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Gene: VPS35 |
Gene summary for VPS35 |
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Gene information | Species | Human | Gene symbol | VPS35 | Gene ID | 55737 |
Gene name | VPS35 retromer complex component | |
Gene Alias | MEM3 | |
Cytomap | 16q11.2 | |
Gene Type | protein-coding | GO ID | GO:0000266 | UniProtAcc | Q96QK1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
55737 | VPS35 | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.15e-04 | 4.80e-01 | -0.0811 |
55737 | VPS35 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.01e-07 | 5.20e-01 | -0.1088 |
55737 | VPS35 | HTA11_347_2000001011 | Human | Colorectum | AD | 8.49e-16 | 5.65e-01 | -0.1954 |
55737 | VPS35 | HTA11_6801_2000001011 | Human | Colorectum | SER | 1.96e-03 | 6.25e-01 | 0.0171 |
55737 | VPS35 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.06e-06 | 5.11e-01 | 0.294 |
55737 | VPS35 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.74e-14 | 9.51e-01 | 0.281 |
55737 | VPS35 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.13e-04 | 4.63e-01 | 0.3859 |
55737 | VPS35 | A015-C-203 | Human | Colorectum | FAP | 1.32e-07 | -7.45e-02 | -0.1294 |
55737 | VPS35 | A002-C-201 | Human | Colorectum | FAP | 3.82e-02 | -1.29e-01 | 0.0324 |
55737 | VPS35 | A001-C-108 | Human | Colorectum | FAP | 1.61e-03 | -7.15e-02 | -0.0272 |
55737 | VPS35 | A002-C-205 | Human | Colorectum | FAP | 4.61e-05 | -2.50e-02 | -0.1236 |
55737 | VPS35 | A015-C-006 | Human | Colorectum | FAP | 7.13e-03 | -9.74e-02 | -0.0994 |
55737 | VPS35 | A002-C-114 | Human | Colorectum | FAP | 6.16e-04 | 4.67e-03 | -0.1561 |
55737 | VPS35 | A015-C-104 | Human | Colorectum | FAP | 5.04e-10 | -3.78e-02 | -0.1899 |
55737 | VPS35 | A002-C-016 | Human | Colorectum | FAP | 2.34e-03 | -9.22e-02 | 0.0521 |
55737 | VPS35 | A015-C-002 | Human | Colorectum | FAP | 4.12e-02 | 8.22e-02 | -0.0763 |
55737 | VPS35 | A002-C-116 | Human | Colorectum | FAP | 2.35e-11 | -7.03e-02 | -0.0452 |
55737 | VPS35 | A014-C-008 | Human | Colorectum | FAP | 1.33e-02 | 6.47e-02 | -0.191 |
55737 | VPS35 | A018-E-020 | Human | Colorectum | FAP | 2.69e-03 | -4.56e-02 | -0.2034 |
55737 | VPS35 | F034 | Human | Colorectum | FAP | 1.60e-05 | 1.29e-03 | -0.0665 |
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∗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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003133112 | Liver | Cirrhotic | positive regulation of cellular catabolic process | 190/4634 | 427/18723 | 1.94e-19 | 4.18e-17 | 190 |
GO:003164712 | Liver | Cirrhotic | regulation of protein stability | 144/4634 | 298/18723 | 6.74e-19 | 1.28e-16 | 144 |
GO:190336212 | Liver | Cirrhotic | regulation of cellular protein catabolic process | 124/4634 | 255/18723 | 9.85e-17 | 1.26e-14 | 124 |
GO:00901507 | Liver | Cirrhotic | establishment of protein localization to membrane | 123/4634 | 260/18723 | 1.85e-15 | 2.15e-13 | 123 |
GO:004573212 | Liver | Cirrhotic | positive regulation of protein catabolic process | 112/4634 | 231/18723 | 3.89e-15 | 4.21e-13 | 112 |
GO:001623611 | Liver | Cirrhotic | macroautophagy | 129/4634 | 291/18723 | 1.75e-13 | 1.41e-11 | 129 |
GO:190336412 | Liver | Cirrhotic | positive regulation of cellular protein catabolic process | 80/4634 | 155/18723 | 5.04e-13 | 3.86e-11 | 80 |
GO:00068397 | Liver | Cirrhotic | mitochondrial transport | 112/4634 | 254/18723 | 1.03e-11 | 6.66e-10 | 112 |
GO:001050611 | Liver | Cirrhotic | regulation of autophagy | 132/4634 | 317/18723 | 2.17e-11 | 1.33e-09 | 132 |
GO:199077811 | Liver | Cirrhotic | protein localization to cell periphery | 135/4634 | 333/18723 | 1.18e-10 | 6.21e-09 | 135 |
GO:007265911 | Liver | Cirrhotic | protein localization to plasma membrane | 119/4634 | 284/18723 | 1.30e-10 | 6.80e-09 | 119 |
