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Gene: RNMT |
Gene summary for RNMT |
Gene summary. |
Gene information | Species | Human | Gene symbol | RNMT | Gene ID | 8731 |
Gene name | RNA guanine-7 methyltransferase | |
Gene Alias | CMT1 | |
Cytomap | 18p11.21 | |
Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | A8K946 |
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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 |
8731 | RNMT | LZE2D | Human | Esophagus | HGIN | 6.71e-05 | 7.70e-01 | 0.0642 |
8731 | RNMT | LZE2T | Human | Esophagus | ESCC | 3.37e-09 | 1.31e+00 | 0.082 |
8731 | RNMT | LZE4T | Human | Esophagus | ESCC | 1.55e-13 | 5.53e-01 | 0.0811 |
8731 | RNMT | LZE5T | Human | Esophagus | ESCC | 9.98e-10 | 4.06e-01 | 0.0514 |
8731 | RNMT | LZE7T | Human | Esophagus | ESCC | 4.38e-10 | 7.24e-01 | 0.0667 |
8731 | RNMT | LZE8T | Human | Esophagus | ESCC | 2.78e-10 | 3.42e-01 | 0.067 |
8731 | RNMT | LZE20T | Human | Esophagus | ESCC | 1.41e-10 | 2.24e-01 | 0.0662 |
8731 | RNMT | LZE21D1 | Human | Esophagus | HGIN | 8.90e-04 | 4.70e-01 | 0.0632 |
8731 | RNMT | LZE22D1 | Human | Esophagus | HGIN | 2.35e-05 | 1.35e-01 | 0.0595 |
8731 | RNMT | LZE22T | Human | Esophagus | ESCC | 1.97e-02 | 2.85e-01 | 0.068 |
8731 | RNMT | LZE24T | Human | Esophagus | ESCC | 2.67e-17 | 4.21e-01 | 0.0596 |
8731 | RNMT | LZE21T | Human | Esophagus | ESCC | 8.21e-10 | 6.35e-01 | 0.0655 |
8731 | RNMT | LZE6T | Human | Esophagus | ESCC | 1.77e-08 | 2.41e-01 | 0.0845 |
8731 | RNMT | P1T-E | Human | Esophagus | ESCC | 1.83e-19 | 8.87e-01 | 0.0875 |
8731 | RNMT | P2T-E | Human | Esophagus | ESCC | 1.08e-41 | 8.59e-01 | 0.1177 |
8731 | RNMT | P4T-E | Human | Esophagus | ESCC | 6.77e-38 | 9.03e-01 | 0.1323 |
8731 | RNMT | P5T-E | Human | Esophagus | ESCC | 1.64e-63 | 1.29e+00 | 0.1327 |
8731 | RNMT | P8T-E | Human | Esophagus | ESCC | 1.33e-38 | 6.62e-01 | 0.0889 |
8731 | RNMT | P9T-E | Human | Esophagus | ESCC | 1.25e-31 | 7.98e-01 | 0.1131 |
8731 | RNMT | P10T-E | Human | Esophagus | ESCC | 5.07e-43 | 7.59e-01 | 0.116 |
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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:19908308 | Esophagus | HGIN | cellular response to leukemia inhibitory factor | 23/2587 | 94/18723 | 3.92e-03 | 3.54e-02 | 23 |
GO:19908238 | Esophagus | HGIN | response to leukemia inhibitory factor | 23/2587 | 95/18723 | 4.51e-03 | 3.93e-02 | 23 |
GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
GO:00015101 | Esophagus | ESCC | RNA methylation | 58/8552 | 83/18723 | 6.87e-06 | 6.94e-05 | 58 |
GO:199082316 | Esophagus | ESCC | response to leukemia inhibitory factor | 60/8552 | 95/18723 | 4.41e-04 | 2.48e-03 | 60 |
GO:199083015 | Esophagus | ESCC | cellular response to leukemia inhibitory factor | 59/8552 | 94/18723 | 6.19e-04 | 3.32e-03 | 59 |
GO:0043414 | Liver | NAFLD | macromolecule methylation | 47/1882 | 316/18723 | 4.08e-03 | 3.41e-02 | 47 |
GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
GO:0001510 | Liver | HCC | RNA methylation | 53/7958 | 83/18723 | 6.96e-05 | 6.29e-04 | 53 |
GO:00094511 | Oral cavity | OSCC | RNA modification | 95/7305 | 167/18723 | 2.05e-06 | 2.62e-05 | 95 |
GO:19908237 | Oral cavity | OSCC | response to leukemia inhibitory factor | 58/7305 | 95/18723 | 1.10e-05 | 1.14e-04 | 58 |
GO:19908307 | Oral cavity | OSCC | cellular response to leukemia inhibitory factor | 57/7305 | 94/18723 | 1.75e-05 | 1.71e-04 | 57 |
GO:00434142 | Oral cavity | OSCC | macromolecule methylation | 149/7305 | 316/18723 | 1.82e-03 | 8.60e-03 | 149 |
GO:00322591 | Oral cavity | OSCC | methylation | 168/7305 | 364/18723 | 3.03e-03 | 1.31e-02 | 168 |
GO:199082315 | Oral cavity | EOLP | response to leukemia inhibitory factor | 26/2218 | 95/18723 | 2.91e-05 | 4.20e-04 | 26 |
