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Gene: SLC39A5 |
Gene summary for SLC39A5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLC39A5 | Gene ID | 283375 |
| Gene name | solute carrier family 39 member 5 | |
| Gene Alias | LZT-Hs7 | |
| Cytomap | 12q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000041 | UniProtAcc | A0A024RB24 |
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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 |
| 283375 | SLC39A5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.68e-05 | 4.20e-01 | -0.1808 |
| 283375 | SLC39A5 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.81e-13 | 5.83e-01 | -0.1954 |
| 283375 | SLC39A5 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.78e-07 | 5.12e-01 | -0.1464 |
| 283375 | SLC39A5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 9.08e-03 | 3.75e-01 | -0.059 |
| 283375 | SLC39A5 | HTA11_10623_2000001011 | Human | Colorectum | AD | 4.87e-05 | 6.44e-01 | -0.0177 |
| 283375 | SLC39A5 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.04e-02 | -1.87e-01 | 0.294 |
| 283375 | SLC39A5 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.25e-04 | 4.86e-01 | 0.281 |
| 283375 | SLC39A5 | A015-C-203 | Human | Colorectum | FAP | 2.48e-03 | -5.08e-02 | -0.1294 |
| 283375 | SLC39A5 | A001-C-108 | Human | Colorectum | FAP | 6.57e-07 | -1.92e-01 | -0.0272 |
| 283375 | SLC39A5 | A002-C-205 | Human | Colorectum | FAP | 4.94e-05 | -1.99e-01 | -0.1236 |
| 283375 | SLC39A5 | A001-C-104 | Human | Colorectum | FAP | 4.14e-03 | -1.60e-01 | 0.0184 |
| 283375 | SLC39A5 | A015-C-104 | Human | Colorectum | FAP | 6.55e-04 | -9.57e-02 | -0.1899 |
| 283375 | SLC39A5 | A001-C-014 | Human | Colorectum | FAP | 1.11e-03 | -2.09e-01 | 0.0135 |
| 283375 | SLC39A5 | A002-C-016 | Human | Colorectum | FAP | 1.28e-05 | -1.92e-01 | 0.0521 |
| 283375 | SLC39A5 | A002-C-116 | Human | Colorectum | FAP | 4.33e-07 | -1.83e-01 | -0.0452 |
| 283375 | SLC39A5 | A014-C-008 | Human | Colorectum | FAP | 4.23e-02 | -1.94e-01 | -0.191 |
| 283375 | SLC39A5 | A018-E-020 | Human | Colorectum | FAP | 3.71e-02 | -1.16e-01 | -0.2034 |
| 283375 | SLC39A5 | F034 | Human | Colorectum | FAP | 4.25e-04 | -1.26e-01 | -0.0665 |
| 283375 | SLC39A5 | HCC1_Meng | Human | Liver | HCC | 6.79e-72 | 4.58e-01 | 0.0246 |
| 283375 | SLC39A5 | S014 | Human | Liver | HCC | 3.88e-48 | 1.96e+00 | 0.2254 |
| Page: 1 2 |
| 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 | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:0055076 | Colorectum | AD | transition metal ion homeostasis | 53/3918 | 138/18723 | 1.89e-06 | 5.65e-05 | 53 |
| GO:0046916 | Colorectum | AD | cellular transition metal ion homeostasis | 43/3918 | 115/18723 | 3.62e-05 | 6.56e-04 | 43 |
| GO:0055069 | Colorectum | AD | zinc ion homeostasis | 18/3918 | 40/18723 | 5.36e-04 | 5.74e-03 | 18 |
| GO:0006882 | Colorectum | AD | cellular zinc ion homeostasis | 17/3918 | 38/18723 | 8.26e-04 | 8.13e-03 | 17 |
| GO:0007178 | Colorectum | AD | transmembrane receptor protein serine/threonine kinase signaling pathway | 99/3918 | 355/18723 | 9.92e-04 | 9.28e-03 | 99 |
| GO:00550761 | Colorectum | SER | transition metal ion homeostasis | 41/2897 | 138/18723 | 1.66e-05 | 5.05e-04 | 41 |
| GO:00469161 | Colorectum | SER | cellular transition metal ion homeostasis | 33/2897 | 115/18723 | 2.20e-04 | 3.89e-03 | 33 |
| GO:00550691 | Colorectum | SER | zinc ion homeostasis | 15/2897 | 40/18723 | 5.71e-04 | 7.86e-03 | 15 |
| GO:00068821 | Colorectum | SER | cellular zinc ion homeostasis | 14/2897 | 38/18723 | 1.06e-03 | 1.23e-02 | 14 |
| GO:00550762 | Colorectum | MSS | transition metal ion homeostasis | 45/3467 | 138/18723 | 4.99e-05 | 9.02e-04 | 45 |
| GO:00469162 | Colorectum | MSS | cellular transition metal ion homeostasis | 35/3467 | 115/18723 | 1.33e-03 | 1.26e-02 | 35 |
| GO:00071781 | Colorectum | MSS | transmembrane receptor protein serine/threonine kinase signaling pathway | 86/3467 | 355/18723 | 4.04e-03 | 2.95e-02 | 86 |
| GO:00071782 | Colorectum | FAP | transmembrane receptor protein serine/threonine kinase signaling pathway | 81/2622 | 355/18723 | 4.28e-06 | 1.46e-04 | 81 |
| GO:00550764 | Colorectum | FAP | transition metal ion homeostasis | 33/2622 | 138/18723 | 1.22e-03 | 1.14e-02 | 33 |
| GO:0071772 | Colorectum | FAP | response to BMP | 37/2622 | 165/18723 | 2.20e-03 | 1.80e-02 | 37 |
