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Gene: RNF43 |
Gene summary for RNF43 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RNF43 | Gene ID | 54894 |
Gene name | ring finger protein 43 | |
Gene Alias | RNF124 | |
Cytomap | 17q22 | |
Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q68DV7 |
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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 |
54894 | RNF43 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.64e-33 | -8.57e-01 | 0.0155 |
54894 | RNF43 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.60e-24 | -9.92e-01 | -0.1808 |
54894 | RNF43 | HTA11_1938_2000001011 | Human | Colorectum | AD | 9.32e-11 | -7.19e-01 | -0.0811 |
54894 | RNF43 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.13e-08 | -6.22e-01 | -0.1088 |
54894 | RNF43 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.06e-39 | -9.45e-01 | -0.1954 |
54894 | RNF43 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.03e-04 | -1.06e+00 | -0.2602 |
54894 | RNF43 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.27e-06 | -1.05e+00 | -0.2196 |
54894 | RNF43 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.53e-09 | -7.81e-01 | -0.1207 |
54894 | RNF43 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.58e-16 | -9.85e-01 | -0.1526 |
54894 | RNF43 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.27e-27 | -7.71e-01 | -0.1464 |
54894 | RNF43 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.64e-24 | -7.85e-01 | -0.1001 |
54894 | RNF43 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.04e-03 | -4.74e-01 | -0.059 |
54894 | RNF43 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.29e-09 | -1.05e+00 | -0.1706 |
54894 | RNF43 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.83e-11 | -1.09e+00 | -0.2061 |
54894 | RNF43 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.46e-05 | -8.54e-01 | -0.1462 |
54894 | RNF43 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.87e-12 | -8.86e-01 | -0.0842 |
54894 | RNF43 | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.17e-04 | -1.06e+00 | -0.00410000000000005 |
54894 | RNF43 | HTA11_7862_2000001011 | Human | Colorectum | AD | 9.80e-12 | -9.92e-01 | -0.0179 |
54894 | RNF43 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.76e-08 | -4.18e-01 | 0.096 |
54894 | RNF43 | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.88e-05 | -9.09e-01 | 0.0446 |
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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:0043112 | Colorectum | AD | receptor metabolic process | 62/3918 | 166/18723 | 8.18e-07 | 2.85e-05 | 62 |
GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
GO:0032801 | Colorectum | AD | receptor catabolic process | 12/3918 | 28/18723 | 7.21e-03 | 4.39e-02 | 12 |
GO:00160551 | Colorectum | SER | Wnt signaling pathway | 97/2897 | 444/18723 | 2.02e-04 | 3.68e-03 | 97 |
GO:01987381 | Colorectum | SER | cell-cell signaling by wnt | 97/2897 | 446/18723 | 2.39e-04 | 4.11e-03 | 97 |
GO:00301111 | Colorectum | SER | regulation of Wnt signaling pathway | 75/2897 | 328/18723 | 2.47e-04 | 4.20e-03 | 75 |
GO:00301112 | Colorectum | MSS | regulation of Wnt signaling pathway | 98/3467 | 328/18723 | 3.37e-07 | 1.36e-05 | 98 |
GO:00160552 | Colorectum | MSS | Wnt signaling pathway | 124/3467 | 444/18723 | 6.06e-07 | 2.26e-05 | 124 |
GO:01987382 | Colorectum | MSS | cell-cell signaling by wnt | 124/3467 | 446/18723 | 7.83e-07 | 2.77e-05 | 124 |
GO:00431121 | Colorectum | MSS | receptor metabolic process | 57/3467 | 166/18723 | 8.47e-07 | 2.97e-05 | 57 |
GO:0030178 | Colorectum | MSS | negative regulation of Wnt signaling pathway | 48/3467 | 170/18723 | 1.23e-03 | 1.18e-02 | 48 |
GO:00328011 | Colorectum | MSS | receptor catabolic process | 12/3467 | 28/18723 | 2.53e-03 | 2.02e-02 | 12 |
GO:00160553 | Colorectum | FAP | Wnt signaling pathway | 104/2622 | 444/18723 | 4.92e-08 | 3.92e-06 | 104 |
GO:01987383 | Colorectum | FAP | cell-cell signaling by wnt | 104/2622 | 446/18723 | 6.26e-08 | 4.54e-06 | 104 |
GO:00301113 | Colorectum | FAP | regulation of Wnt signaling pathway | 81/2622 | 328/18723 | 1.44e-07 | 9.03e-06 | 81 |
GO:00431122 | Colorectum | FAP | receptor metabolic process | 46/2622 | 166/18723 | 2.70e-06 | 1.02e-04 | 46 |
GO:00301781 | Colorectum | FAP | negative regulation of Wnt signaling pathway | 38/2622 | 170/18723 | 2.06e-03 | 1.70e-02 | 38 |
GO:00160554 | Colorectum | CRC | Wnt signaling pathway | 88/2078 | 444/18723 | 3.91e-08 | 5.28e-06 | 88 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04310 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
hsa043101 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
hsa043102 | Colorectum | MSS | Wnt signaling pathway | 53/1875 | 171/8465 | 4.24e-03 | 1.86e-02 | 1.14e-02 | 53 |
hsa043103 | Colorectum | MSS | Wnt signaling pathway | 53/1875 | 171/8465 | 4.24e-03 | 1.86e-02 | 1.14e-02 | 53 |
hsa043104 | Colorectum | FAP | Wnt signaling pathway | 46/1404 | 171/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 46 |
hsa043105 | Colorectum | FAP | Wnt signaling pathway | 46/1404 | 171/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 46 |
hsa043106 | Colorectum | CRC | Wnt signaling pathway | 40/1091 | 171/8465 | 1.01e-04 | 1.57e-03 | 1.07e-03 | 40 |
hsa043107 | Colorectum | CRC | Wnt signaling pathway | 40/1091 | 171/8465 | 1.01e-04 | 1.57e-03 | 1.07e-03 | 40 |
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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 |
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-DF-A2KZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-DI-A0WH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-E6-A2P8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-EC-A1NJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-EC-A24G-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delG | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-EO-A3KX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
RNF43 | insertion | Frame_Shift_Ins | novel | c.239dupG | p.Leu82IlefsTer14 | p.L82Ifs*14 | Q68DV7 | protein_coding | TCGA-EY-A1G7-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
RNF43 | deletion | Frame_Shift_Del | novel | c.784delN | p.Ser262GlnfsTer157 | p.S262Qfs*157 | Q68DV7 | protein_coding | TCGA-EY-A1GF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-EY-A1H0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | SD | ||
RNF43 | deletion | Frame_Shift_Del | rs781215815 | c.1976delN | p.Gly659ValfsTer41 | p.G659Vfs*41 | Q68DV7 | protein_coding | TCGA-EY-A548-01 | 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 |
54894 | RNF43 | ENZYME, CLINICALLY ACTIONABLE | RNF43-721 | 22977472 |
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