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Gene: DENND4B |
Gene summary for DENND4B |
Gene summary. |
Gene information | Species | Human | Gene symbol | DENND4B | Gene ID | 9909 |
Gene name | DENN domain containing 4B | |
Gene Alias | KIAA0476 | |
Cytomap | 1q21.3 | |
Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | O75064 |
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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 |
9909 | DENND4B | HCC1_Meng | Human | Liver | HCC | 1.04e-16 | 2.19e-02 | 0.0246 |
9909 | DENND4B | HCC1 | Human | Liver | HCC | 4.22e-04 | 2.41e+00 | 0.5336 |
9909 | DENND4B | HCC2 | Human | Liver | HCC | 8.13e-12 | 2.30e+00 | 0.5341 |
9909 | DENND4B | S016 | Human | Liver | HCC | 2.85e-06 | 2.42e-01 | 0.2243 |
9909 | DENND4B | S028 | Human | Liver | HCC | 1.68e-04 | 2.61e-01 | 0.2503 |
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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:000726521 | Liver | HCC | Ras protein signal transduction | 187/7958 | 337/18723 | 8.89e-07 | 1.35e-05 | 187 |
GO:004657811 | Liver | HCC | regulation of Ras protein signal transduction | 100/7958 | 189/18723 | 2.42e-03 | 1.18e-02 | 100 |
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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 |
DENND4B | SNV | Missense_Mutation | rs749288468 | c.1039N>T | p.Arg347Cys | p.R347C | O75064 | protein_coding | tolerated(0.08) | possibly_damaging(0.733) | TCGA-CG-4460-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | capecitabine | PD |
DENND4B | SNV | Missense_Mutation | c.2465N>C | p.Leu822Pro | p.L822P | O75064 | protein_coding | deleterious(0.02) | probably_damaging(0.96) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
DENND4B | SNV | Missense_Mutation | rs368380218 | c.1994C>T | p.Pro665Leu | p.P665L | O75064 | protein_coding | deleterious(0.01) | benign(0.003) | TCGA-CG-5723-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
DENND4B | SNV | Missense_Mutation | novel | c.2725N>G | p.Gln909Glu | p.Q909E | O75064 | protein_coding | tolerated(1) | benign(0.007) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD |
DENND4B | SNV | Missense_Mutation | c.769G>A | p.Val257Ile | p.V257I | O75064 | protein_coding | tolerated(0.06) | benign(0.339) | TCGA-HU-A4GQ-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
DENND4B | SNV | Missense_Mutation | c.4420N>T | p.Arg1474Trp | p.R1474W | O75064 | protein_coding | deleterious(0) | benign(0.018) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | ||
DENND4B | SNV | Missense_Mutation | novel | c.3169N>A | p.Leu1057Met | p.L1057M | O75064 | protein_coding | deleterious(0.04) | benign(0.247) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | |
DENND4B | SNV | Missense_Mutation | novel | c.2095N>G | p.Pro699Ala | p.P699A | O75064 | protein_coding | tolerated(1) | benign(0) | TCGA-VQ-A8PE-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
DENND4B | deletion | Frame_Shift_Del | novel | c.228delN | p.Leu77TrpfsTer222 | p.L77Wfs*222 | O75064 | protein_coding | TCGA-BR-8361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
DENND4B | deletion | Frame_Shift_Del | c.2864delC | p.Pro955LeufsTer5 | p.P955Lfs*5 | O75064 | protein_coding | TCGA-CG-5723-01 | Stomach | stomach 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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