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Gene: RBM42 |
Gene summary for RBM42 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RBM42 | Gene ID | 79171 |
| Gene name | RNA binding motif protein 42 | |
| Gene Alias | RBM42 | |
| Cytomap | 19q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q9BTD8 |
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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 |
| 79171 | RBM42 | LZE2T | Human | Esophagus | ESCC | 7.16e-04 | 4.02e-01 | 0.082 |
| 79171 | RBM42 | LZE4T | Human | Esophagus | ESCC | 4.02e-14 | 5.38e-01 | 0.0811 |
| 79171 | RBM42 | LZE7T | Human | Esophagus | ESCC | 1.33e-07 | 6.86e-01 | 0.0667 |
| 79171 | RBM42 | LZE8T | Human | Esophagus | ESCC | 8.49e-09 | 1.90e-01 | 0.067 |
| 79171 | RBM42 | LZE20T | Human | Esophagus | ESCC | 3.30e-07 | 3.20e-01 | 0.0662 |
| 79171 | RBM42 | LZE22D1 | Human | Esophagus | HGIN | 3.91e-06 | 1.54e-01 | 0.0595 |
| 79171 | RBM42 | LZE22T | Human | Esophagus | ESCC | 4.93e-05 | 6.31e-01 | 0.068 |
| 79171 | RBM42 | LZE24T | Human | Esophagus | ESCC | 4.97e-29 | 9.08e-01 | 0.0596 |
| 79171 | RBM42 | LZE21T | Human | Esophagus | ESCC | 5.55e-04 | 5.70e-01 | 0.0655 |
| 79171 | RBM42 | LZE6T | Human | Esophagus | ESCC | 3.65e-07 | 3.36e-01 | 0.0845 |
| 79171 | RBM42 | P1T-E | Human | Esophagus | ESCC | 1.81e-17 | 7.16e-01 | 0.0875 |
| 79171 | RBM42 | P2T-E | Human | Esophagus | ESCC | 2.58e-47 | 7.85e-01 | 0.1177 |
| 79171 | RBM42 | P4T-E | Human | Esophagus | ESCC | 7.10e-49 | 1.10e+00 | 0.1323 |
| 79171 | RBM42 | P5T-E | Human | Esophagus | ESCC | 7.68e-31 | 8.33e-01 | 0.1327 |
| 79171 | RBM42 | P8T-E | Human | Esophagus | ESCC | 1.75e-73 | 1.42e+00 | 0.0889 |
| 79171 | RBM42 | P9T-E | Human | Esophagus | ESCC | 9.81e-51 | 1.18e+00 | 0.1131 |
| 79171 | RBM42 | P10T-E | Human | Esophagus | ESCC | 1.22e-53 | 1.07e+00 | 0.116 |
| 79171 | RBM42 | P11T-E | Human | Esophagus | ESCC | 1.78e-32 | 1.18e+00 | 0.1426 |
| 79171 | RBM42 | P12T-E | Human | Esophagus | ESCC | 2.79e-53 | 1.16e+00 | 0.1122 |
| 79171 | RBM42 | P15T-E | Human | Esophagus | ESCC | 1.85e-57 | 1.23e+00 | 0.1149 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000838026 | Esophagus | HGIN | RNA splicing | 160/2587 | 434/18723 | 3.74e-34 | 1.12e-30 | 160 |
| GO:000037520 | Esophagus | HGIN | RNA splicing, via transesterification reactions | 115/2587 | 324/18723 | 3.16e-23 | 3.80e-20 | 115 |
| GO:000037720 | Esophagus | HGIN | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
| GO:000039820 | Esophagus | HGIN | mRNA splicing, via spliceosome | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
| GO:004348427 | Esophagus | HGIN | regulation of RNA splicing | 59/2587 | 148/18723 | 3.61e-15 | 7.22e-13 | 59 |
| 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:004802426 | Esophagus | HGIN | regulation of mRNA splicing, via spliceosome | 42/2587 | 101/18723 | 6.35e-12 | 7.78e-10 | 42 |
| GO:190331226 | Esophagus | HGIN | negative regulation of mRNA metabolic process | 29/2587 | 92/18723 | 1.01e-05 | 2.92e-04 | 29 |
| GO:003311926 | Esophagus | HGIN | negative regulation of RNA splicing | 12/2587 | 25/18723 | 4.25e-05 | 1.04e-03 | 12 |
| GO:005068610 | Esophagus | HGIN | negative regulation of mRNA processing | 12/2587 | 29/18723 | 2.48e-04 | 4.38e-03 | 12 |