GO:000703411 | Liver | Cirrhotic | vacuolar transport | 75/4634 | 157/18723 | 3.13e-10 | 1.53e-08 | 75 |
GO:007099712 | Liver | Cirrhotic | neuron death | 141/4634 | 361/18723 | 9.56e-10 | 4.38e-08 | 141 |
GO:001648211 | Liver | Cirrhotic | cytosolic transport | 74/4634 | 168/18723 | 3.34e-08 | 1.12e-06 | 74 |
GO:19012147 | Liver | Cirrhotic | regulation of neuron death | 122/4634 | 319/18723 | 5.17e-08 | 1.62e-06 | 122 |
GO:001619711 | Liver | Cirrhotic | endosomal transport | 93/4634 | 230/18723 | 1.01e-07 | 2.93e-06 | 93 |
GO:00619515 | Liver | Cirrhotic | establishment of protein localization to plasma membrane | 33/4634 | 60/18723 | 5.09e-07 | 1.14e-05 | 33 |
GO:00108216 | Liver | Cirrhotic | regulation of mitochondrion organization | 62/4634 | 144/18723 | 1.09e-06 | 2.22e-05 | 62 |
GO:009887611 | Liver | Cirrhotic | vesicle-mediated transport to the plasma membrane | 59/4634 | 136/18723 | 1.46e-06 | 2.88e-05 | 59 |
GO:00162414 | Liver | Cirrhotic | regulation of macroautophagy | 60/4634 | 141/18723 | 2.57e-06 | 4.63e-05 | 60 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa041441 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa041444 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa041445 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa041446 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
hsa041447 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
hsa041448 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
hsa041449 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
hsa0414429 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
hsa04144113 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
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 |
hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
hsa0414413 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
hsa0414422 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
hsa0414428 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
hsa0414436 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
VPS35 | SNV | Missense_Mutation | rs868056476 | c.1807N>A | p.Ala603Thr | p.A603T | Q96QK1 | protein_coding | tolerated(0.15) | probably_damaging(0.991) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VPS35 | SNV | Missense_Mutation | c.2209N>A | p.Ala737Thr | p.A737T | Q96QK1 | protein_coding | tolerated(0.31) | benign(0) | TCGA-BH-A0C1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
VPS35 | SNV | Missense_Mutation | c.1747N>G | p.Leu583Val | p.L583V | Q96QK1 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VPS35 | SNV | Missense_Mutation | c.514A>G | p.Thr172Ala | p.T172A | Q96QK1 | protein_coding | tolerated(0.86) | benign(0.001) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VPS35 | SNV | Missense_Mutation | novel | c.183G>T | p.Lys61Asn | p.K61N | Q96QK1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
VPS35 | SNV | Missense_Mutation | c.676C>T | p.Arg226Cys | p.R226C | Q96QK1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
VPS35 | SNV | Missense_Mutation | novel | c.587N>A | p.Arg196Gln | p.R196Q | Q96QK1 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
VPS35 | SNV | Missense_Mutation | c.286N>A | p.Glu96Lys | p.E96K | Q96QK1 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD | |
VPS35 | SNV | Missense_Mutation | novel | c.1961N>T | p.Ala654Val | p.A654V | Q96QK1 | protein_coding | tolerated(0.09) | possibly_damaging(0.447) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
VPS35 | SNV | Missense_Mutation | c.434N>T | p.Arg145Met | p.R145M | Q96QK1 | protein_coding | deleterious(0) | possibly_damaging(0.886) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
55737 | VPS35 | ENZYME | MELAGATRAN | MELAGATRAN | 22494098 |
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