| GO:0071773 | Colorectum | FAP | cellular response to BMP stimulus | 37/2622 | 165/18723 | 2.20e-03 | 1.80e-02 | 37 |
| GO:0030509 | Colorectum | FAP | BMP signaling pathway | 34/2622 | 152/18723 | 3.38e-03 | 2.47e-02 | 34 |
| GO:005507612 | Liver | HCC | transition metal ion homeostasis | 81/7958 | 138/18723 | 8.87e-05 | 7.72e-04 | 81 |
| GO:004691611 | Liver | HCC | cellular transition metal ion homeostasis | 67/7958 | 115/18723 | 4.64e-04 | 3.08e-03 | 67 |
| GO:00000411 | Liver | HCC | transition metal ion transport | 59/7958 | 105/18723 | 3.18e-03 | 1.47e-02 | 59 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05012 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
| hsa050121 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
| hsa050122 | Colorectum | SER | Parkinson disease | 132/1580 | 266/8465 | 2.72e-31 | 9.03e-29 | 6.55e-29 | 132 |
| hsa050102 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
| hsa050123 | Colorectum | SER | Parkinson disease | 132/1580 | 266/8465 | 2.72e-31 | 9.03e-29 | 6.55e-29 | 132 |
| hsa050103 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
| hsa050124 | Colorectum | MSS | Parkinson disease | 140/1875 | 266/8465 | 2.32e-28 | 7.79e-26 | 4.77e-26 | 140 |
| hsa050104 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
| hsa050125 | Colorectum | MSS | Parkinson disease | 140/1875 | 266/8465 | 2.32e-28 | 7.79e-26 | 4.77e-26 | 140 |
| hsa050105 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
| hsa050128 | Colorectum | FAP | Parkinson disease | 80/1404 | 266/8465 | 2.04e-08 | 6.20e-07 | 3.77e-07 | 80 |
| hsa050108 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
| hsa050129 | Colorectum | FAP | Parkinson disease | 80/1404 | 266/8465 | 2.04e-08 | 6.20e-07 | 3.77e-07 | 80 |
| hsa050109 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
| hsa0501222 | Liver | HCC | Parkinson disease | 198/4020 | 266/8465 | 9.40e-20 | 1.58e-17 | 8.76e-18 | 198 |
| hsa0501022 | Liver | HCC | Alzheimer disease | 254/4020 | 384/8465 | 3.75e-14 | 8.97e-13 | 4.99e-13 | 254 |
| hsa0501232 | Liver | HCC | Parkinson disease | 198/4020 | 266/8465 | 9.40e-20 | 1.58e-17 | 8.76e-18 | 198 |
| hsa0501032 | Liver | HCC | Alzheimer disease | 254/4020 | 384/8465 | 3.75e-14 | 8.97e-13 | 4.99e-13 | 254 |
| Page: 1 2 |
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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 |
| SLC39A5 | SNV | Missense_Mutation | rs764042659 | c.1258N>T | p.Val420Phe | p.V420F | Q6ZMH5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A09M-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | CR |
| SLC39A5 | SNV | Missense_Mutation | rs764042659 | c.1258N>T | p.Val420Phe | p.V420F | Q6ZMH5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
| SLC39A5 | SNV | Missense_Mutation | c.161N>A | p.Thr54Asn | p.T54N | Q6ZMH5 | protein_coding | deleterious(0.01) | possibly_damaging(0.63) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| SLC39A5 | SNV | Missense_Mutation | rs751626086 | c.61N>C | p.Trp21Arg | p.W21R | Q6ZMH5 | protein_coding | tolerated_low_confidence(0.21) | benign(0.003) | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| SLC39A5 | SNV | Missense_Mutation | rs745642336 | c.718N>T | p.Arg240Cys | p.R240C | Q6ZMH5 | protein_coding | deleterious(0.04) | possibly_damaging(0.663) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SLC39A5 | SNV | Missense_Mutation | rs764042659 | c.1258N>T | p.Val420Phe | p.V420F | Q6ZMH5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0DQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SLC39A5 | SNV | Missense_Mutation | c.379C>T | p.His127Tyr | p.H127Y | Q6ZMH5 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| SLC39A5 | SNV | Missense_Mutation | c.938N>C | p.Leu313Pro | p.L313P | Q6ZMH5 | protein_coding | tolerated(0.26) | possibly_damaging(0.761) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| SLC39A5 | SNV | Missense_Mutation | novel | c.1436N>A | p.Gly479Glu | p.G479E | Q6ZMH5 | protein_coding | deleterious(0.01) | benign(0.419) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SLC39A5 | SNV | Missense_Mutation | c.800N>T | p.Pro267Leu | p.P267L | Q6ZMH5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EA-A5O9-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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