| GO:004802510 | Esophagus | HGIN | negative regulation of mRNA splicing, via spliceosome | 9/2587 | 20/18723 | 7.18e-04 | 9.60e-03 | 9 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
| GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:1903311110 | Esophagus | ESCC | regulation of mRNA metabolic process | 210/8552 | 288/18723 | 3.25e-21 | 5.56e-19 | 210 |
| GO:0043484111 | Esophagus | ESCC | regulation of RNA splicing | 116/8552 | 148/18723 | 3.18e-16 | 2.38e-14 | 116 |
| GO:0050684110 | Esophagus | ESCC | regulation of mRNA processing | 109/8552 | 137/18723 | 3.51e-16 | 2.59e-14 | 109 |
| GO:0048024111 | Esophagus | ESCC | regulation of mRNA splicing, via spliceosome | 78/8552 | 101/18723 | 8.72e-11 | 2.66e-09 | 78 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| RBM42 | TREG | Liver | Cirrhotic | RPS4Y1,CD300C,TIMP2, etc. | 4.62e-02 |  |
| RBM42 | CD8TEXP | Liver | Cirrhotic | RPS4Y1,CD300C,TIMP2, etc. | 1.16e-01 | |
| RBM42 | CD8TEXINT | Liver | HCC | RPS4Y1,CD300C,TIMP2, etc. | 1.19e-01 |  |
| RBM42 | TREG | Liver | HCC | RPS4Y1,CD300C,TIMP2, etc. | 7.39e-02 | |
| RBM42 | pDC | Liver | NAFLD | RPS4Y1,CD300C,TIMP2, etc. | 4.59e-01 |  |
| ∗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. |
| Page: 1 |
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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 |
| RBM42 | SNV | Missense_Mutation | c.688G>C | p.Glu230Gln | p.E230Q | Q9BTD8 | protein_coding | tolerated(0.14) | benign(0.143) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| RBM42 | SNV | Missense_Mutation | novel | c.1115N>T | p.Ser372Ile | p.S372I | Q9BTD8 | protein_coding | deleterious(0) | benign(0.005) | TCGA-HN-A2NL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| RBM42 | SNV | Missense_Mutation | c.1274N>A | p.Gly425Asp | p.G425D | Q9BTD8 | protein_coding | deleterious(0) | benign(0.031) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RBM42 | SNV | Missense_Mutation | novel | c.1015G>A | p.Glu339Lys | p.E339K | Q9BTD8 | protein_coding | tolerated(0.11) | possibly_damaging(0.899) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RBM42 | SNV | Missense_Mutation | c.167T>C | p.Ile56Thr | p.I56T | Q9BTD8 | protein_coding | tolerated(0.12) | benign(0.438) | TCGA-A6-6137-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | SD | |
| RBM42 | SNV | Missense_Mutation | c.116C>T | p.Ala39Val | p.A39V | Q9BTD8 | protein_coding | deleterious(0) | possibly_damaging(0.77) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RBM42 | SNV | Missense_Mutation | rs538251490 | c.433C>T | p.Arg145Trp | p.R145W | Q9BTD8 | protein_coding | deleterious(0.02) | probably_damaging(0.952) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| RBM42 | SNV | Missense_Mutation | rs376033321 | c.535N>A | p.Gly179Ser | p.G179S | Q9BTD8 | protein_coding | deleterious(0.04) | possibly_damaging(0.638) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| RBM42 | SNV | Missense_Mutation | rs370094400 | c.1396N>A | p.Val466Met | p.V466M | Q9BTD8 | protein_coding | deleterious(0) | benign(0.246) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RBM42 | SNV | Missense_Mutation | c.529N>T | p.Ala177Ser | p.A177S | Q9BTD8 | protein_coding | tolerated(0.28) | probably_damaging(0.935) | TCGA-AZ-6598-01 | 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 |
| Page: 1 |
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