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Gene: VPS4A |
Gene summary for VPS4A |
Gene summary. |
Gene information | Species | Human | Gene symbol | VPS4A | Gene ID | 27183 |
Gene name | vacuolar protein sorting 4 homolog A | |
Gene Alias | CIMDAG | |
Cytomap | 16q22.1 | |
Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | A0A024R705 |
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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 |
27183 | VPS4A | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.12e-03 | 2.67e-01 | -0.1808 |
27183 | VPS4A | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.54e-02 | 2.41e-01 | -0.0811 |
27183 | VPS4A | HTA11_347_2000001011 | Human | Colorectum | AD | 4.36e-09 | 2.67e-01 | -0.1954 |
27183 | VPS4A | HTA11_411_2000001011 | Human | Colorectum | SER | 3.82e-03 | 4.16e-01 | -0.2602 |
27183 | VPS4A | HTA11_83_2000001011 | Human | Colorectum | SER | 4.58e-03 | 2.58e-01 | -0.1526 |
27183 | VPS4A | HTA11_696_2000001011 | Human | Colorectum | AD | 3.80e-09 | 2.83e-01 | -0.1464 |
27183 | VPS4A | HTA11_866_2000001011 | Human | Colorectum | AD | 2.73e-03 | 1.43e-01 | -0.1001 |
27183 | VPS4A | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.00e-06 | 2.82e-01 | -0.059 |
27183 | VPS4A | HTA11_2992_2000001011 | Human | Colorectum | SER | 5.34e-03 | 4.37e-01 | -0.1706 |
27183 | VPS4A | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.33e-04 | 1.97e-01 | 0.0674 |
27183 | VPS4A | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.53e-02 | 1.71e-01 | 0.294 |
27183 | VPS4A | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.05e-18 | 5.40e-01 | 0.3859 |
27183 | VPS4A | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.27e-04 | 2.55e-01 | 0.3005 |
27183 | VPS4A | LZE4T | Human | Esophagus | ESCC | 2.21e-10 | 2.46e-01 | 0.0811 |
27183 | VPS4A | LZE7T | Human | Esophagus | ESCC | 8.08e-04 | 1.23e-01 | 0.0667 |
27183 | VPS4A | LZE8T | Human | Esophagus | ESCC | 3.82e-02 | -3.35e-02 | 0.067 |
27183 | VPS4A | LZE20T | Human | Esophagus | ESCC | 1.72e-03 | 2.75e-01 | 0.0662 |
27183 | VPS4A | LZE22D1 | Human | Esophagus | HGIN | 2.01e-04 | 1.48e-01 | 0.0595 |
27183 | VPS4A | LZE22T | Human | Esophagus | ESCC | 2.37e-07 | 6.93e-01 | 0.068 |
27183 | VPS4A | LZE24T | Human | Esophagus | ESCC | 7.00e-22 | 5.55e-01 | 0.0596 |
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Transcriptomic changes along malignancy continuum. |
∗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:19019908 | Thyroid | PTC | regulation of mitotic cell cycle phase transition | 138/5968 | 299/18723 | 1.44e-07 | 2.78e-06 | 138 |
GO:000704115 | Thyroid | PTC | lysosomal transport | 63/5968 | 114/18723 | 1.97e-07 | 3.54e-06 | 63 |
GO:1903076112 | Thyroid | PTC | regulation of protein localization to plasma membrane | 58/5968 | 104/18723 | 3.91e-07 | 6.51e-06 | 58 |
GO:000703210 | Thyroid | PTC | endosome organization | 48/5968 | 82/18723 | 5.65e-07 | 9.04e-06 | 48 |
GO:00002818 | Thyroid | PTC | mitotic cytokinesis | 43/5968 | 71/18723 | 5.93e-07 | 9.47e-06 | 43 |
GO:0030865110 | Thyroid | PTC | cortical cytoskeleton organization | 38/5968 | 61/18723 | 9.77e-07 | 1.46e-05 | 38 |
GO:199018215 | Thyroid | PTC | exosomal secretion | 17/5968 | 20/18723 | 1.39e-06 | 1.98e-05 | 17 |
GO:00457867 | Thyroid | PTC | negative regulation of cell cycle | 166/5968 | 385/18723 | 1.93e-06 | 2.64e-05 | 166 |
GO:19019878 | Thyroid | PTC | regulation of cell cycle phase transition | 167/5968 | 390/18723 | 2.97e-06 | 3.87e-05 | 167 |
GO:00482846 | Thyroid | PTC | organelle fusion | 71/5968 | 141/18723 | 3.68e-06 | 4.70e-05 | 71 |
GO:004409110 | Thyroid | PTC | membrane biogenesis | 34/5968 | 55/18723 | 4.64e-06 | 5.69e-05 | 34 |
GO:009773415 | Thyroid | PTC | extracellular exosome biogenesis | 17/5968 | 21/18723 | 5.13e-06 | 6.22e-05 | 17 |
GO:014011210 | Thyroid | PTC | extracellular vesicle biogenesis | 18/5968 | 23/18723 | 6.38e-06 | 7.63e-05 | 18 |
GO:001906816 | Thyroid | PTC | virion assembly | 24/5968 | 35/18723 | 9.08e-06 | 1.03e-04 | 24 |
