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Gene: LAMP2 |
Gene summary for LAMP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LAMP2 | Gene ID | 3920 |
| Gene name | lysosomal associated membrane protein 2 | |
| Gene Alias | CD107b | |
| Cytomap | Xq24 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | P13473 |
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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 |
| 3920 | LAMP2 | CA_HPV_3 | Human | Cervix | CC | 2.94e-04 | 1.14e-01 | 0.0414 |
| 3920 | LAMP2 | CCII_1 | Human | Cervix | CC | 4.13e-06 | -4.29e-01 | 0.3249 |
| 3920 | LAMP2 | Tumor | Human | Cervix | CC | 2.87e-14 | 4.58e-01 | 0.1241 |
| 3920 | LAMP2 | sample3 | Human | Cervix | CC | 4.57e-19 | 5.72e-01 | 0.1387 |
| 3920 | LAMP2 | T3 | Human | Cervix | CC | 3.91e-23 | 5.81e-01 | 0.1389 |
| 3920 | LAMP2 | AEH-subject2 | Human | Endometrium | AEH | 1.52e-08 | -3.20e-01 | -0.2525 |
| 3920 | LAMP2 | AEH-subject3 | Human | Endometrium | AEH | 4.23e-03 | -1.73e-01 | -0.2576 |
| 3920 | LAMP2 | EEC-subject2 | Human | Endometrium | EEC | 1.89e-09 | -2.61e-01 | -0.2607 |
| 3920 | LAMP2 | EEC-subject3 | Human | Endometrium | EEC | 8.04e-23 | -2.77e-01 | -0.2525 |
| 3920 | LAMP2 | EEC-subject4 | Human | Endometrium | EEC | 3.30e-04 | 1.54e-02 | -0.2571 |
| 3920 | LAMP2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.09e-24 | -7.35e-02 | -0.1869 |
| 3920 | LAMP2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 6.43e-28 | -1.39e-01 | -0.1875 |
| 3920 | LAMP2 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.63e-29 | 4.86e-02 | -0.1883 |
| 3920 | LAMP2 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 4.19e-19 | 4.57e-02 | -0.1934 |
| 3920 | LAMP2 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 2.24e-44 | -2.90e-01 | -0.1917 |
| 3920 | LAMP2 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 4.35e-33 | -4.05e-01 | -0.1916 |
| 3920 | LAMP2 | LZE4T | Human | Esophagus | ESCC | 5.43e-06 | 4.05e-01 | 0.0811 |
| 3920 | LAMP2 | LZE5T | Human | Esophagus | ESCC | 2.53e-03 | 3.40e-01 | 0.0514 |
| 3920 | LAMP2 | LZE7T | Human | Esophagus | ESCC | 3.14e-03 | 2.91e-01 | 0.0667 |
| 3920 | LAMP2 | LZE8T | Human | Esophagus | ESCC | 9.25e-11 | -1.74e-01 | 0.067 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
| GO:007149610 | Cervix | CC | cellular response to external stimulus | 78/2311 | 320/18723 | 1.82e-09 | 1.98e-07 | 78 |
| GO:00316689 | Cervix | CC | cellular response to extracellular stimulus | 59/2311 | 246/18723 | 3.03e-07 | 1.24e-05 | 59 |
| GO:000660510 | Cervix | CC | protein targeting | 68/2311 | 314/18723 | 2.17e-06 | 6.55e-05 | 68 |
| GO:003166710 | Cervix | CC | response to nutrient levels | 92/2311 | 474/18723 | 5.80e-06 | 1.42e-04 | 92 |
| GO:00170388 | Cervix | CC | protein import | 48/2311 | 206/18723 | 8.62e-06 | 1.98e-04 | 48 |
| GO:00092678 | Cervix | CC | cellular response to starvation | 39/2311 | 156/18723 | 1.04e-05 | 2.32e-04 | 39 |
| GO:003164710 | Cervix | CC | regulation of protein stability | 63/2311 | 298/18723 | 1.14e-05 | 2.45e-04 | 63 |
| GO:00425948 | Cervix | CC | response to starvation | 46/2311 | 197/18723 | 1.24e-05 | 2.59e-04 | 46 |
| GO:00316698 | Cervix | CC | cellular response to nutrient levels | 49/2311 | 215/18723 | 1.32e-05 | 2.68e-04 | 49 |
| GO:005082110 | Cervix | CC | protein stabilization | 43/2311 | 191/18723 | 5.90e-05 | 8.54e-04 | 43 |
| GO:002241110 | Cervix | CC | cellular component disassembly | 83/2311 | 443/18723 | 6.04e-05 | 8.68e-04 | 83 |
| GO:00726655 | Cervix | CC | protein localization to vacuole | 20/2311 | 67/18723 | 1.12e-04 | 1.40e-03 | 20 |
| GO:00162367 | Cervix | CC | macroautophagy | 58/2311 | 291/18723 | 1.40e-04 | 1.70e-03 | 58 |
| GO:00616847 | Cervix | CC | chaperone-mediated autophagy | 8/2311 | 16/18723 | 2.73e-04 | 2.99e-03 | 8 |
| GO:00070347 | Cervix | CC | vacuolar transport | 34/2311 | 157/18723 | 7.03e-04 | 6.40e-03 | 34 |
| GO:00066235 | Cervix | CC | protein targeting to vacuole | 12/2311 | 37/18723 | 1.15e-03 | 9.39e-03 | 12 |
| GO:00726665 | Cervix | CC | establishment of protein localization to vacuole | 14/2311 | 49/18723 | 1.84e-03 | 1.37e-02 | 14 |
