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Gene: RNASE4 |
Gene summary for RNASE4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RNASE4 | Gene ID | 6038 |
Gene name | ribonuclease A family member 4 | |
Gene Alias | RAB1 | |
Cytomap | 14q11.2 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | P34096 |
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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 |
6038 | RNASE4 | LZE4T | Human | Esophagus | ESCC | 2.45e-09 | 2.80e-01 | 0.0811 |
6038 | RNASE4 | LZE5T | Human | Esophagus | ESCC | 5.52e-13 | 7.68e-01 | 0.0514 |
6038 | RNASE4 | LZE24T | Human | Esophagus | ESCC | 4.99e-09 | 2.95e-01 | 0.0596 |
6038 | RNASE4 | P1T-E | Human | Esophagus | ESCC | 2.97e-02 | 1.36e-01 | 0.0875 |
6038 | RNASE4 | P2T-E | Human | Esophagus | ESCC | 1.00e-04 | 1.25e-01 | 0.1177 |
6038 | RNASE4 | P4T-E | Human | Esophagus | ESCC | 2.23e-06 | 1.74e-01 | 0.1323 |
6038 | RNASE4 | P8T-E | Human | Esophagus | ESCC | 6.34e-33 | 6.53e-01 | 0.0889 |
6038 | RNASE4 | P9T-E | Human | Esophagus | ESCC | 2.41e-06 | 1.99e-01 | 0.1131 |
6038 | RNASE4 | P10T-E | Human | Esophagus | ESCC | 2.39e-09 | 2.19e-01 | 0.116 |
6038 | RNASE4 | P11T-E | Human | Esophagus | ESCC | 2.46e-02 | 1.22e-01 | 0.1426 |
6038 | RNASE4 | P12T-E | Human | Esophagus | ESCC | 1.05e-13 | 4.12e-01 | 0.1122 |
6038 | RNASE4 | P15T-E | Human | Esophagus | ESCC | 1.87e-22 | 4.48e-01 | 0.1149 |
6038 | RNASE4 | P16T-E | Human | Esophagus | ESCC | 7.31e-12 | 1.59e-01 | 0.1153 |
6038 | RNASE4 | P17T-E | Human | Esophagus | ESCC | 1.49e-05 | 3.20e-01 | 0.1278 |
6038 | RNASE4 | P19T-E | Human | Esophagus | ESCC | 6.53e-04 | 2.73e-01 | 0.1662 |
6038 | RNASE4 | P21T-E | Human | Esophagus | ESCC | 6.02e-06 | 1.61e-01 | 0.1617 |
6038 | RNASE4 | P22T-E | Human | Esophagus | ESCC | 1.33e-17 | 3.41e-01 | 0.1236 |
6038 | RNASE4 | P23T-E | Human | Esophagus | ESCC | 1.48e-05 | 2.26e-01 | 0.108 |
6038 | RNASE4 | P26T-E | Human | Esophagus | ESCC | 4.22e-18 | 3.55e-01 | 0.1276 |
6038 | RNASE4 | P28T-E | Human | Esophagus | ESCC | 1.81e-06 | 2.40e-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 |
Cervix | N_HPV | |
Endometrium | AEH | |
Endometrium | EEC | |
Prostate | BPH | |
Prostate | Tumor |
∗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:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
GO:00063793 | Esophagus | ESCC | mRNA cleavage | 17/8552 | 22/18723 | 2.60e-03 | 1.11e-02 | 17 |
GO:0090501 | Liver | Cirrhotic | RNA phosphodiester bond hydrolysis | 54/4634 | 152/18723 | 1.89e-03 | 1.19e-02 | 54 |
GO:00905011 | Liver | HCC | RNA phosphodiester bond hydrolysis | 101/7958 | 152/18723 | 1.99e-09 | 5.63e-08 | 101 |
GO:0090305 | Liver | HCC | nucleic acid phosphodiester bond hydrolysis | 152/7958 | 261/18723 | 1.90e-07 | 3.46e-06 | 152 |
GO:0090502 | Liver | HCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 52/7958 | 82/18723 | 1.06e-04 | 9.08e-04 | 52 |
GO:0006379 | Liver | HCC | mRNA cleavage | 17/7958 | 22/18723 | 9.84e-04 | 5.70e-03 | 17 |
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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 |
RNASE4 | SNV | Missense_Mutation | c.391N>A | p.Val131Ile | p.V131I | P34096 | protein_coding | tolerated(1) | benign(0.044) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
RNASE4 | SNV | Missense_Mutation | c.73N>T | p.Pro25Ser | p.P25S | P34096 | protein_coding | deleterious(0.02) | possibly_damaging(0.893) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
RNASE4 | SNV | Missense_Mutation | rs771543461 | c.244N>T | p.Arg82Cys | p.R82C | P34096 | protein_coding | deleterious(0) | possibly_damaging(0.754) | TCGA-CM-6169-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Ancillary | leucovorin | SD |
RNASE4 | SNV | Missense_Mutation | c.320C>T | p.Thr107Ile | p.T107I | P34096 | protein_coding | deleterious(0.01) | probably_damaging(0.952) | TCGA-AH-6897-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
RNASE4 | SNV | Missense_Mutation | c.245N>A | p.Arg82His | p.R82H | P34096 | protein_coding | tolerated(0.13) | benign(0.001) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
RNASE4 | SNV | Missense_Mutation | novel | c.380G>T | p.Ser127Ile | p.S127I | P34096 | protein_coding | tolerated(0.15) | benign(0.063) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
RNASE4 | SNV | Missense_Mutation | novel | c.279N>T | p.Lys93Asn | p.K93N | P34096 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RNASE4 | SNV | Missense_Mutation | novel | c.383N>T | p.Thr128Ile | p.T128I | P34096 | protein_coding | tolerated(0.11) | possibly_damaging(0.587) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
RNASE4 | SNV | Missense_Mutation | rs775063092 | c.250A>G | p.Ile84Val | p.I84V | P34096 | protein_coding | tolerated(0.67) | possibly_damaging(0.536) | TCGA-D1-A15X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RNASE4 | SNV | Missense_Mutation | novel | c.409G>T | p.Gly137Cys | p.G137C | P34096 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-EO-A3AZ-01 | Endometrium | uterine corpus endometrioid carcinoma | 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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