GO:007170914 | Thyroid | PTC | membrane assembly | 31/5968 | 50/18723 | 1.12e-05 | 1.23e-04 | 31 |
GO:0031032110 | Thyroid | PTC | actomyosin structure organization | 91/5968 | 196/18723 | 1.35e-05 | 1.45e-04 | 91 |
GO:000091019 | Thyroid | PTC | cytokinesis | 82/5968 | 173/18723 | 1.37e-05 | 1.47e-04 | 82 |
GO:1903900113 | Thyroid | PTC | regulation of viral life cycle | 72/5968 | 148/18723 | 1.49e-05 | 1.58e-04 | 72 |
GO:19035439 | Thyroid | PTC | positive regulation of exosomal secretion | 13/5968 | 15/18723 | 1.81e-05 | 1.87e-04 | 13 |
GO:007266518 | Thyroid | PTC | protein localization to vacuole | 38/5968 | 67/18723 | 2.28e-05 | 2.28e-04 | 38 |
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Enriched KEGG pathways. |
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 |
hsa041442 | Colorectum | SER | Endocytosis | 81/1580 | 251/8465 | 1.14e-07 | 2.36e-06 | 1.71e-06 | 81 |
hsa04217 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
hsa041443 | Colorectum | SER | Endocytosis | 81/1580 | 251/8465 | 1.14e-07 | 2.36e-06 | 1.71e-06 | 81 |
hsa042171 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
hsa041444 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa03250 | Colorectum | MSS | Viral life cycle - HIV-1 | 23/1875 | 63/8465 | 6.55e-03 | 2.64e-02 | 1.62e-02 | 23 |
hsa041445 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa032501 | Colorectum | MSS | Viral life cycle - HIV-1 | 23/1875 | 63/8465 | 6.55e-03 | 2.64e-02 | 1.62e-02 | 23 |
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 |
hsa032509 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
hsa0325014 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
hsa0414422 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa032502 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0325011 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
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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 |
VPS4A | SNV | Missense_Mutation | novel | c.940C>G | p.Leu314Val | p.L314V | Q9UN37 | protein_coding | deleterious(0) | benign(0.076) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
VPS4A | SNV | Missense_Mutation | rs757227102 | c.52G>A | p.Glu18Lys | p.E18K | Q9UN37 | protein_coding | tolerated(0.11) | possibly_damaging(0.595) | TCGA-A2-A0YD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
VPS4A | SNV | Missense_Mutation | c.1135N>G | p.Pro379Ala | p.P379A | Q9UN37 | protein_coding | deleterious(0.03) | possibly_damaging(0.839) | TCGA-E2-A1B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Adriamycin | SD | |
VPS4A | insertion | Nonsense_Mutation | novel | c.158_159insCATGGTGAAACTCTGTCTGCACTAAAAATACAAAAATTAGCC | p.Lys53delinsAsnMetValLysLeuCysLeuHisTerLysTyrLysAsnTerPro | p.K53delinsNMVKLCLH*KYKN*P | Q9UN37 | protein_coding | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
VPS4A | insertion | Nonsense_Mutation | novel | c.476_477insAGGCTGAAGGGCCAGCTTGTGACTTTCCGTCT | p.Trp160GlyfsTer2 | p.W160Gfs*2 | Q9UN37 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
VPS4A | SNV | Missense_Mutation | novel | c.733C>T | p.Arg245Trp | p.R245W | Q9UN37 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VPS4A | SNV | Missense_Mutation | novel | c.944C>T | p.Thr315Met | p.T315M | Q9UN37 | protein_coding | deleterious(0) | benign(0.276) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VPS4A | SNV | Missense_Mutation | c.802N>T | p.Leu268Phe | p.L268F | Q9UN37 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-IR-A3LL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
VPS4A | SNV | Missense_Mutation | c.441N>G | p.Ile147Met | p.I147M | Q9UN37 | protein_coding | tolerated(0.09) | benign(0.097) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
VPS4A | SNV | Missense_Mutation | c.632N>G | p.Asn211Ser | p.N211S | Q9UN37 | protein_coding | tolerated(0.26) | benign(0.005) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <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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