coding | tolerated(0.08) | benign(0.003) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LOX | SNV | Missense_Mutation | c.842N>A | p.Arg281Gln | p.R281Q | P28300 | protein_coding | deleterious(0.02) | possibly_damaging(0.821) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
| LOX | SNV | Missense_Mutation | rs566461481 | c.364N>T | p.Arg122Cys | p.R122C | P28300 | protein_coding | deleterious(0.01) | benign(0.001) | TCGA-CK-5913-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LOX | SNV | Missense_Mutation | c.76G>A | p.Ala26Thr | p.A26T | P28300 | protein_coding | tolerated(0.61) | benign(0) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LOX | SNV | Missense_Mutation | c.842N>A | p.Arg281Gln | p.R281Q | P28300 | protein_coding | deleterious(0.02) | possibly_damaging(0.821) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | 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 |
| 4015 | LOX | ENZYME, DRUGGABLE GENOME | inhibitor | 385612244 | ||
| 4015 | LOX | ENZYME, DRUGGABLE GENOME | inhibitor | 385612245 |
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