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Gene: VPS45 |
Gene summary for VPS45 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VPS45 | Gene ID | 11311 |
| Gene name | vacuolar protein sorting 45 homolog | |
| Gene Alias | H1 | |
| Cytomap | 1q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | B7Z5D4 |
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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 |
| 11311 | VPS45 | CCI_1 | Human | Cervix | CC | 2.09e-08 | 8.19e-01 | 0.528 |
| 11311 | VPS45 | CCI_2 | Human | Cervix | CC | 1.52e-09 | 8.12e-01 | 0.5249 |
| 11311 | VPS45 | CCI_3 | Human | Cervix | CC | 2.30e-12 | 8.13e-01 | 0.516 |
| 11311 | VPS45 | LZE4T | Human | Esophagus | ESCC | 1.38e-06 | 1.25e-01 | 0.0811 |
| 11311 | VPS45 | LZE5T | Human | Esophagus | ESCC | 1.17e-03 | 2.61e-01 | 0.0514 |
| 11311 | VPS45 | LZE20T | Human | Esophagus | ESCC | 2.79e-04 | 1.50e-01 | 0.0662 |
| 11311 | VPS45 | LZE24T | Human | Esophagus | ESCC | 5.96e-07 | 1.72e-01 | 0.0596 |
| 11311 | VPS45 | P1T-E | Human | Esophagus | ESCC | 4.98e-04 | 2.84e-01 | 0.0875 |
| 11311 | VPS45 | P2T-E | Human | Esophagus | ESCC | 1.01e-15 | 2.68e-01 | 0.1177 |
| 11311 | VPS45 | P4T-E | Human | Esophagus | ESCC | 1.80e-07 | 1.95e-01 | 0.1323 |
| 11311 | VPS45 | P5T-E | Human | Esophagus | ESCC | 4.54e-14 | 2.26e-01 | 0.1327 |
| 11311 | VPS45 | P8T-E | Human | Esophagus | ESCC | 9.68e-15 | 2.24e-01 | 0.0889 |
| 11311 | VPS45 | P9T-E | Human | Esophagus | ESCC | 2.59e-11 | 1.22e-01 | 0.1131 |
| 11311 | VPS45 | P10T-E | Human | Esophagus | ESCC | 1.40e-13 | 2.48e-01 | 0.116 |
| 11311 | VPS45 | P11T-E | Human | Esophagus | ESCC | 1.77e-11 | 3.29e-01 | 0.1426 |
| 11311 | VPS45 | P12T-E | Human | Esophagus | ESCC | 6.85e-13 | 1.58e-01 | 0.1122 |
| 11311 | VPS45 | P15T-E | Human | Esophagus | ESCC | 1.36e-19 | 3.44e-01 | 0.1149 |
| 11311 | VPS45 | P16T-E | Human | Esophagus | ESCC | 4.96e-24 | 2.98e-01 | 0.1153 |
| 11311 | VPS45 | P17T-E | Human | Esophagus | ESCC | 8.71e-07 | 2.82e-01 | 0.1278 |
| 11311 | VPS45 | P19T-E | Human | Esophagus | ESCC | 2.99e-03 | 2.67e-01 | 0.1662 |
| Page: 1 2 3 4 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414418 | Cervix | CC | Endocytosis | 64/1267 | 251/8465 | 6.97e-06 | 6.10e-05 | 3.61e-05 | 64 |
| hsa0414419 | Cervix | CC | Endocytosis | 64/1267 | 251/8465 | 6.97e-06 | 6.10e-05 | 3.61e-05 | 64 |
| hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| Page: 1 |
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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 |
| VPS45 | SNV | Missense_Mutation | novel | c.362A>G | p.Glu121Gly | p.E121G | Q9NRW7 | protein_coding | deleterious(0.02) | benign(0.345) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| VPS45 | SNV | Missense_Mutation | c.82G>A | p.Asp28Asn | p.D28N | Q9NRW7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS45 | SNV | Missense_Mutation | c.1282G>C | p.Glu428Gln | p.E428Q | Q9NRW7 | protein_coding | tolerated(0.26) | benign(0.038) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VPS45 | SNV | Missense_Mutation | novel | c.781N>A | p.Glu261Lys | p.E261K | Q9NRW7 | protein_coding | deleterious(0.02) | benign(0.223) | TCGA-E2-A2P6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| VPS45 | insertion | In_Frame_Ins | novel | c.1241_1242insGTTCTGCTGCATAATAAATATAAATCTATACTA | p.Gly414_Val415insPheCysCysIleIleAsnIleAsnLeuTyrTyr | p.G414_V415insFCCIININLYY | Q9NRW7 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| VPS45 | insertion | In_Frame_Ins | novel | c.142_143insTGGGCTTCAGGCTGCCGCTGGGCCTCCAGCACC | p.Glu48delinsValGlyPheArgLeuProLeuGlyLeuGlnHisGln | p.E48delinsVGFRLPLGLQHQ | Q9NRW7 | protein_coding | TCGA-A8-A0A4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR | ||
| VPS45 | SNV | Missense_Mutation | novel | c.673C>T | p.Pro225Ser | p.P225S | Q9NRW7 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| VPS45 | SNV | Missense_Mutation | novel | c.1043T>G | p.Leu348Arg | p.L348R | Q9NRW7 | protein_coding | deleterious(0) | possibly_damaging(0.739) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| VPS45 | SNV | Missense_Mutation | novel | c.1454A>G | p.Asn485Ser | p.N485S | Q9NRW7 | protein_coding | tolerated(1) | benign(0.006) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| VPS45 | SNV | Missense_Mutation | c.361N>C | p.Glu121Gln | p.E121Q | Q9NRW7 | protein_coding | deleterious(0.04) | benign(0.173) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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