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Gene: RNF40 |
Gene summary for RNF40 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RNF40 | Gene ID | 9810 |
Gene name | ring finger protein 40 | |
Gene Alias | BRE1B | |
Cytomap | 16p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | A8K6K1 |
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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 |
9810 | RNF40 | LZE2T | Human | Esophagus | ESCC | 5.07e-03 | 3.92e-01 | 0.082 |
9810 | RNF40 | LZE4T | Human | Esophagus | ESCC | 2.20e-09 | 1.97e-01 | 0.0811 |
9810 | RNF40 | LZE7T | Human | Esophagus | ESCC | 9.74e-10 | 4.62e-01 | 0.0667 |
9810 | RNF40 | LZE8T | Human | Esophagus | ESCC | 2.10e-10 | 2.83e-01 | 0.067 |
9810 | RNF40 | LZE20T | Human | Esophagus | ESCC | 5.29e-04 | 1.34e-01 | 0.0662 |
9810 | RNF40 | LZE22D1 | Human | Esophagus | HGIN | 2.88e-02 | 8.90e-02 | 0.0595 |
9810 | RNF40 | LZE22T | Human | Esophagus | ESCC | 2.43e-04 | 2.62e-01 | 0.068 |
9810 | RNF40 | LZE24T | Human | Esophagus | ESCC | 5.49e-35 | 9.65e-01 | 0.0596 |
9810 | RNF40 | LZE21T | Human | Esophagus | ESCC | 5.07e-04 | 2.70e-01 | 0.0655 |
9810 | RNF40 | LZE6T | Human | Esophagus | ESCC | 2.88e-05 | 1.77e-01 | 0.0845 |
9810 | RNF40 | P1T-E | Human | Esophagus | ESCC | 1.44e-16 | 5.40e-01 | 0.0875 |
9810 | RNF40 | P2T-E | Human | Esophagus | ESCC | 4.83e-38 | 7.07e-01 | 0.1177 |
9810 | RNF40 | P4T-E | Human | Esophagus | ESCC | 6.65e-21 | 4.18e-01 | 0.1323 |
9810 | RNF40 | P5T-E | Human | Esophagus | ESCC | 9.89e-16 | 1.88e-01 | 0.1327 |
9810 | RNF40 | P8T-E | Human | Esophagus | ESCC | 6.92e-22 | 4.55e-01 | 0.0889 |
9810 | RNF40 | P9T-E | Human | Esophagus | ESCC | 3.22e-12 | 2.47e-01 | 0.1131 |
9810 | RNF40 | P10T-E | Human | Esophagus | ESCC | 6.13e-16 | 1.95e-01 | 0.116 |
9810 | RNF40 | P11T-E | Human | Esophagus | ESCC | 5.15e-19 | 6.53e-01 | 0.1426 |
9810 | RNF40 | P12T-E | Human | Esophagus | ESCC | 5.30e-34 | 6.67e-01 | 0.1122 |
9810 | RNF40 | P15T-E | Human | Esophagus | ESCC | 1.21e-31 | 5.18e-01 | 0.1149 |
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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:004217627 | Esophagus | HGIN | regulation of protein catabolic process | 119/2587 | 391/18723 | 8.09e-18 | 2.43e-15 | 119 |
GO:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
GO:190331120 | Esophagus | HGIN | regulation of mRNA metabolic process | 91/2587 | 288/18723 | 5.06e-15 | 9.78e-13 | 91 |
GO:005068419 | Esophagus | HGIN | regulation of mRNA processing | 55/2587 | 137/18723 | 2.17e-14 | 3.94e-12 | 55 |
GO:004586227 | Esophagus | HGIN | positive regulation of proteolysis | 107/2587 | 372/18723 | 2.61e-14 | 4.60e-12 | 107 |
GO:190336227 | Esophagus | HGIN | regulation of cellular protein catabolic process | 81/2587 | 255/18723 | 1.16e-13 | 1.93e-11 | 81 |
GO:190332027 | Esophagus | HGIN | regulation of protein modification by small protein conjugation or removal | 78/2587 | 242/18723 | 1.40e-13 | 2.26e-11 | 78 |
GO:000989626 | Esophagus | HGIN | positive regulation of catabolic process | 126/2587 | 492/18723 | 1.46e-12 | 2.09e-10 | 126 |
GO:003133126 | Esophagus | HGIN | positive regulation of cellular catabolic process | 112/2587 | 427/18723 | 5.15e-12 | 6.72e-10 | 112 |
GO:190305027 | Esophagus | HGIN | regulation of proteolysis involved in cellular protein catabolic process | 70/2587 | 221/18723 | 6.21e-12 | 7.76e-10 | 70 |
GO:006113627 | Esophagus | HGIN | regulation of proteasomal protein catabolic process | 60/2587 | 187/18723 | 1.10e-10 | 1.12e-08 | 60 |