| GO:00614623 | Cervix | CC | protein localization to lysosome | 13/2311 | 46/18723 | 2.95e-03 | 1.94e-02 | 13 |
| GO:00066223 | Cervix | CC | protein targeting to lysosome | 8/2311 | 23/18723 | 4.70e-03 | 2.82e-02 | 8 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414520 | Cervix | CC | Phagosome | 47/1267 | 152/8465 | 3.95e-07 | 4.26e-06 | 2.52e-06 | 47 |
| hsa05152 | Cervix | CC | Tuberculosis | 42/1267 | 180/8465 | 1.78e-03 | 7.21e-03 | 4.26e-03 | 42 |
| hsa04145110 | Cervix | CC | Phagosome | 47/1267 | 152/8465 | 3.95e-07 | 4.26e-06 | 2.52e-06 | 47 |
| hsa051521 | Cervix | CC | Tuberculosis | 42/1267 | 180/8465 | 1.78e-03 | 7.21e-03 | 4.26e-03 | 42 |
| hsa0414524 | Endometrium | AEH | Phagosome | 41/1197 | 152/8465 | 2.12e-05 | 2.22e-04 | 1.63e-04 | 41 |
| hsa04145111 | Endometrium | AEH | Phagosome | 41/1197 | 152/8465 | 2.12e-05 | 2.22e-04 | 1.63e-04 | 41 |
| hsa0414525 | Endometrium | EEC | Phagosome | 42/1237 | 152/8465 | 2.01e-05 | 2.28e-04 | 1.70e-04 | 42 |
| hsa0414534 | Endometrium | EEC | Phagosome | 42/1237 | 152/8465 | 2.01e-05 | 2.28e-04 | 1.70e-04 | 42 |
| hsa041426 | Esophagus | HGIN | Lysosome | 33/1383 | 132/8465 | 6.65e-03 | 4.37e-02 | 3.47e-02 | 33 |
| hsa0414213 | Esophagus | HGIN | Lysosome | 33/1383 | 132/8465 | 6.65e-03 | 4.37e-02 | 3.47e-02 | 33 |
| hsa0414222 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0414530 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
| hsa051527 | Esophagus | ESCC | Tuberculosis | 111/4205 | 180/8465 | 7.14e-04 | 2.32e-03 | 1.19e-03 | 111 |
| hsa0414232 | Esophagus | ESCC | Lysosome | 102/4205 | 132/8465 | 5.11e-11 | 7.13e-10 | 3.65e-10 | 102 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa04145114 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
| hsa0515212 | Esophagus | ESCC | Tuberculosis | 111/4205 | 180/8465 | 7.14e-04 | 2.32e-03 | 1.19e-03 | 111 |
| hsa041424 | Liver | Cirrhotic | Lysosome | 68/2530 | 132/8465 | 1.34e-07 | 1.97e-06 | 1.21e-06 | 68 |
| hsa0414514 | Liver | Cirrhotic | Phagosome | 73/2530 | 152/8465 | 1.61e-06 | 1.78e-05 | 1.10e-05 | 73 |
| Page: 1 2 3 |
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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 |
| LAMP2 | SNV | Missense_Mutation | c.325N>C | p.Tyr109His | p.Y109H | P13473 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LAMP2 | SNV | Missense_Mutation | c.80N>G | p.Tyr27Cys | p.Y27C | P13473 | protein_coding | tolerated(0.1) | benign(0.015) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LAMP2 | SNV | Missense_Mutation | c.320C>T | p.Ser107Phe | p.S107F | P13473 | protein_coding | deleterious(0.01) | possibly_damaging(0.789) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| LAMP2 | insertion | Nonsense_Mutation | novel | c.463_464insAGTCTGTCTCCTAGCTTTTACTCCCCATTGCCTTTGCTCT | p.Ser155LysfsTer5 | p.S155Kfs*5 | P13473 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| LAMP2 | SNV | Missense_Mutation | novel | c.1211N>T | p.Ser404Ile | p.S404I | P13473 | protein_coding | deleterious(0.01) | possibly_damaging(0.676) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LAMP2 | SNV | Missense_Mutation | c.376N>C | p.Phe126Leu | p.F126L | P13473 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-5667-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| LAMP2 | SNV | Missense_Mutation | c.40N>A | p.Leu14Ile | p.L14I | P13473 | protein_coding | tolerated(0.07) | benign(0.265) | TCGA-AY-6196-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| LAMP2 | SNV | Missense_Mutation | c.35C>T | p.Ser12Leu | p.S12L | P13473 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LAMP2 | SNV | Missense_Mutation | novel | c.1081A>C | p.Lys361Gln | p.K361Q | P13473 | protein_coding | tolerated(0.13) | benign(0.196) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| LAMP2 | SNV | Missense_Mutation | c.269T>C | p.Val90Ala | p.V90A | P13473 | protein_coding | deleterious(0.02) | benign(0.118) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| Page: 1 |
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