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Gene: VPS11 |
Gene summary for VPS11 |
Gene summary. |
Gene information | Species | Human | Gene symbol | VPS11 | Gene ID | 55823 |
Gene name | VPS11 core subunit of CORVET and HOPS complexes | |
Gene Alias | END1 | |
Cytomap | 11q23.3 | |
Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | B7Z879 |
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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 |
55823 | VPS11 | HCC1_Meng | Human | Liver | HCC | 8.53e-16 | 2.26e-02 | 0.0246 |
55823 | VPS11 | HCC1 | Human | Liver | HCC | 1.10e-02 | 1.57e+00 | 0.5336 |
55823 | VPS11 | HCC2 | Human | Liver | HCC | 1.81e-05 | 2.42e+00 | 0.5341 |
55823 | VPS11 | S014 | Human | Liver | HCC | 7.04e-07 | 3.07e-01 | 0.2254 |
55823 | VPS11 | S015 | Human | Liver | HCC | 1.22e-04 | 3.06e-01 | 0.2375 |
55823 | VPS11 | S016 | Human | Liver | HCC | 2.49e-09 | 3.59e-01 | 0.2243 |
55823 | VPS11 | S028 | Human | Liver | HCC | 7.06e-10 | 3.84e-01 | 0.2503 |
55823 | VPS11 | S029 | Human | Liver | HCC | 3.45e-14 | 4.55e-01 | 0.2581 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:007259422 | Liver | HCC | establishment of protein localization to organelle | 299/7958 | 422/18723 | 1.06e-32 | 6.10e-30 | 299 |
GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
GO:004217622 | Liver | HCC | regulation of protein catabolic process | 267/7958 | 391/18723 | 2.45e-25 | 7.38e-23 | 267 |
GO:190382922 | Liver | HCC | positive regulation of cellular protein localization | 199/7958 | 276/18723 | 1.15e-23 | 2.62e-21 | 199 |
GO:003164722 | Liver | HCC | regulation of protein stability | 211/7958 | 298/18723 | 2.29e-23 | 5.01e-21 | 211 |
GO:000660512 | Liver | HCC | protein targeting | 219/7958 | 314/18723 | 7.74e-23 | 1.49e-20 | 219 |
GO:003238621 | Liver | HCC | regulation of intracellular transport | 231/7958 | 337/18723 | 1.99e-22 | 3.40e-20 | 231 |
GO:000683912 | Liver | HCC | mitochondrial transport | 184/7958 | 254/18723 | 2.30e-22 | 3.83e-20 | 184 |
GO:190336222 | Liver | HCC | regulation of cellular protein catabolic process | 182/7958 | 255/18723 | 5.91e-21 | 8.52e-19 | 182 |
GO:003315721 | Liver | HCC | regulation of intracellular protein transport | 165/7958 | 229/18723 | 8.37e-20 | 1.15e-17 | 165 |
GO:003238821 | Liver | HCC | positive regulation of intracellular transport | 148/7958 | 202/18723 | 5.15e-19 | 6.66e-17 | 148 |
GO:007265512 | Liver | HCC | establishment of protein localization to mitochondrion | 98/7958 | 120/18723 | 1.18e-18 | 1.46e-16 | 98 |
GO:007058512 | Liver | HCC | protein localization to mitochondrion | 101/7958 | 125/18723 | 1.53e-18 | 1.86e-16 | 101 |
GO:004573222 | Liver | HCC | positive regulation of protein catabolic process | 163/7958 | 231/18723 | 4.00e-18 | 4.69e-16 | 163 |
GO:009031621 | Liver | HCC | positive regulation of intracellular protein transport | 121/7958 | 160/18723 | 1.27e-17 | 1.39e-15 | 121 |
GO:190495122 | Liver | HCC | positive regulation of establishment of protein localization | 207/7958 | 319/18723 | 3.95e-16 | 3.29e-14 | 207 |
GO:000662612 | Liver | HCC | protein targeting to mitochondrion | 82/7958 | 100/18723 | 4.93e-16 | 4.05e-14 | 82 |
GO:190336422 | Liver | HCC | positive regulation of cellular protein catabolic process | 115/7958 | 155/18723 | 9.30e-16 | 7.19e-14 | 115 |
GO:001605021 | Liver | HCC | vesicle organization | 194/7958 | 300/18723 | 5.58e-15 | 3.97e-13 | 194 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513242 | Liver | HCC | Salmonella infection | 178/4020 | 249/8465 | 5.90e-15 | 1.98e-13 | 1.10e-13 | 178 |
hsa0513252 | Liver | HCC | Salmonella infection | 178/4020 | 249/8465 | 5.90e-15 | 1.98e-13 | 1.10e-13 | 178 |
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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 |
VPS11 | SNV | Missense_Mutation | novel | c.2446A>C | p.Ile816Leu | p.I816L | protein_coding | deleterious(0.01) | possibly_damaging(0.452) | TCGA-AA-3833-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
VPS11 | SNV | Missense_Mutation | rs782468120 | c.1098N>C | p.Lys366Asn | p.K366N | protein_coding | deleterious(0) | possibly_damaging(0.485) | TCGA-AA-3982-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
VPS11 | SNV | Missense_Mutation | novel | c.1101N>T | p.Lys367Asn | p.K367N | protein_coding | deleterious(0) | probably_damaging(0.926) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
VPS11 | SNV | Missense_Mutation | rs782051419 | c.1942N>A | p.Ala648Thr | p.A648T | protein_coding | tolerated(0.56) | benign(0.01) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VPS11 | SNV | Missense_Mutation | novel | c.1645N>A | p.Gly549Ser | p.G549S | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
VPS11 | SNV | Missense_Mutation | novel | c.971N>T | p.Ser324Ile | p.S324I | protein_coding | deleterious(0) | probably_damaging(0.934) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VPS11 | SNV | Missense_Mutation | novel | c.1846N>T | p.Pro616Ser | p.P616S | protein_coding | tolerated(0.6) | benign(0.005) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
VPS11 | SNV | Missense_Mutation | rs782053536 | c.329N>G | p.Asn110Ser | p.N110S | protein_coding | tolerated(0.07) | benign(0.037) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
VPS11 | SNV | Missense_Mutation | novel | c.960C>A | p.Phe320Leu | p.F320L | protein_coding | tolerated(0.33) | benign(0.101) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
VPS11 | SNV | Missense_Mutation | novel | c.109N>C | p.Ser37Pro | p.S37P | protein_coding | tolerated(0.27) | benign(0) | TCGA-D5-6534-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
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