GO:004573227 | Esophagus | HGIN | positive regulation of protein catabolic process | 69/2587 | 231/18723 | 1.66e-10 | 1.64e-08 | 69 |
GO:003139627 | Esophagus | HGIN | regulation of protein ubiquitination | 64/2587 | 210/18723 | 3.02e-10 | 2.71e-08 | 64 |
GO:190336427 | Esophagus | HGIN | positive regulation of cellular protein catabolic process | 51/2587 | 155/18723 | 1.01e-09 | 8.15e-08 | 51 |
GO:190180020 | Esophagus | HGIN | positive regulation of proteasomal protein catabolic process | 41/2587 | 114/18723 | 2.25e-09 | 1.67e-07 | 41 |
GO:190305219 | Esophagus | HGIN | positive regulation of proteolysis involved in cellular protein catabolic process | 45/2587 | 133/18723 | 3.55e-09 | 2.53e-07 | 45 |
GO:000020916 | Esophagus | HGIN | protein polyubiquitination | 58/2587 | 236/18723 | 6.29e-06 | 1.97e-04 | 58 |
GO:190331226 | Esophagus | HGIN | negative regulation of mRNA metabolic process | 29/2587 | 92/18723 | 1.01e-05 | 2.92e-04 | 29 |
GO:00165708 | Esophagus | HGIN | histone modification | 92/2587 | 463/18723 | 1.70e-04 | 3.30e-03 | 92 |
GO:19033228 | Esophagus | HGIN | positive regulation of protein modification by small protein conjugation or removal | 35/2587 | 138/18723 | 2.11e-04 | 3.88e-03 | 35 |
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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 |
RNF40 | SNV | Missense_Mutation | c.963N>T | p.Gln321His | p.Q321H | O75150 | protein_coding | tolerated(0.14) | probably_damaging(0.952) | TCGA-85-8355-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
RNF40 | SNV | Missense_Mutation | rs564561453 | c.2507G>A | p.Arg836Gln | p.R836Q | O75150 | protein_coding | tolerated(0.09) | benign(0.007) | TCGA-CQ-7072-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
RNF40 | SNV | Missense_Mutation | novel | c.1020N>C | p.Glu340Asp | p.E340D | O75150 | protein_coding | tolerated(0.05) | probably_damaging(0.987) | TCGA-CR-7376-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
RNF40 | SNV | Missense_Mutation | rs560357910 | c.859N>A | p.Glu287Lys | p.E287K | O75150 | protein_coding | tolerated(0.34) | possibly_damaging(0.885) | TCGA-CV-7254-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
RNF40 | SNV | Missense_Mutation | rs556209638 | c.329N>A | p.Arg110Gln | p.R110Q | O75150 | protein_coding | tolerated(1) | benign(0.003) | TCGA-CV-A45U-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
RNF40 | SNV | Missense_Mutation | novel | c.407N>A | p.Thr136Asn | p.T136N | O75150 | protein_coding | tolerated(0.47) | benign(0.003) | TCGA-CV-A45W-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
RNF40 | SNV | Missense_Mutation | novel | c.526G>A | p.Glu176Lys | p.E176K | O75150 | protein_coding | deleterious(0.01) | probably_damaging(0.991) | TCGA-P3-A6T5-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
RNF40 | SNV | Missense_Mutation | novel | c.329N>T | p.Arg110Leu | p.R110L | O75150 | protein_coding | deleterious(0.02) | benign(0.168) | TCGA-YL-A8HK-01 | Prostate | prostate adenocarcinoma | Male | <65 | 9 | Hormone Therapy | casodex | PD |
RNF40 | SNV | Missense_Mutation | c.2297N>G | p.Glu766Gly | p.E766G | O75150 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-BR-4368-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
RNF40 | SNV | Missense_Mutation | c.1004N>A | p.Leu335Gln | p.L335Q | O75150 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-BR-7703-01 | 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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