GO:199083014 | Oral cavity | EOLP | cellular response to leukemia inhibitory factor | 25/2218 | 94/18723 | 6.89e-05 | 8.53e-04 | 25 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030159 | Esophagus | HGIN | mRNA surveillance pathway | 30/1383 | 97/8465 | 2.48e-04 | 2.69e-03 | 2.14e-03 | 30 |
hsa0301514 | Esophagus | HGIN | mRNA surveillance pathway | 30/1383 | 97/8465 | 2.48e-04 | 2.69e-03 | 2.14e-03 | 30 |
hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa030154 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa0301511 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa0301521 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa0301531 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030158 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
hsa0301513 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
hsa0301541 | Oral cavity | EOLP | mRNA surveillance pathway | 30/1218 | 97/8465 | 2.26e-05 | 1.20e-04 | 7.07e-05 | 30 |
hsa0301551 | Oral cavity | EOLP | mRNA surveillance pathway | 30/1218 | 97/8465 | 2.26e-05 | 1.20e-04 | 7.07e-05 | 30 |
hsa030156 | Oral cavity | NEOLP | mRNA surveillance pathway | 25/1112 | 97/8465 | 5.70e-04 | 3.18e-03 | 2.00e-03 | 25 |
hsa030157 | Oral cavity | NEOLP | mRNA surveillance pathway | 25/1112 | 97/8465 | 5.70e-04 | 3.18e-03 | 2.00e-03 | 25 |
hsa030155 | Prostate | BPH | mRNA surveillance pathway | 32/1718 | 97/8465 | 2.20e-03 | 8.63e-03 | 5.34e-03 | 32 |
hsa0301512 | Prostate | BPH | mRNA surveillance pathway | 32/1718 | 97/8465 | 2.20e-03 | 8.63e-03 | 5.34e-03 | 32 |
hsa0301522 | Prostate | Tumor | mRNA surveillance pathway | 33/1791 | 97/8465 | 2.18e-03 | 8.60e-03 | 5.33e-03 | 33 |
hsa0301532 | Prostate | Tumor | mRNA surveillance pathway | 33/1791 | 97/8465 | 2.18e-03 | 8.60e-03 | 5.33e-03 | 33 |
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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 |
RNMT | deletion | Frame_Shift_Del | c.1233_1239delNNNNNNN | p.Leu412GlufsTer31 | p.L412Efs*31 | O43148 | protein_coding | TCGA-55-A491-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
RNMT | deletion | Frame_Shift_Del | c.931delN | p.Gly312AlafsTer13 | p.G312Afs*13 | O43148 | protein_coding | TCGA-60-2726-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |||
RNMT | SNV | Missense_Mutation | novel | c.941T>C | p.Phe314Ser | p.F314S | O43148 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CV-6003-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
RNMT | SNV | Missense_Mutation | novel | c.605N>G | p.Leu202Trp | p.L202W | O43148 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-UF-A71A-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
RNMT | SNV | Missense_Mutation | rs868206894 | c.404C>T | p.Pro135Leu | p.P135L | O43148 | protein_coding | deleterious(0.04) | benign(0.178) | TCGA-UF-A7JA-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RNMT | deletion | Frame_Shift_Del | c.1174delN | p.Thr394HisfsTer19 | p.T394Hfs*19 | O43148 | protein_coding | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
RNMT | SNV | Missense_Mutation | novel | c.1072N>C | p.Tyr358His | p.Y358H | O43148 | protein_coding | deleterious(0) | possibly_damaging(0.449) | TCGA-XJ-A9DQ-01 | Prostate | prostate adenocarcinoma | Male | <65 | 6 | Unknown | Unknown | SD |
RNMT | SNV | Missense_Mutation | rs772399725 | c.59N>T | p.Ala20Val | p.A20V | O43148 | protein_coding | tolerated_low_confidence(0.21) | benign(0.012) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
RNMT | SNV | Missense_Mutation | rs576605287 | c.815G>A | p.Arg272His | p.R272H | O43148 | protein_coding | tolerated(0.31) | benign(0.007) | TCGA-B7-5816-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RNMT | SNV | Missense_Mutation | c.550A>G | p.Ile184Val | p.I184V | O43148 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-BR-6452-01 | Stomach | stomach 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 |
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