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Gene: BEST4 |
Gene summary for BEST4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | BEST4 | Gene ID | 266675 |
Gene name | bestrophin 4 | |
Gene Alias | VMD2L2 | |
Cytomap | 1p34.1 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q8NFU0 |
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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 |
266675 | BEST4 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.73e-07 | 1.08e+00 | -0.1954 |
266675 | BEST4 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.91e-02 | 1.60e+00 | -0.2061 |
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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:0015698 | Colorectum | AD | inorganic anion transport | 52/3918 | 180/18723 | 6.83e-03 | 4.22e-02 | 52 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
BEST4 | SNV | Missense_Mutation | novel | c.949N>T | p.Asp317Tyr | p.D317Y | Q8NFU0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A6IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
BEST4 | insertion | Nonsense_Mutation | novel | c.80_81insTACACAAGCATCCCGCTGCCAGACCAGCTGATGTGCGTC | p.Ser27_Ile28insThrGlnAlaSerArgCysGlnThrSerTerCysAlaSer | p.S27_I28insTQASRCQTS*CAS | Q8NFU0 | protein_coding | TCGA-A2-A0CM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | PD | ||
BEST4 | deletion | Frame_Shift_Del | novel | c.421delC | p.Arg141AlafsTer34 | p.R141Afs*34 | Q8NFU0 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
BEST4 | SNV | Missense_Mutation | c.220G>A | p.Asp74Asn | p.D74N | Q8NFU0 | protein_coding | tolerated(0.32) | benign(0.02) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
BEST4 | SNV | Missense_Mutation | novel | c.331N>G | p.Ser111Ala | p.S111A | Q8NFU0 | protein_coding | tolerated(0.14) | benign(0.19) | TCGA-ZJ-AB0I-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
BEST4 | SNV | Missense_Mutation | rs773733162 | c.764N>A | p.Arg255His | p.R255H | Q8NFU0 | protein_coding | deleterious(0.01) | probably_damaging(0.973) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
BEST4 | SNV | Missense_Mutation | c.317N>C | p.Leu106Pro | p.L106P | Q8NFU0 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
BEST4 | SNV | Missense_Mutation | c.616G>A | p.Ala206Thr | p.A206T | Q8NFU0 | protein_coding | tolerated(0.33) | benign(0.041) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
BEST4 | SNV | Missense_Mutation | c.1068C>A | p.Asp356Glu | p.D356E | Q8NFU0 | protein_coding | tolerated(0.74) | benign(0) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
BEST4 | SNV | Missense_Mutation | c.212N>A | p.Arg71His | p.R71H | Q8NFU0 | protein_coding | tolerated(0.2) | benign(0.055) | TCGA-F4-6570-01 | 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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